Starting phenix.real_space_refine on Tue Jan 14 14:36:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s37_19690/01_2025/8s37_19690.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s37_19690/01_2025/8s37_19690.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8s37_19690/01_2025/8s37_19690.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s37_19690/01_2025/8s37_19690.map" model { file = "/net/cci-nas-00/data/ceres_data/8s37_19690/01_2025/8s37_19690.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s37_19690/01_2025/8s37_19690.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.016 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 106 5.49 5 S 93 5.16 5 C 15482 2.51 5 N 4409 2.21 5 O 4994 1.98 5 H 23920 0.53 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-5571/modules/chem_data/mon_lib" Total number of atoms: 49005 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 5252 Classifications: {'peptide': 342} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 327} Chain: "B" Number of atoms: 5276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 5276 Classifications: {'peptide': 343} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 328} Chain: "C" Number of atoms: 5276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 5276 Classifications: {'peptide': 343} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 328} Chain: "D" Number of atoms: 5269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 5269 Classifications: {'peptide': 343} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 328} Chain: "E" Number of atoms: 3752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 3752 Classifications: {'peptide': 253} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 238} Chain breaks: 1 Chain: "F" Number of atoms: 3625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 3625 Classifications: {'peptide': 235} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 215} Chain: "G" Number of atoms: 4209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 4209 Classifications: {'peptide': 263} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 246} Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 1186 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: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 1164 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "J" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 1047 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "L" Number of atoms: 3061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3061 Classifications: {'peptide': 201} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain breaks: 3 Chain: "M" Number of atoms: 9887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 9887 Classifications: {'peptide': 624} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 26, 'TRANS': 597} 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 28910 SG CYS G 30 46.992 79.866 21.657 1.00186.24 S ATOM 28942 SG CYS G 33 44.731 77.220 21.885 1.00185.91 S ATOM 29322 SG CYS G 58 44.146 79.751 19.009 1.00177.46 S ATOM 29370 SG CYS G 61 43.297 80.810 22.438 1.00156.63 S Time building chain proxies: 17.49, per 1000 atoms: 0.36 Number of scatterers: 49005 At special positions: 0 Unit cell: (101.2, 134.2, 192.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 93 16.00 P 106 15.00 O 4994 8.00 N 4409 7.00 C 15482 6.00 H 23920 1.00 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: 10.13 Conformation dependent library (CDL) restraints added in 2.8 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 58 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 61 " Number of angles added : 6 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5400 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 29 sheets defined 44.4% alpha, 16.4% beta 30 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 20.14 Creating SS restraints... Processing helix chain 'A' and resid 44 through 65 removed outlier: 3.546A pdb=" N ILE A 48 " --> pdb=" O PRO A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 85 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 Processing helix chain 'A' and resid 154 through 159 Processing helix chain 'A' and resid 161 through 196 removed outlier: 4.006A pdb=" N ARG A 167 " --> pdb=" O ASP A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 199 No H-bonds generated for 'chain 'A' and resid 197 through 199' Processing helix chain 'A' and resid 203 through 225 removed outlier: 3.565A pdb=" N GLN A 208 " --> pdb=" O LYS A 204 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ILE A 209 " --> pdb=" O ALA A 205 " (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 334 removed outlier: 3.501A pdb=" N PHE A 326 " --> pdb=" O GLY A 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 65 removed outlier: 3.509A pdb=" N ILE B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 85 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 160 removed outlier: 3.562A pdb=" N GLU B 158 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE B 159 " --> pdb=" O LEU B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 196 Processing helix chain 'B' and resid 200 through 224 Processing helix chain 'B' and resid 258 through 275 removed outlier: 3.681A pdb=" N ALA B 274 " --> pdb=" O ILE B 270 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU B 275 " --> pdb=" O ARG B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 285 Processing helix chain 'B' and resid 322 through 334 removed outlier: 3.814A pdb=" N PHE B 326 " --> pdb=" O GLY B 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 65 Processing helix chain 'C' and resid 75 through 84 Processing helix chain 'C' and resid 96 through 100 Processing helix chain 'C' and resid 101 through 110 removed outlier: 4.257A pdb=" N GLU C 105 " --> pdb=" O ASN C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 116 Processing helix chain 'C' and resid 148 through 153 Processing helix chain 'C' and resid 156 through 160 removed outlier: 3.605A pdb=" N PHE C 159 " --> pdb=" O LEU C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 197 removed outlier: 4.015A pdb=" N ALA C 191 " --> pdb=" O THR C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 225 removed outlier: 4.039A pdb=" N ALA C 205 " --> pdb=" O LYS C 201 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU C 206 " --> pdb=" O ASP C 202 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 275 removed outlier: 3.731A pdb=" N GLU C 275 " --> pdb=" O ARG C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 removed outlier: 4.272A pdb=" N CYS C 286 " --> pdb=" O ASN C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 335 removed outlier: 3.598A pdb=" N PHE C 326 " --> pdb=" O GLY C 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 65 removed outlier: 3.601A pdb=" N ILE D 48 " --> pdb=" O PRO D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 83 Processing helix chain 'D' and resid 101 through 110 removed outlier: 4.480A pdb=" N GLU D 105 " --> pdb=" O ASN D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 117 Processing helix chain 'D' and resid 148 through 153 Processing helix chain 'D' and resid 154 through 159 Processing helix chain 'D' and resid 161 through 198 Processing helix chain 'D' and resid 203 through 224 removed outlier: 3.819A pdb=" N LEU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) 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 removed outlier: 3.765A pdb=" N PHE D 326 " --> pdb=" O GLY D 