Starting phenix.real_space_refine on Wed Jun 18 15:49:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tib_25616/06_2025/7tib_25616.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tib_25616/06_2025/7tib_25616.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tib_25616/06_2025/7tib_25616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tib_25616/06_2025/7tib_25616.map" model { file = "/net/cci-nas-00/data/ceres_data/7tib_25616/06_2025/7tib_25616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tib_25616/06_2025/7tib_25616.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 55 5.49 5 Mg 4 5.21 5 S 101 5.16 5 C 13381 2.51 5 N 3631 2.21 5 O 4205 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 174 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21377 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3923 Classifications: {'peptide': 495} Link IDs: {'PTRANS': 19, 'TRANS': 475} Chain: "B" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2505 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 9, 'TRANS': 309} Chain: "C" Number of atoms: 2586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2586 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 12, 'TRANS': 314} Chain: "D" Number of atoms: 2687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2687 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 327} Chain: "E" Number of atoms: 2716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2716 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 14, 'TRANS': 328} Chain breaks: 1 Chain: "F" Number of atoms: 2003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2003 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "G" Number of atoms: 1983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1983 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 8, 'TRANS': 243} Chain breaks: 1 Chain: "H" Number of atoms: 1964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1964 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 8, 'TRANS': 241} Chain breaks: 3 Chain: "I" Number of atoms: 488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 488 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "J" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 367 Classifications: {'DNA': 18} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 17} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.43, per 1000 atoms: 0.58 Number of scatterers: 21377 At special positions: 0 Unit cell: (127.2, 133.56, 125.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 101 16.00 P 55 15.00 Mg 4 11.99 O 4205 8.00 N 3631 7.00 C 13381 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.95 Conformation dependent library (CDL) restraints added in 2.6 seconds 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4910 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 16 sheets defined 52.9% alpha, 15.0% beta 8 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 7.03 Creating SS restraints... Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 306 through 310 removed outlier: 3.537A pdb=" N VAL A 310 " --> pdb=" O LEU A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 326 Processing helix chain 'A' and resid 326 through 333 removed outlier: 3.708A pdb=" N ASN A 333 " --> pdb=" O ASN A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 370 Processing helix chain 'A' and resid 384 through 391 Processing helix chain 'A' and resid 392 through 396 removed outlier: 3.726A pdb=" N LEU A 396 " --> pdb=" O LYS A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 407 removed outlier: 4.153A pdb=" N PHE A 405 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 417 removed outlier: 3.974A pdb=" N LYS A 417 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 429 Processing helix chain 'A' and resid 435 through 444 removed outlier: 3.861A pdb=" N GLN A 439 " --> pdb=" O GLY A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 467 Processing helix chain 'A' and resid 479 through 494 removed outlier: 3.822A pdb=" N ILE A 483 " --> pdb=" O ASP A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 511 Processing helix chain 'A' and resid 513 through 525 Processing helix chain 'A' and resid 535 through 543 Processing helix chain 'A' and resid 552 through 559 Processing helix chain 'A' and resid 565 through 570 removed outlier: 4.176A pdb=" N ARG A 570 " --> pdb=" O ASP A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 584 removed outlier: 4.146A pdb=" N ASP A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 595 Processing helix chain 'A' and resid 609 through 632 Processing helix chain 'A' and resid 637 through 639 No H-bonds generated for 'chain 'A' and resid 637 through 639' Processing helix chain 'A' and resid 640 through 649 Processing helix chain 'A' and resid 649 through 657 Processing helix chain 'A' and resid 668 through 695 removed outlier: 5.442A pdb=" N LEU A 692 " --> pdb=" O TYR A 688 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N GLY A 693 " --> pdb=" O HIS A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 705 removed outlier: 3.597A pdb=" N ASP A 704 " --> pdb=" O GLY A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 