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 65 removed outlier: 3.843A 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 98 through 110 removed outlier: 3.953A pdb=" N ALA E 102 " --> pdb=" O GLY E 98 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ALA E 104 " --> pdb=" O ILE E 100 " (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: 3.851A 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 235 removed outlier: 4.290A pdb=" N GLY F 235 " --> pdb=" O SER F 231 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 12 Processing helix chain 'G' and resid 13 through 17 Processing helix chain 'G' and resid 36 through 40 removed outlier: 3.541A pdb=" N GLU G 39 " --> pdb=" O ALA G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 63 removed outlier: 3.779A 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 108 through 115 Processing helix chain 'G' and resid 116 through 123 removed outlier: 4.021A pdb=" N PHE G 120 " --> pdb=" O PRO G 116 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASP G 121 " --> pdb=" O GLU G 117 " (cutoff:3.500A) removed outlier: 4.289A 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 163 Processing helix chain 'G' and resid 191 through 203 removed outlier: 3.557A 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 237 Processing helix chain 'G' and resid 239 through 245 Processing helix chain 'G' and resid 249 through 263 Processing helix chain 'L' and resid 44 through 64 removed outlier: 3.779A 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 271 Processing helix chain 'L' and resid 322 through 334 removed outlier: 4.101A pdb=" N GLU L 334 " --> pdb=" O LYS L 330 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 6 Processing helix chain 'M' and resid 15 through 31 Processing helix chain 'M' and resid 45 through 59 Proline residue: M 53 - end of helix removed outlier: 3.747A pdb=" N LEU M 59 " --> pdb=" O LEU M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 72 through 95 Proline residue: M 85 - end of helix removed outlier: 3.918A pdb=" N GLU M 88 " --> pdb=" O ARG M 84 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLN M 93 " --> pdb=" O GLN M 89 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N CYS M 94 " --> pdb=" O ILE M 90 " (cutoff:3.500A) Processing helix chain 'M' and resid 112 through 126 removed outlier: 3.711A pdb=" N LEU M 119 " --> pdb=" O VAL M 115 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU M 120 " --> pdb=" O ARG M 116 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE M 124 " --> pdb=" O LEU M 120 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR M 125 " --> pdb=" O MET M 121 " (cutoff:3.500A) Processing helix chain 'M' and resid 129 through 139 removed outlier: 3.542A pdb=" N TRP M 139 " --> pdb=" O LYS M 135 " (cutoff:3.500A) Processing helix chain 'M' and resid 142 through 150 removed outlier: 4.124A pdb=" N GLU M 148 " --> pdb=" O VAL M 144 " (cutoff:3.500A) Processing helix chain 'M' and resid 158 through 163 removed outlier: 4.251A pdb=" N VAL M 162 " --> pdb=" O THR M 158 " (cutoff:3.500A) Processing helix chain 'M' and resid 171 through 182 removed outlier: 3.644A pdb=" N ASP M 175 " --> pdb=" O GLN M 171 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N SER M 182 " --> pdb=" O LEU M 178 " (cutoff:3.500A) Processing helix chain 'M' and resid 190 through 196 removed outlier: 4.102A pdb=" N MET M 194 " --> pdb=" O HIS M 190 " (cutoff:3.500A) Processing helix chain 'M' and resid 216 through 228 removed outlier: 4.061A pdb=" N VAL M 226 " --> pdb=" O ASP M 222 " (cutoff:3.500A) Processing helix chain 'M' and resid 233 through 241 Processing helix chain 'M' and resid 246 through 265 removed outlier: 3.625A pdb=" N VAL M 250 " --> pdb=" O PRO M 246 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N HIS M 251 " --> pdb=" O ARG M 247 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N VAL M 252 " --> pdb=" O ASN M 248 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR M 261 " --> pdb=" O MET M 257 " (cutoff:3.500A) Processing helix chain 'M' and resid 272 through 291 removed outlier: 4.232A pdb=" N VAL M 276 " --> pdb=" O THR M 272 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL M 289 " --> pdb=" O ALA M 285 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG M 291 " --> pdb=" O SER M 287 " (cutoff:3.500A) Processing helix chain 'M' and resid 295 through 316 removed outlier: 3.894A pdb=" N GLY M 316 " --> pdb=" O LEU M 312 " (cutoff:3.500A) Processing helix chain 'M' and resid 336 through 350 removed outlier: 4.092A pdb=" N GLY M 344 " --> pdb=" O GLY M 340 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TRP M 350 " --> pdb=" O TYR M 346 " (cutoff:3.500A) Processing helix chain 'M' and resid 365 through 370 Processing helix chain 'M' and resid 370 through 377 Processing helix chain 'M' and resid 380 through 384 removed outlier: 3.537A pdb=" N THR M 383 " --> pdb=" O THR M 380 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ILE M 384 " --> pdb=" O SER M 381 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 380 through 384' Processing helix chain 'M' and resid 420 through 433 Processing helix chain 'M' and resid 444 through 455 Processing helix chain 'M' and resid 470 through 481 removed outlier: 4.127A pdb=" N ILE M 474 " --> pdb=" O ALA M 470 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU M 480 " --> pdb=" O LYS M 476 " (cutoff:3.500A) Processing helix chain 'M' and resid 488 through 492 removed outlier: 3.692A pdb=" N VAL M 492 " --> pdb=" O GLY M 489 " (cutoff:3.500A) Processing helix chain 'M' and resid 521 through 533 Processing helix chain 'M' and resid 538 through 566 removed outlier: 3.785A pdb=" N GLY M 565 " --> pdb=" O SER M 561 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE M 566 " --> pdb=" O VAL M 562 " (cutoff:3.500A) Processing helix chain 'M' and resid 592 through 599 Processing helix chain 'M' and resid 603 through 609 Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 132 removed outlier: 4.834A pdb=" N ILE A 127 " --> pdb=" O SER A 253 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N SER A 253 " --> pdb=" O ILE A 127 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ASN A 129 " --> pdb=" O ARG A 251 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ARG A 251 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR A 297 " --> pdb=" O THR A 307 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N THR A 307 " --> pdb=" O THR A 297 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 17 Processing sheet with id=AA3, first strand: chain 'B' and resid 125 through 127 Processing sheet with id=AA4, first strand: chain 'B' and resid 125 through 127 removed outlier: 6.713A pdb=" N GLU B 247 " --> pdb=" O THR B 12 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N THR B 12 " --> pdb=" O GLU B 247 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N SER B 249 " --> pdb=" O ILE B 10 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE B 10 " --> pdb=" O SER B 249 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ARG B 251 " --> pdb=" O GLY B 8 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N GLY B 8 " --> pdb=" O ARG B 251 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N SER B 253 " --> pdb=" O PHE B 6 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N PHE B 6 " --> pdb=" O SER B 253 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LYS B 255 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU B 4 " --> pdb=" O LYS B 255 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N THR B 297 " --> pdb=" O THR B 307 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N THR B 307 " --> pdb=" O THR B 297 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 138 through 142 Processing sheet with id=AA6, first strand: chain 'B' and resid 145 through 146 Processing sheet with id=AA7, first strand: chain 'C' and resid 125 through 132 removed outlier: 5.287A pdb=" N ARG C 251 " --> pdb=" O GLY C 128 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA C 130 " --> pdb=" O SER C 249 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N SER C 249 " --> pdb=" O ALA C 130 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N GLU C 247 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLU C 247 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N THR C 12 " --> pdb=" O GLU C 247 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N SER C 249 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE C 10 " --> pdb=" O SER C 249 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N ARG C 251 " --> pdb=" O GLY C 8 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N GLY C 8 " --> pdb=" O ARG C 251 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N SER C 253 " --> pdb=" O PHE C 6 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N PHE C 6 " --> pdb=" O SER C 253 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LYS C 255 " --> pdb=" O LEU C 4 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU C 4 " --> pdb=" O LYS C 255 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N THR C 297 " --> pdb=" O THR C 307 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N THR C 307 " --> pdb=" O THR C 297 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 16 through 17 Processing sheet with id=AA9, first strand: chain 'C' and resid 144 through 146 Processing sheet with id=AB1, first strand: chain 'D' and resid 125 through 127 Processing sheet with id=AB2, first strand: chain 'D' and resid 125 through 127 removed outlier: 7.139A pdb=" N GLU D 247 " --> pdb=" O THR D 12 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N THR D 12 " --> pdb=" O GLU D 247 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N SER D 249 " --> pdb=" O ILE D 10 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE D 10 " --> pdb=" O SER D 249 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ARG D 251 " --> pdb=" O GLY D 8 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N GLY D 8 " --> pdb=" O ARG D 251 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N SER D 253 " --> pdb=" O PHE D 6 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N PHE D 6 " --> pdb=" O SER D 253 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LYS D 255 " --> pdb=" O LEU D 4 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU D 4 " --> pdb=" O LYS D 255 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N THR D 297 " --> pdb=" O THR D 307 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N THR D 307 " --> pdb=" O THR D 297 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 138 through 142 Processing sheet with id=AB4, first strand: chain 'E' and resid 125 through 127 Processing sheet with id=AB5, first strand: chain 'E' and resid 125 through 127 removed outlier: 7.000A pdb=" N GLU E 247 " --> pdb=" O THR E 12 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N THR E 12 " --> pdb=" O GLU E 247 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N SER E 249 " --> pdb=" O ILE E 10 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE E 10 " --> pdb=" O SER E 249 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ARG E 251 " --> pdb=" O GLY E 8 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N GLY E 8 " --> pdb=" O ARG E 251 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N SER E 253 " --> pdb=" O PHE E 6 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N PHE E 6 " --> pdb=" O SER E 253 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LYS E 255 " --> pdb=" O LEU E 4 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU E 4 " --> pdb=" O LYS E 255 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N THR E 297 " --> pdb=" O THR E 307 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N THR E 307 " --> pdb=" O THR E 297 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 138 through 141 Processing sheet with id=AB7, first strand: chain 'F' and resid 167 through 174 removed outlier: 5.713A pdb=" N ASN F 169 " --> pdb=" O SER F 12 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER F 12 " --> pdb=" O ASN F 169 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 56 through 57 Processing sheet with id=AB9, first strand: chain 'F' and resid 80 through 86 Processing sheet with id=AC1, first strand: chain 'F' and resid 103 through 104 Processing sheet with id=AC2, first strand: chain 'F' and resid 182 through 183 Processing sheet with id=AC3, first strand: chain 'F' and resid 191 through 192 Processing sheet with id=AC4, first strand: chain 'G' and resid 45 through 48 Processing sheet with id=AC5, first strand: chain 'G' and resid 124 through 127 removed outlier: 4.100A pdb=" N GLU G 124 " --> pdb=" O SER G 103 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N LEU G 146 " --> pdb=" O TYR G 173 " (cutoff:3.500A) removed outlier: 8.977A pdb=" N CYS G 175 " --> pdb=" O LEU G 146 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N TYR G 148 " --> pdb=" O CYS G 175 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 125 through 132 removed outlier: 5.852A pdb=" N VAL L 125 " --> pdb=" O LYS L 255 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LYS L 255 " --> pdb=" O VAL L 125 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ILE L 127 " --> pdb=" O SER L 253 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N SER L 253 " --> pdb=" O ILE L 127 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ASN L 129 " --> pdb=" O ARG L 251 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ARG L 251 " --> pdb=" O ASN L 129 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN L 256 " --> pdb=" O ARG L 2 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ARG L 2 " --> pdb=" O ASN L 256 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY L 309 " --> pdb=" O VAL L 295 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N THR L 297 " --> pdb=" O THR L 307 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N THR L 307 " --> pdb=" O THR L 297 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 138 through 141 Processing sheet with id=AC8, first strand: chain 'M' and resid 185 through 188 removed outlier: 5.943A pdb=" N ALA M 36 " --> pdb=" O LEU M 355 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N SER M 357 " --> pdb=" O ALA M 36 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE M 38 " --> pdb=" O SER M 357 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N LYS M 388 " --> pdb=" O VAL M 35 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU M 37 " --> pdb=" O LYS M 388 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N PHE M 390 " --> pdb=" O LEU M 37 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N SER M 39 " --> pdb=" O PHE M 390 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 319 through 323 Processing sheet with id=AD1, first strand: chain 'M' and resid 463 through 464 removed outlier: 6.262A pdb=" N TYR M 463 " --> pdb=" O ILE M 486 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ALA M 438 " --> pdb=" O LEU M 485 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N SER M 487 " --> pdb=" O ALA M 438 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL M 440 " --> pdb=" O SER M 487 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N SER M 397 " --> pdb=" O VAL M 573 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ILE M 575 " --> pdb=" O SER M 397 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LYS M 399 " --> pdb=" O ILE M 575 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ILE M 577 " --> pdb=" O LYS M 399 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N THR M 401 " --> pdb=" O ILE M 577 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU M 611 " --> pdb=" O LEU M 400 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 411 through 413 removed outlier: 7.435A pdb=" N ILE M 418 " --> pdb=" O ASN M 412 " (cutoff:3.500A) 1100 hydrogen bonds defined for protein. 