714 removed outlier: 4.104A pdb=" N LYS A 711 " --> pdb=" O PRO A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 721 removed outlier: 3.785A pdb=" N LEU A 718 " --> pdb=" O LEU A 714 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS A 719 " --> pdb=" O ASP A 715 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY A 721 " --> pdb=" O PHE A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 735 removed outlier: 3.630A pdb=" N TYR A 735 " --> pdb=" O VAL A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 746 removed outlier: 3.709A pdb=" N MET A 746 " --> pdb=" O TRP A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 762 Processing helix chain 'A' and resid 763 through 775 removed outlier: 3.587A pdb=" N ASN A 775 " --> pdb=" O THR A 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 19 through 23 removed outlier: 3.604A pdb=" N ILE B 23 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 55 through 68 Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 85 through 99 removed outlier: 4.079A pdb=" N ILE B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LYS B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 119 Processing helix chain 'B' and resid 120 through 134 removed outlier: 3.767A pdb=" N ARG B 128 " --> pdb=" O GLN B 124 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ARG B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR B 134 " --> pdb=" O THR B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 150 Processing helix chain 'B' and resid 151 through 157 removed outlier: 3.775A pdb=" N ARG B 157 " --> pdb=" O PRO B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 183 Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 201 through 217 Processing helix chain 'B' and resid 220 through 228 Processing helix chain 'B' and resid 231 through 241 removed outlier: 3.605A pdb=" N ILE B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 255 Processing helix chain 'B' and resid 262 through 276 Processing helix chain 'B' and resid 281 through 300 removed outlier: 3.624A pdb=" N ARG B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 320 removed outlier: 3.676A pdb=" N LEU B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 322 No H-bonds generated for 'chain 'B' and resid 321 through 322' Processing helix chain 'C' and resid 9 through 13 removed outlier: 3.571A pdb=" N ASN C 12 " --> pdb=" O SER C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 23 through 27 removed outlier: 3.766A pdb=" N VAL C 27 " --> pdb=" O LEU C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 44 removed outlier: 3.508A pdb=" N THR C 36 " --> pdb=" O GLU C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 72 Processing helix chain 'C' and resid 74 through 78 Processing helix chain 'C' and resid 89 through 103 removed outlier: 4.016A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 122 removed outlier: 3.534A pdb=" N ALA C 121 " --> pdb=" O GLU C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 137 removed outlier: 4.410A pdb=" N ARG C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU C 135 " --> pdb=" O ARG C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 159 Processing helix chain 'C' and resid 170 through 185 Processing helix chain 'C' and resid 190 through 200 Processing helix chain 'C' and resid 204 through 219 Processing helix chain 'C' and resid 228 through 237 Processing helix chain 'C' and resid 240 through 253 Processing helix chain 'C' and resid 255 through 270 removed outlier: 3.732A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 286 Processing helix chain 'C' and resid 293 through 311 Processing helix chain 'C' and resid 315 through 332 Processing helix chain 'D' and resid 15 through 24 Processing helix chain 'D' and resid 26 through 31 Processing helix chain 'D' and resid 42 through 55 removed outlier: 3.737A pdb=" N VAL D 46 " --> pdb=" O GLN D 42 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL D 48 " --> pdb=" O HIS D 44 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER D 55 " --> pdb=" O LYS D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 88 Proline residue: D 85 - end of helix Processing helix chain 'D' and resid 102 through 116 removed outlier: 3.870A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 removed outlier: 3.695A pdb=" N LEU D 126 " --> pdb=" O SER D 122 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASN D 128 " --> pdb=" O HIS D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 145 removed outlier: 3.562A pdb=" N SER D 144 " --> pdb=" O GLU D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 160 removed outlier: 3.571A pdb=" N LEU D 153 " --> pdb=" O ALA D 149 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG D 154 " --> pdb=" O GLN D 150 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ARG D 155 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N THR D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR D 160 " --> pdb=" O THR D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'D' and resid 177 through 184 Processing helix chain 'D' and resid 193 through 208 removed outlier: 5.155A pdb=" N ASP D 199 " --> pdb=" O SER D 195 