3114 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 82 hydrogen bonds 164 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 17.27 Time building geometry restraints manager: 12.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 23901 1.03 - 1.23: 59 1.23 - 1.42: 10851 1.42 - 1.62: 14752 1.62 - 1.81: 163 Bond restraints: 49726 Sorted by residual: bond pdb=" C1' DC J 15 " pdb=" N1 DC J 15 " ideal model delta sigma weight residual 1.490 1.546 -0.056 3.00e-02 1.11e+03 3.45e+00 bond pdb=" C1' DT J 8 " pdb=" N1 DT J 8 " ideal model delta sigma weight residual 1.490 1.539 -0.049 3.00e-02 1.11e+03 2.72e+00 bond pdb=" C1' DT J 22 " pdb=" N1 DT J 22 " ideal model delta sigma weight residual 1.490 1.539 -0.049 3.00e-02 1.11e+03 2.67e+00 bond pdb=" C3' DA J -7 " pdb=" O3' DA J -7 " ideal model delta sigma weight residual 1.422 1.471 -0.049 3.00e-02 1.11e+03 2.64e+00 bond pdb=" C3' DA J 20 " pdb=" O3' DA J 20 " ideal model delta sigma weight residual 1.422 1.470 -0.048 3.00e-02 1.11e+03 2.60e+00 ... (remaining 49721 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.33: 89939 7.33 - 14.66: 1 14.66 - 21.99: 0 21.99 - 29.31: 0 29.31 - 36.64: 3 Bond angle restraints: 89943 Sorted by residual: angle pdb=" C ASP M 168 " pdb=" CA ASP M 168 " pdb=" HA ASP M 168 " ideal model delta sigma weight residual 109.00 72.36 36.64 3.00e+00 1.11e-01 1.49e+02 angle pdb=" N ASP M 168 " pdb=" CA ASP M 168 " pdb=" HA ASP M 168 " ideal model delta sigma weight residual 110.00 75.18 34.82 3.00e+00 1.11e-01 1.35e+02 angle pdb=" CB ASP M 168 " pdb=" CA ASP M 168 " pdb=" HA ASP M 168 " ideal model delta sigma weight residual 109.00 78.70 30.30 3.00e+00 1.11e-01 1.02e+02 angle pdb=" CA GLN M 460 " pdb=" CB GLN M 460 " pdb=" CG GLN M 460 " ideal model delta sigma weight residual 114.10 120.48 -6.38 2.00e+00 2.50e-01 1.02e+01 angle pdb=" N ASP M 168 " pdb=" CA ASP M 168 " pdb=" C ASP M 168 " ideal model delta sigma weight residual 110.80 117.36 -6.56 2.13e+00 2.20e-01 9.48e+00 ... (remaining 89938 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.48: 22115 35.48 - 70.97: 949 70.97 - 106.45: 35 106.45 - 141.93: 2 141.93 - 177.42: 5 Dihedral angle restraints: 23106 sinusoidal: 13388 harmonic: 9718 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 33.83 166.17 1 1.50e+01 4.44e-03 8.41e+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 -77.20 -82.80 1 1.50e+01 4.44e-03 3.73e+01 dihedral pdb=" O4' C H 1 " pdb=" C1' C H 1 " pdb=" N1 C H 1 " pdb=" C2 C H 1 " ideal model delta sinusoidal sigma weight residual -160.00 -87.00 -73.00 1 1.50e+01 4.44e-03 3.02e+01 ... (remaining 23103 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3668 0.079 - 0.158: 307 0.158 - 0.237: 2 0.237 - 0.316: 0 0.316 - 0.395: 1 Chirality restraints: 3978 Sorted by residual: chirality pdb=" CA ASP M 168 " pdb=" N ASP M 168 " pdb=" C ASP M 168 " pdb=" CB ASP M 168 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.89e+00 chirality pdb=" CB ILE M 79 " pdb=" CA ILE M 79 " pdb=" CG1 ILE M 79 " pdb=" CG2 ILE M 79 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.74e-01 chirality pdb=" CA PRO M 461 " pdb=" N PRO M 461 " pdb=" C PRO M 461 " pdb=" CB PRO M 461 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.16 2.00e-01 2.50e+01 6.70e-01 ... (remaining 3975 not shown) Planarity restraints: 7122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR D 294 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.73e+00 pdb=" C THR D 294 " 0.045 2.00e-02 2.50e+03 pdb=" O THR D 294 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL D 295 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR L 294 " -0.011 2.00e-02 2.50e+03 2.30e-02 5.30e+00 pdb=" C THR L 294 " 0.040 2.00e-02 2.50e+03 pdb=" O THR L 294 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL L 295 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU E 14 " 0.037 5.00e-02 4.00e+02 5.61e-02 5.03e+00 pdb=" N PRO E 15 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO E 15 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 15 " 0.031 5.00e-02 4.00e+02 ... (remaining 7119 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 2673 2.19 - 2.79: 100636 2.79 - 3.39: 145078 3.39 - 4.00: 192255 4.00 - 4.60: 293044 Nonbonded interactions: 733686 Sorted by model distance: nonbonded pdb=" H HIS M 33 " pdb=" O ARG M 351 " model vdw 1.584 2.450 nonbonded pdb=" H ALA C 282 " pdb=" OP1 A H 15 " model vdw 1.601 2.450 nonbonded pdb=" O THR C 12 " pdb=" H GLY C 245 " model vdw 1.617 2.450 nonbonded pdb=" H HIS B 281 " pdb=" OP2 G H 9 " model vdw 1.627 2.450 nonbonded pdb="HO2' C H 19 " pdb=" O4' C H 20 " model vdw 1.627 2.450 ... (remaining 733681 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 25 or (resid 26 and (name N or name CA or name C \ or name O or name CB or name OG1 or name CG2)) or resid 27 through 196 or (resi \ d 197 and (name N or name CA or name C or name O or name CB or name CG or name C \ D or name CE or name NZ or name HA or name HB2 or name HB3 or name HG2 or name H \ G3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ1 or name HZ2 or na \ me HZ3)) or resid 198 through 342)) selection = (chain 'B' and (resid 1 through 25 or (resid 26 and (name N or name CA or name C \ or name O or name CB or name OG1 or name CG2)) or resid 27 through 196 or (resi \ d 197 and (name N or name CA or name C or name O or name CB or name CG or name C \ D or name CE or name NZ or name HA or name HB2 or name HB3 or name HG2 or name H \ G3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ1 or name HZ2 or na \ me HZ3)) or resid 198 through 342)) selection = (chain 'C' and (resid 1 through 25 or (resid 26 and (name N or name CA or name C \ or name O or name CB or name OG1 or name CG2)) or resid 27 through 196 or (resi \ d 197 and (name N or name CA or name C or name O or name CB or name CG or name C \ D or name CE or name NZ or name HA or name HB2 or name HB3 or name HG2 or name H \ G3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ1 or name HZ2 or na \ me HZ3)) or resid 198 through 342)) selection = (chain 'D' and (resid 1 through 78 or (resid 79 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE \ 1)) or resid 80 through 342)) } 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: 1.850 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: 0.640 Extract box with map and model: 1.340 Check model and map are aligned: 0.270 Set scattering table: 0.350 Process input model: 109.500 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.140 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:9.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 25806 Z= 0.235 Angle : 0.660 7.956 35390 Z= 0.357 Chirality : 0.043 0.395 3978 Planarity : 0.005 0.056 4253 Dihedral : 16.547 177.416 9981 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 0.31 % Favored : 99.55 % Rotamer: Outliers : 0.90 % Allowed : 7.23 % Favored : 91.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.15), residues: 2921 helix: -0.20 (0.15), residues: 1135 sheet: -0.45 (0.25), residues: 385 loop : -1.11 (0.17), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 119 HIS 0.007 0.001 HIS C 281 PHE 0.015 0.001 PHE M 338 TYR 0.017 0.001 TYR M 50 ARG 0.003 0.000 ARG D 152 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 171 time to evaluate : 2.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 MET cc_start: 0.9230 (mmm) cc_final: 0.8799 (mmm) REVERT: B 1 MET cc_start: 0.9071 (tpp) cc_final: 0.8641 (tpp) REVERT: B 140 MET cc_start: 0.9407 (mmm) cc_final: 0.8863 (mmm) REVERT: B 290 GLU cc_start: 0.8913 (pt0) cc_final: 0.8574 (pp20) REVERT: C 196 MET cc_start: 0.9431 (ttp) cc_final: 0.9115 (tpp) REVERT: C 224 GLN cc_start: 0.9680 (tt0) cc_final: 0.9406 (tm-30) REVERT: D 81 MET cc_start: 0.9211 (tpp) cc_final: 0.8956 (tpp) REVERT: D 181 ASP cc_start: 0.9069 (OUTLIER) cc_final: 0.8783 (p0) REVERT: E 37 PHE cc_start: 0.9373 (t80) cc_final: 0.9152 (t80) REVERT: E 339 ASP cc_start: 0.8723 (t0) cc_final: 0.8181 (t0) REVERT: F 42 GLU cc_start: 0.9131 (mp0) cc_final: 0.8915 (mp0) REVERT: F 122 MET cc_start: 0.9215 (tpp) cc_final: 0.8975 (tpp) REVERT: F 142 GLU cc_start: 0.9341 (mp0) cc_final: 0.9124 (mp0) REVERT: F 145 GLU cc_start: 0.8974 (tm-30) cc_final: 0.8716 (tm-30) REVERT: F 166 GLU cc_start: 0.9218 (tt0) cc_final: 0.8788 (tt0) REVERT: F 184 GLU cc_start: 0.8887 (pm20) cc_final: 0.8651 (pm20) REVERT: G 170 ASP cc_start: 0.9476 (m-30) cc_final: 0.9106 (p0) REVERT: G 178 GLN cc_start: 0.9061 (mm-40) cc_final: 0.8672 (mm-40) REVERT: L 330 LYS cc_start: 0.9717 (tppp) cc_final: 0.9411 (tppt) REVERT: M 194 MET cc_start: 0.7976 (OUTLIER) cc_final: 0.7636 (pmm) outliers start: 22 outliers final: 9 residues processed: 186 average time/residue: 2.0547 time to fit residues: 456.7299 Evaluate side-chains 150 residues out of total 2449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 2.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain L residue 252 MET Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 173 ILE Chi-restraints excluded: chain M residue 194 MET Chi-restraints excluded: chain M residue 508 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 254 optimal weight: 9.9990 chunk 228 optimal weight: 10.0000 chunk 126 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 153 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 chunk 235 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 273 optimal weight: 9.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN C 250 HIS F 169 ASN ** M 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 209 ASN M 417 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.069595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.046088 restraints weight = 306156.764| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 4.66 r_work: 0.2845 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 25806 Z= 0.321 Angle : 0.608 6.683 35390 Z= 0.328 Chirality : 0.042 0.407 3978 Planarity : 0.005 0.068 4253 Dihedral : 18.061 178.672 4504 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.53 % Favored : 96.34 % Rotamer: Outliers : 1.02 % Allowed : 9.47 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: -0.16 (0.16), residues: 2921 helix: 0.92 (0.15), residues: 1140 sheet: -0.68 (0.25), residues: 408 loop : -0.74 (0.17), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 293 HIS 0.004 0.001 HIS E 54 PHE 0.011 0.001 PHE C 43 TYR 0.014 0.001 TYR M 50 ARG 0.004 0.001 ARG C 212 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 2.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 MET cc_start: 0.9065 (tpp) cc_final: 0.8479 (tpp) REVERT: B 290 GLU cc_start: 0.8903 (pt0) cc_final: 0.8545 (pp20) REVERT: C 81 MET cc_start: 0.8982 (tpp) cc_final: 0.8774 (tpp) REVERT: C 140 MET cc_start: 0.9389 (mmm) cc_final: 0.9160 (mmm) REVERT: C 196 MET cc_start: 0.9403 (ttp) cc_final: 0.9183 (tpp) REVERT: C 224 GLN cc_start: 0.9650 (tt0) cc_final: 0.9262 (tm-30) REVERT: D 81 MET cc_start: 0.9148 (tpp) cc_final: 0.8885 (tpp) REVERT: D 157 MET cc_start: 0.8924 (mmm) cc_final: 0.8361 (mpp) REVERT: D 181 ASP cc_start: 0.8982 (OUTLIER) cc_final: 0.8771 (p0) REVERT: F 32 GLU cc_start: 0.9361 (tp30) cc_final: 0.8542 (tp30) REVERT: F 42 GLU cc_start: 0.9105 (mp0) cc_final: 0.8829 (mp0) REVERT: F 84 MET cc_start: 0.9089 (ttm) cc_final: 0.8704 (tmt) REVERT: F 142 GLU cc_start: 0.9333 (mp0) cc_final: 0.9111 (mp0) REVERT: G 170 ASP cc_start: 0.9515 (m-30) cc_final: 0.9209 (p0) REVERT: G 177 ASP cc_start: 0.7916 (OUTLIER) cc_final: 0.7235 (p0) REVERT: G 178 GLN cc_start: 0.9035 (mm-40) cc_final: 0.8629 (mm-40) REVERT: G 189 MET cc_start: 0.8847 (tpt) cc_final: 0.8645 (mmm) REVERT: L 330 LYS cc_start: 0.9679 (tppp) cc_final: 0.9352 (tppt) REVERT: M 450 MET cc_start: 0.9473 (mtp) cc_final: 0.9050 (mtm) outliers start: 25 outliers final: 9 residues processed: 158 average time/residue: 2.1494 time to fit residues: 404.9566 Evaluate side-chains 139 residues out of total 2449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 2.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain L residue 135 ASP Chi-restraints excluded: chain L residue 252 MET Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 147 GLU Chi-restraints excluded: chain M residue 508 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 114 optimal weight: 2.9990 chunk 295 optimal weight: 8.9990 chunk 253 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 290 optimal weight: 2.9990 chunk 139 optimal weight: 7.9990 chunk 260 optimal weight: 8.9990 chunk 140 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 156 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 256 ASN ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 200 GLN ** M 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.068811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.045081 restraints weight = 312079.071| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 4.67 r_work: 0.2812 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 25806 Z= 0.298 Angle : 0.582 7.660 35390 Z= 0.311 Chirality : 0.041 0.408 3978 Planarity : 0.004 0.059 4253 Dihedral : 18.047 178.605 4496 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.73 % Favored : 96.13 % Rotamer: Outliers : 1.10 % Allowed : 10.37 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: 0.25 (0.16), residues: 2921 helix: 1.41 (0.15), residues: 1141 sheet: -0.68 (0.25), residues: 404 loop : -0.58 (0.17), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 293 HIS 0.005 0.001 HIS E 54 PHE 0.016 0.001 PHE E 272 TYR 0.014 0.001 TYR M 50 ARG 0.003 0.000 ARG G 35 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 2.