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 225 Processing helix chain 'D' and resid 227 through 246 removed outlier: 3.700A pdb=" N LEU D 245 " --> pdb=" O GLY D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 260 removed outlier: 3.958A pdb=" N LEU D 259 " --> pdb=" O GLN D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 277 Processing helix chain 'D' and resid 279 through 291 Processing helix chain 'D' and resid 296 through 311 Processing helix chain 'D' and resid 315 through 334 Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'E' and resid 12 through 16 removed outlier: 3.595A pdb=" N LEU E 16 " --> pdb=" O LEU E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 32 removed outlier: 4.447A pdb=" N GLN E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 61 Processing helix chain 'E' and resid 62 through 66 removed outlier: 3.531A pdb=" N VAL E 65 " --> pdb=" O GLY E 62 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR E 66 " --> pdb=" O PRO E 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 66' Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.564A pdb=" N ASP E 100 " --> pdb=" O THR E 97 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 97 through 101' Processing helix chain 'E' and resid 102 through 103 No H-bonds generated for 'chain 'E' and resid 102 through 103' Processing helix chain 'E' and resid 104 through 119 removed outlier: 3.748A pdb=" N VAL E 108 " --> pdb=" O ASN E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 146 Processing helix chain 'E' and resid 147 through 161 removed outlier: 4.045A pdb=" N ARG E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU E 159 " --> pdb=" O ARG E 155 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR E 161 " --> pdb=" O THR E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 184 Processing helix chain 'E' and resid 194 through 209 Processing helix chain 'E' and resid 216 through 227 removed outlier: 3.846A pdb=" N LYS E 220 " --> pdb=" O LYS E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 244 Processing helix chain 'E' and resid 257 through 273 Processing helix chain 'E' and resid 275 through 291 removed outlier: 3.539A pdb=" N GLU E 281 " --> pdb=" O ASN E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 309 Processing helix chain 'E' and resid 314 through 335 Processing helix chain 'E' and resid 337 through 353 removed outlier: 3.726A pdb=" N HIS E 341 " --> pdb=" O LYS E 337 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY E 344 " --> pdb=" O PHE E 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 18 removed outlier: 3.616A pdb=" N LYS F 13 " --> pdb=" O ALA F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 81 removed outlier: 3.575A pdb=" N CYS F 81 " --> pdb=" O LYS F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 152 Processing helix chain 'F' and resid 209 through 216 removed outlier: 3.830A pdb=" N ASP F 214 " --> pdb=" O LYS F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 221 removed outlier: 3.718A pdb=" N SER F 220 " --> pdb=" O LYS F 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 19 removed outlier: 4.470A pdb=" N PHE G 12 " --> pdb=" O GLU G 8 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N PHE G 19 " --> pdb=" O ILE G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 80 Processing helix chain 'G' and resid 141 through 153 removed outlier: 3.662A pdb=" N GLN G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 194 removed outlier: 3.682A pdb=" N SER G 194 " --> pdb=" O PRO G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 217 removed outlier: 3.927A pdb=" N LEU G 212 " --> pdb=" O GLY G 208 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS G 217 " --> pdb=" O LEU G 213 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 19 removed outlier: 4.452A pdb=" N PHE H 12 " --> pdb=" O GLU H 8 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE H 19 " --> pdb=" O ILE H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 82 removed outlier: 3.782A pdb=" N GLY H 82 " --> pdb=" O ILE H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 152 Processing helix chain 'H' and resid 209 through 216 removed outlier: 3.699A pdb=" N ASP H 214 " --> pdb=" O LYS H 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 217 through 221 removed outlier: 4.404A pdb=" N SER H 220 " --> pdb=" O LYS H 217 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU H 221 " --> pdb=" O GLY H 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 217 through 221' Processing sheet with id=AA1, first strand: chain 'A' and resid 373 through 377 removed outlier: 8.003A pdb=" N ILE A 452 " --> pdb=" O PHE A 419 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ILE A 421 " --> pdb=" O ILE A 452 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ILE A 454 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N MET A 423 " --> pdb=" O ILE A 454 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 497 through 498 removed outlier: 7.746A pdb=" N LYS A 497 " --> pdb=" O ILE A 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 599 through 601 Processing sheet with id=AA4, first strand: chain 'B' and resid 75 through 78 removed outlier: 