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 MET cc_start: 0.9107 (tpp) cc_final: 0.8621 (tpp) REVERT: B 290 GLU cc_start: 0.8934 (pt0) cc_final: 0.8580 (pp20) REVERT: C 224 GLN cc_start: 0.9613 (tt0) cc_final: 0.9196 (tm-30) REVERT: D 81 MET cc_start: 0.9124 (tpp) cc_final: 0.8922 (tpp) REVERT: D 181 ASP cc_start: 0.8933 (OUTLIER) cc_final: 0.8694 (p0) REVERT: D 311 ILE cc_start: 0.9666 (OUTLIER) cc_final: 0.9464 (pt) REVERT: E 37 PHE cc_start: 0.9403 (t80) cc_final: 0.9155 (t80) REVERT: F 32 GLU cc_start: 0.9377 (tp30) cc_final: 0.8570 (tp30) REVERT: F 42 GLU cc_start: 0.9144 (mp0) cc_final: 0.8901 (mp0) REVERT: F 84 MET cc_start: 0.9100 (ttm) cc_final: 0.8754 (tmt) REVERT: F 186 MET cc_start: 0.9258 (mmm) cc_final: 0.9036 (mmm) REVERT: G 177 ASP cc_start: 0.7898 (OUTLIER) cc_final: 0.7196 (p0) REVERT: G 178 GLN cc_start: 0.9073 (mm-40) cc_final: 0.8696 (mm-40) REVERT: G 189 MET cc_start: 0.8815 (tpt) cc_final: 0.8556 (mmm) REVERT: L 330 LYS cc_start: 0.9661 (tppp) cc_final: 0.9322 (tppt) REVERT: M 194 MET cc_start: 0.8296 (pmm) cc_final: 0.7923 (pmm) outliers start: 27 outliers final: 11 residues processed: 148 average time/residue: 2.1056 time to fit residues: 374.7018 Evaluate side-chains 140 residues out of total 2449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 2.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain L residue 135 ASP Chi-restraints excluded: chain L residue 252 MET Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain M residue 508 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 178 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 chunk 271 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 198 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 123 optimal weight: 9.9990 chunk 126 optimal weight: 4.9990 chunk 265 optimal weight: 9.9990 chunk 240 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 HIS B 84 GLN ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.066380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.042784 restraints weight = 315712.564| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 4.49 r_work: 0.2719 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 25806 Z= 0.496 Angle : 0.669 8.085 35390 Z= 0.361 Chirality : 0.044 0.398 3978 Planarity : 0.005 0.052 4253 Dihedral : 18.205 179.759 4496 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.17 % Favored : 94.69 % Rotamer: Outliers : 1.22 % Allowed : 11.27 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: 0.06 (0.16), residues: 2921 helix: 1.30 (0.15), residues: 1144 sheet: -0.70 (0.25), residues: 377 loop : -0.77 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 350 HIS 0.007 0.001 HIS E 54 PHE 0.016 0.002 PHE A 265 TYR 0.013 0.002 TYR M 607 ARG 0.005 0.001 ARG L 33 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 2.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 MET cc_start: 0.9128 (tpp) cc_final: 0.8698 (tpp) REVERT: B 290 GLU cc_start: 0.9049 (pt0) cc_final: 0.8623 (pp20) REVERT: C 136 ASN cc_start: 0.9320 (p0) cc_final: 0.9111 (p0) REVERT: C 140 MET cc_start: 0.9458 (mmm) cc_final: 0.9240 (mmm) REVERT: C 224 GLN cc_start: 0.9595 (tt0) cc_final: 0.9213 (tm-30) REVERT: C 252 MET cc_start: 0.9145 (mtm) cc_final: 0.8725 (mtt) REVERT: D 181 ASP cc_start: 0.8906 (OUTLIER) cc_final: 0.8664 (p0) REVERT: D 311 ILE cc_start: 0.9666 (OUTLIER) cc_final: 0.9432 (pt) REVERT: E 328 MET cc_start: 0.9195 (OUTLIER) cc_final: 0.8969 (mmt) REVERT: F 32 GLU cc_start: 0.9401 (tp30) cc_final: 0.8631 (tp30) REVERT: F 84 MET cc_start: 0.9148 (ttm) cc_final: 0.8792 (ttp) REVERT: G 89 TRP cc_start: 0.9138 (OUTLIER) cc_final: 0.8894 (m-10) REVERT: G 189 MET cc_start: 0.8837 (tpt) cc_final: 0.8599 (mmm) REVERT: L 330 LYS cc_start: 0.9638 (tppp) cc_final: 0.9304 (tppt) REVERT: M 450 MET cc_start: 0.9666 (mtm) cc_final: 0.9317 (mtm) outliers start: 30 outliers final: 16 residues processed: 145 average time/residue: 2.0887 time to fit residues: 364.6943 Evaluate side-chains 139 residues out of total 2449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 2.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 328 MET Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain G residue 89 TRP Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain L residue 135 ASP Chi-restraints excluded: chain L residue 252 MET Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain M residue 257 MET Chi-restraints excluded: chain M residue 389 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 269 optimal weight: 9.9990 chunk 201 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 218 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 180 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 chunk 277 optimal weight: 8.9990 chunk 264 optimal weight: 20.0000 chunk 124 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.067499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.044266 restraints weight = 311299.103| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 4.33 r_work: 0.2760 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25806 Z= 0.278 Angle : 0.585 8.606 35390 Z= 0.310 Chirality : 0.041 0.403 3978 Planarity : 0.004 0.064 4253 Dihedral : 18.160 177.356 4492 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.21 % Favored : 95.65 % Rotamer: Outliers : 1.06 % Allowed : 12.62 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: 0.27 (0.16), residues: 2921 helix: 1.55 (0.16), residues: 1138 sheet: -0.80 (0.25), residues: 378 loop : -0.65 (0.17), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 119 HIS 0.005 0.001 HIS D 281 PHE 0.013 0.001 PHE D 150 TYR 0.012 0.001 TYR M 50 ARG 0.004 0.000 ARG L 33 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 2.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 MET cc_start: 0.9107 (tpp) cc_final: 0.8691 (tpp) REVERT: B 290 GLU cc_start: 0.9005 (pt0) cc_final: 0.8608 (pp20) REVERT: C 81 MET cc_start: 0.8945 (tpp) cc_final: 0.8734 (tpp) REVERT: C 140 MET cc_start: 0.9406 (mmm) cc_final: 0.9184 (mmm) REVERT: C 224 GLN cc_start: 0.9590 (tt0) cc_final: 0.9176 (tm-30) REVERT: C 252 MET cc_start: 0.9095 (mtm) cc_final: 0.8655 (mtt) REVERT: D 181 ASP cc_start: 0.8842 (OUTLIER) cc_final: 0.8580 (p0) REVERT: E 328 MET cc_start: 0.9224 (OUTLIER) cc_final: 0.8919 (mmt) REVERT: F 32 GLU cc_start: 0.9349 (tp30) cc_final: 0.8500 (tp30) REVERT: F 84 MET cc_start: 0.9101 (ttm) cc_final: 0.8717 (tmt) REVERT: F 142 GLU cc_start: 0.9291 (mp0) cc_final: 0.8933 (pm20) REVERT: G 39 GLU cc_start: 0.6265 (OUTLIER) cc_final: 0.5657 (pp20) REVERT: G 178 GLN cc_start: 0.9023 (mm-40) cc_final: 0.8567 (mm-40) REVERT: G 189 MET cc_start: 0.8851 (tpt) cc_final: 0.8602 (mmm) REVERT: L 330 LYS cc_start: 0.9631 (tppp) cc_final: 0.9273 (tppt) outliers start: 26 outliers final: 11 residues processed: 146 average time/residue: 2.0701 time to fit residues: 364.3690 Evaluate side-chains 136 residues out of total 2449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 2.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 328 MET Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain G residue 39 GLU Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain L residue 252 MET Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain M residue 194 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 247 optimal weight: 0.9980 chunk 221 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 293 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 241 optimal weight: 10.0000 chunk 147 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 170 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 ASN ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.067248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.043736 restraints weight = 311682.101| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 4.52 r_work: 0.2753 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 25806 Z= 0.303 Angle : 0.588 8.803 35390 Z= 0.311 Chirality : 0.041 0.402 3978 Planarity : 0.004 0.057 4253 Dihedral : 18.140 176.854 4492 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.79 % Favored : 95.07 % Rotamer: Outliers : 1.06 % Allowed : 13.27 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: 0.32 (0.16), residues: 2921 helix: 1.63 (0.16), residues: 1134 sheet: -0.84 (0.25), residues: 370 loop : -0.64 (0.17), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 293 HIS 0.005 0.001 HIS E 54 PHE 0.012 0.001 PHE D 150 TYR 0.013 0.001 TYR F 157 ARG 0.004 0.000 ARG L 33 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 2.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 MET cc_start: 0.9134 (mmm) cc_final: 0.8733 (mmm) REVERT: B 1 MET cc_start: 0.9193 (tpp) cc_final: 0.8780 (tpp) REVERT: B 81 MET cc_start: 0.9123 (tpp) cc_final: 0.8668 (tpp) REVERT: B 290 GLU cc_start: 0.9011 (pt0) cc_final: 0.8602 (pp20) REVERT: C 81 MET cc_start: 0.8993 (tpp) cc_final: 0.8750 (tpp) REVERT: C 224 GLN cc_start: 0.9577 (tt0) cc_final: 0.9172 (tm-30) REVERT: C 252 MET cc_start: 0.9123 (mtm) cc_final: 0.8660 (mtt) REVERT: D 81 MET cc_start: 0.9124 (tpp) cc_final: 0.8901 (tpp) REVERT: D 181 ASP cc_start: 0.8838 (OUTLIER) cc_final: 0.8580 (p0) REVERT: F 32 GLU cc_start: 0.9328 (tp30) cc_final: 0.8509 (tp30) REVERT: F 84 MET cc_start: 0.9091 (ttm) cc_final: 0.8857 (ttt) REVERT: G 39 GLU cc_start: 0.6381 (OUTLIER) cc_final: 0.5616 (pp20) REVERT: G 177 ASP cc_start: 0.8155 (OUTLIER) cc_final: 0.7927 (p0) REVERT: G 189 MET cc_start: 0.8830 (tpt) cc_final: 0.8566 (mmm) outliers start: 26 outliers final: 14 residues processed: 145 average time/residue: 2.0799 time to fit residues: 368.7662 Evaluate side-chains 142 residues out of total 2449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 2.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 85 ARG Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain G residue 39 GLU Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain L residue 252 MET Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain M residue 194 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 207 optimal weight: 4.9990 chunk 172 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 242 optimal weight: 8.9990 chunk 151 optimal weight: 6.9990 chunk 133 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 233 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 chunk 290 optimal weight: 0.7980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 285 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.067295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.044166 restraints weight = 311365.120| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 4.56 r_work: 0.2783 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 25806 Z= 0.296 Angle : 0.590 8.721 35390 Z= 0.311 Chirality : 0.041 0.402 3978 Planarity : 0.004 0.056 4253 Dihedral : 18.149 176.671 4492 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.86 % Favored : 95.00 % Rotamer: Outliers : 1.14 % Allowed : 13.47 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: 0.37 (0.16), residues: 2921 helix: 1.70 (0.16), residues: 1134 sheet: -0.84 (0.25), residues: 374 loop : -0.62 (0.17), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 89 HIS 0.005 0.001 HIS D 281 PHE 0.017 0.001 PHE M 146 TYR 0.013 0.001 TYR M 50 ARG 0.004 0.000 ARG L 33 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 2.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.9209 (tpp) cc_final: 0.8769 (tpp) REVERT: B 81 MET cc_start: 0.9122 (tpp) cc_final: 0.8645 (tpp) REVERT: B 290 GLU cc_start: 0.9020 (pt0) cc_final: 0.8602 (pp20) REVERT: C 224 GLN cc_start: 0.9569 (tt0) cc_final: 0.9176 (tm-30) REVERT: C 252 MET cc_start: 0.9108 (mtm) cc_final: 0.8605 (mtt) REVERT: C 295 VAL cc_start: 0.9683 (OUTLIER) cc_final: 0.9400 (p) REVERT: D 81 MET cc_start: 0.9066 (tpp) cc_final: 0.8787 (tpp) REVERT: D 181 ASP cc_start: 0.8845 (OUTLIER) cc_final: 0.8610 (p0) REVERT: E 328 MET cc_start: 0.9198 (OUTLIER) cc_final: 0.8853 (mmt) REVERT: F 32 GLU cc_start: 0.9321 (tp30) cc_final: 0.8541 (tp30) REVERT: F 84 MET cc_start: 0.9113 (ttm) cc_final: 0.8854 (ttt) REVERT: F 112 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9275 (tm) REVERT: F 142 GLU cc_start: 0.9296 (mp0) cc_final: 0.8988 (pm20) REVERT: F 158 ASP cc_start: 0.8791 (p0) cc_final: 0.8453 (p0) REVERT: F 201 LYS cc_start: 0.9476 (mppt) cc_final: 0.9045 (mmpt) REVERT: G 177 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.8056 (p0) REVERT: G 189 MET cc_start: 0.8846 (tpt) cc_final: 0.8587 (mmm) outliers start: 28 outliers final: 16 residues processed: 149 average time/residue: 2.0385 time to fit residues: 363.5416 Evaluate side-chains 145 residues out of total 2449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 2.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 328 MET Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 85 ARG Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain G residue 39 GLU Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain L residue 252 MET Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain M residue 194 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 179 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 158 optimal weight: 0.9980 chunk 78 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 292 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 199 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.067589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.044444 restraints weight = 311037.373| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 4.53 r_work: 0.2790 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25806 Z= 0.263 Angle : 0.591 10.418 35390 Z= 0.308 Chirality : 0.041 0.402 3978 Planarity : 0.004 0.057 4253 Dihedral : 18.144 176.224 4492 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.03 % Favored : 94.83 % Rotamer: Outliers : 1.22 % Allowed : 13.84 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: 0.39 (0.16), residues: 2921 helix: 1.75 (0.16), residues: 1134 sheet: -0.91 (0.25), residues: 365 loop : -0.61 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 89 HIS 0.005 0.001 HIS E 54 PHE 0.013 0.001 PHE M 220 TYR 0.013 0.001 TYR M 50 ARG 0.003 0.000 ARG L 33 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 2.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.9203 (tpp) cc_final: 0.8757 (tpp) REVERT: B 81 MET cc_start: 0.9125 (tpp) cc_final: 0.8607 (tpp) REVERT: B 290 GLU cc_start: 0.9018 (pt0) cc_final: 0.8599 (pp20) REVERT: C 224 GLN cc_start: 0.9569 (tt0) cc_final: 0.9173 (tm-30) REVERT: C 252 MET cc_start: 0.9093 (mtm) cc_final: 0.8588 (mtt) REVERT: C 295 VAL cc_start: 0.9672 (OUTLIER) cc_final: 0.9396 (p) REVERT: D 81 MET cc_start: 0.9073 (tpp) cc_final: 0.8791 (tpp) REVERT: D 181 ASP cc_start: 0.8854 (OUTLIER) cc_final: 0.8616 (p0) REVERT: E 328 MET cc_start: 0.9212 (OUTLIER) cc_final: 0.8874 (mmt) REVERT: F 32 GLU cc_start: 0.9308 (tp30) cc_final: 0.8516 (tp30) REVERT: F 84 MET cc_start: 0.9108 (ttm) cc_final: 0.8844 (ttt) REVERT: F 112 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9279 (tm) REVERT: G 189 MET cc_start: 0.8775 (tpt) cc_final: 0.8510 (mmm) outliers start: 30 outliers final: 20 residues processed: 151 average time/residue: 1.9502 time to fit residues: 354.3235 Evaluate side-chains 150 residues out of total 2449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 2.