6.305A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE B 46 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 79 through 82 removed outlier: 6.570A pdb=" N LYS C 112 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N CYS C 144 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE C 114 " --> pdb=" O CYS C 144 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N LEU C 146 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N LEU C 116 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU C 49 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ALA C 147 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N PHE C 51 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU C 50 " --> pdb=" O PHE C 164 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 92 through 95 removed outlier: 6.213A pdb=" N LEU D 62 " --> pdb=" O PHE D 187 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 69 through 76 removed outlier: 3.568A pdb=" N VAL E 88 " --> pdb=" O GLU E 95 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LEU E 94 " --> pdb=" O ILE E 139 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ASN E 141 " --> pdb=" O LEU E 94 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE E 96 " --> pdb=" O ASN E 141 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU E 40 " --> pdb=" O ILE E 188 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 212 through 213 removed outlier: 5.992A pdb=" N GLN E 212 " --> pdb=" O LEU E 248 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'F' and resid 57 through 62 removed outlier: 4.940A pdb=" N LEU F 88 " --> pdb=" O PHE F 6 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ASP H 172 " --> pdb=" O SER H 157 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N SER H 157 " --> pdb=" O ASP H 172 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 66 through 71 removed outlier: 5.649A pdb=" N LEU F 25 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N VAL F 40 " --> pdb=" O LEU F 25 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ASN F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLN F 38 " --> pdb=" O ASN F 27 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ASP F 240 " --> pdb=" O ARG F 224 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ARG F 224 " --> pdb=" O ASP F 240 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 203 through 208 removed outlier: 5.543A pdb=" N SER F 157 " --> pdb=" O ASP F 172 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP F 172 " --> pdb=" O SER F 157 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LEU G 88 " --> pdb=" O PHE G 6 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLU G 3 " --> pdb=" O TYR G 60 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N TYR G 60 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LYS G 5 " --> pdb=" O GLN G 58 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 66 through 71 removed outlier: 6.362A pdb=" N LEU G 25 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N VAL G 40 " --> pdb=" O LEU G 25 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASN G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN G 38 " --> pdb=" O ASN G 27 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N SER G 230 " --> pdb=" O PRO G 234 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASP G 240 " --> pdb=" O ARG G 224 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ARG G 224 " --> pdb=" O ASP G 240 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 178 through 182 Processing sheet with id=AB5, first strand: chain 'H' and resid 57 through 62 removed outlier: 6.415A pdb=" N LYS H 5 " --> pdb=" O GLN H 58 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TYR H 60 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLU H 3 " --> pdb=" O TYR H 60 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 47 through 53 removed outlier: 3.796A pdb=" N ASN H 27 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N VAL H 40 " --> pdb=" O LEU H 25 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LEU H 25 " --> pdb=" O VAL H 40 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 196 through 199 1085 hydrogen bonds defined for protein. 3081 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 20 hydrogen bonds 40 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 8.24 Time building geometry restraints manager: 5.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 7004 1.36 - 1.51: 5611 1.51 - 1.66: 9032 1.66 - 1.80: 96 1.80 - 1.95: 63 Bond restraints: 21806 Sorted by residual: bond pdb=" C4 ADP E 401 " pdb=" C5 ADP E 401 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.01e+00 bond pdb=" C3' DT J 19 " pdb=" C2' DT J 19 " ideal model delta sigma weight residual 1.525 1.543 -0.018 2.00e-02 2.50e+03 8.51e-01 bond pdb=" CA ILE G 195 " pdb=" CB ILE G 195 " ideal model delta sigma weight residual 1.530 1.540 -0.009 1.05e-02 9.07e+03 7.89e-01 bond pdb=" CA ILE F 111 " pdb=" CB ILE F 111 " ideal model delta sigma weight residual 1.540 1.528 0.012 1.36e-02 5.41e+03 7.84e-01 bond pdb=" N PRO A 780 " pdb=" CA PRO A 780 " ideal model delta sigma weight residual 1.469 1.480 -0.011 1.28e-02 6.10e+03 7.79e-01 ... (remaining 