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 328 MET Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 85 ARG Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain G residue 39 GLU Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain L residue 252 MET Chi-restraints excluded: chain L residue 292 HIS Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain M residue 194 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 207 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 151 optimal weight: 7.9990 chunk 266 optimal weight: 30.0000 chunk 226 optimal weight: 9.9990 chunk 237 optimal weight: 9.9990 chunk 217 optimal weight: 7.9990 chunk 184 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.066776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.043865 restraints weight = 310875.717| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 4.43 r_work: 0.2751 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 25806 Z= 0.347 Angle : 0.621 10.542 35390 Z= 0.325 Chirality : 0.042 0.398 3978 Planarity : 0.004 0.051 4253 Dihedral : 18.181 176.945 4492 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.41 % Favored : 94.45 % Rotamer: Outliers : 1.14 % Allowed : 14.09 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: 0.31 (0.16), residues: 2921 helix: 1.68 (0.15), residues: 1138 sheet: -0.91 (0.25), residues: 361 loop : -0.69 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 89 HIS 0.005 0.001 HIS G 3 PHE 0.017 0.001 PHE M 220 TYR 0.012 0.001 TYR M 50 ARG 0.004 0.000 ARG L 33 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 3.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 MET cc_start: 0.9073 (tpp) cc_final: 0.8591 (tpp) REVERT: B 140 MET cc_start: 0.9166 (mmm) cc_final: 0.8267 (mmm) REVERT: B 290 GLU cc_start: 0.9086 (pt0) cc_final: 0.8591 (pp20) REVERT: C 224 GLN cc_start: 0.9561 (tt0) cc_final: 0.9167 (tm-30) REVERT: C 252 MET cc_start: 0.9142 (mtm) cc_final: 0.8600 (mtt) REVERT: C 295 VAL cc_start: 0.9680 (OUTLIER) cc_final: 0.9408 (p) REVERT: D 181 ASP cc_start: 0.8850 (OUTLIER) cc_final: 0.8612 (p0) REVERT: E 328 MET cc_start: 0.9206 (OUTLIER) cc_final: 0.8838 (mmt) REVERT: F 32 GLU cc_start: 0.9328 (tp30) cc_final: 0.8565 (tp30) REVERT: F 84 MET cc_start: 0.9093 (ttm) cc_final: 0.8777 (ttt) REVERT: F 142 GLU cc_start: 0.9316 (mp0) cc_final: 0.9046 (pm20) REVERT: G 22 GLU cc_start: 0.9173 (mm-30) cc_final: 0.8901 (pp20) REVERT: G 177 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.8051 (p0) REVERT: G 189 MET cc_start: 0.8740 (tpt) cc_final: 0.8476 (mmm) REVERT: M 194 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.7832 (pmt) REVERT: M 198 MET cc_start: 0.7727 (pmm) cc_final: 0.7116 (pmm) REVERT: M 311 MET cc_start: 0.8160 (ppp) cc_final: 0.7949 (mmp) outliers start: 28 outliers final: 18 residues processed: 151 average time/residue: 2.0619 time to fit residues: 372.5376 Evaluate side-chains 148 residues out of total 2449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 2.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 328 MET Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 85 ARG Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain G residue 39 GLU Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain L residue 252 MET Chi-restraints excluded: chain L residue 292 HIS Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain M residue 194 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 18 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 64 optimal weight: 0.0980 chunk 69 optimal weight: 0.6980 chunk 273 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 274 optimal weight: 8.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 HIS ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.068714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.045635 restraints weight = 307615.699| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 4.59 r_work: 0.2829 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25806 Z= 0.175 Angle : 0.586 10.940 35390 Z= 0.300 Chirality : 0.041 0.406 3978 Planarity : 0.004 0.067 4253 Dihedral : 18.107 174.567 4492 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.55 % Favored : 95.31 % Rotamer: Outliers : 0.94 % Allowed : 14.33 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: 0.49 (0.16), residues: 2921 helix: 1.87 (0.16), residues: 1130 sheet: -0.96 (0.26), residues: 368 loop : -0.55 (0.17), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 293 HIS 0.005 0.001 HIS D 281 PHE 0.014 0.001 PHE M 220 TYR 0.014 0.001 TYR M 50 ARG 0.004 0.000 ARG E 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 2.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.9217 (tpp) cc_final: 0.8833 (tpp) REVERT: B 81 MET cc_start: 0.9082 (tpp) cc_final: 0.8583 (tpp) REVERT: B 290 GLU cc_start: 0.9018 (pt0) cc_final: 0.8581 (pp20) REVERT: C 224 GLN cc_start: 0.9566 (tt0) cc_final: 0.9123 (tm-30) REVERT: C 252 MET cc_start: 0.9041 (mtm) cc_final: 0.8610 (mtt) REVERT: C 295 VAL cc_start: 0.9655 (OUTLIER) cc_final: 0.9394 (p) REVERT: D 181 ASP cc_start: 0.8859 (OUTLIER) cc_final: 0.8621 (p0) REVERT: D 247 GLU cc_start: 0.9277 (mm-30) cc_final: 0.8849 (mm-30) REVERT: E 328 MET cc_start: 0.9202 (OUTLIER) cc_final: 0.8842 (mmt) REVERT: F 32 GLU cc_start: 0.9288 (tp30) cc_final: 0.8487 (tp30) REVERT: F 84 MET cc_start: 0.9060 (ttm) cc_final: 0.8614 (tmt) REVERT: G 189 MET cc_start: 0.8751 (tpt) cc_final: 0.8476 (mmm) REVERT: M 194 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.7973 (pmt) REVERT: M 532 GLU cc_start: 0.9228 (mp0) cc_final: 0.9027 (mp0) outliers start: 23 outliers final: 17 residues processed: 149 average time/residue: 2.0585 time to fit residues: 367.0785 Evaluate side-chains 146 residues out of total 2449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 2.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 328 MET Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 85 ARG Chi-restraints excluded: chain G residue 39 GLU Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain L residue 252 MET Chi-restraints excluded: chain L residue 292 HIS Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain M residue 194 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 214 optimal weight: 4.9990 chunk 256 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 265 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 171 optimal weight: 4.9990 chunk 219 optimal weight: 6.9990 chunk 138 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 246 optimal weight: 0.9990 chunk 174 optimal weight: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 HIS ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.067218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.044415 restraints weight = 309235.050| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 4.31 r_work: 0.2787 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 25806 Z= 0.317 Angle : 0.612 11.140 35390 Z= 0.318 Chirality : 0.041 0.401 3978 Planarity : 0.004 0.052 4253 Dihedral : 18.136 176.689 4492 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.93 % Favored : 94.93 % Rotamer: Outliers : 0.98 % Allowed : 14.54 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: 0.48 (0.16), residues: 2921 helix: 1.84 (0.16), residues: 1131 sheet: -0.80 (0.26), residues: 351 loop : -0.61 (0.17), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 89 HIS 0.007 0.001 HIS M 268 PHE 0.014 0.001 PHE M 220 TYR 0.012 0.001 TYR M 50 ARG 0.004 0.000 ARG L 33 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22912.87 seconds wall clock time: 391 minutes 11.50 seconds (23471.50 seconds total)