21801 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 29184 1.70 - 3.40: 417 3.40 - 5.10: 45 5.10 - 6.80: 12 6.80 - 8.50: 1 Bond angle restraints: 29659 Sorted by residual: angle pdb=" N VAL B 303 " pdb=" CA VAL B 303 " pdb=" C VAL B 303 " ideal model delta sigma weight residual 111.91 108.30 3.61 8.90e-01 1.26e+00 1.64e+01 angle pdb=" N VAL H 45 " pdb=" CA VAL H 45 " pdb=" C VAL H 45 " ideal model delta sigma weight residual 113.53 109.91 3.62 9.80e-01 1.04e+00 1.36e+01 angle pdb=" C SER A 634 " pdb=" N GLU A 635 " pdb=" CA GLU A 635 " ideal model delta sigma weight residual 121.54 128.22 -6.68 1.91e+00 2.74e-01 1.22e+01 angle pdb=" N ASN B 321 " pdb=" CA ASN B 321 " pdb=" C ASN B 321 " ideal model delta sigma weight residual 112.97 109.89 3.08 1.06e+00 8.90e-01 8.42e+00 angle pdb=" CA GLU F 129 " pdb=" CB GLU F 129 " pdb=" CG GLU F 129 " ideal model delta sigma weight residual 114.10 119.66 -5.56 2.00e+00 2.50e-01 7.74e+00 ... (remaining 29654 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.56: 12372 26.56 - 53.12: 802 53.12 - 79.68: 101 79.68 - 106.25: 18 106.25 - 132.81: 4 Dihedral angle restraints: 13297 sinusoidal: 5755 harmonic: 7542 Sorted by residual: dihedral pdb=" C5' ADP E 401 " pdb=" O5' ADP E 401 " pdb=" PA ADP E 401 " pdb=" O2A ADP E 401 " ideal model delta sinusoidal sigma weight residual -60.00 72.81 -132.81 1 2.00e+01 2.50e-03 4.03e+01 dihedral pdb=" O2A ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PA ADP E 401 " pdb=" PB ADP E 401 " ideal model delta sinusoidal sigma weight residual -60.00 46.54 -106.54 1 2.00e+01 2.50e-03 3.08e+01 dihedral pdb=" O1B ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PB ADP E 401 " pdb=" PA ADP E 401 " ideal model delta sinusoidal sigma weight residual -60.00 29.75 -89.75 1 2.00e+01 2.50e-03 2.39e+01 ... (remaining 13294 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2139 0.028 - 0.056: 861 0.056 - 0.085: 282 0.085 - 0.113: 144 0.113 - 0.141: 25 Chirality restraints: 3451 Sorted by residual: chirality pdb=" CA VAL E 122 " pdb=" N VAL E 122 " pdb=" C VAL E 122 " pdb=" CB VAL E 122 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.96e-01 chirality pdb=" CA GLU F 129 " pdb=" N GLU F 129 " pdb=" C GLU F 129 " pdb=" CB GLU F 129 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.93e-01 chirality pdb=" CA ILE G 111 " pdb=" N ILE G 111 " pdb=" C ILE G 111 " pdb=" CB ILE G 111 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 ... (remaining 3448 not shown) Planarity restraints: 3618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 221 " -0.034 5.00e-02 4.00e+02 5.25e-02 4.40e+00 pdb=" N PRO C 222 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO C 222 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 222 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 10 " 0.019 2.00e-02 2.50e+03 1.02e-02 2.61e+00 pdb=" N1 DT I 10 " -0.025 2.00e-02 2.50e+03 pdb=" C2 DT I 10 " -0.000 2.00e-02 2.50e+03 pdb=" O2 DT I 10 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DT I 10 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DT I 10 " 0.003 2.00e-02 2.50e+03 pdb=" O4 DT I 10 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DT I 10 " 0.001 2.00e-02 2.50e+03 pdb=" C7 DT I 10 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DT I 10 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN H 201 " 0.024 5.00e-02 4.00e+02 3.66e-02 2.14e+00 pdb=" N PRO H 202 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO H 202 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO H 202 " 0.020 5.00e-02 4.00e+02 ... (remaining 3615 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 303 2.66 - 3.22: 19599 3.22 - 3.78: 33296 3.78 - 4.34: 46224 4.34 - 4.90: 75141 Nonbonded interactions: 174563 Sorted by model distance: nonbonded pdb=" OG1 THR B 56 " pdb="MG MG B 402 " model vdw 2.099 2.170 nonbonded pdb=" O3G AGS B 401 " pdb="MG MG B 402 " model vdw 2.104 2.170 nonbonded pdb=" OG1 THR C 60 " pdb="MG MG C 402 " model vdw 2.106 2.170 nonbonded pdb=" O3G AGS D 401 " pdb="MG MG D 402 " model vdw 2.146 2.170 nonbonded pdb=" O3G AGS C 401 " pdb="MG MG C 402 " model vdw 2.150 2.170 ... (remaining 174558 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 'F' and (resid 1 through 82 or resid 85 through 104 or resid 106 through \ 173 or resid 177 through 240 or resid 244 through 255)) selection = (chain 'G' and (resid 1 through 82 or resid 85 through 104 or resid 106 through \ 240 or resid 244 through 255)) selection = (chain 'H' and (resid 1 through 173 or resid 177 through 255)) } 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.870 Check model and map are aligned: 0.160 Set scattering table: 0.220 Process input model: 52.700 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 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 : 0.002 0.032 21806 Z= 0.116 Angle : 0.530 8.499 29659 Z= 0.317 Chirality : 0.038 0.141 3451 Planarity : 0.003 0.052 3618 Dihedral : 16.862 132.807 8387 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.09 % Allowed : 9.02 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.97 (0.15), residues: 2555 helix: -0.62 (0.14), residues: 1202 sheet: -1.27 (0.20), residues: 525 loop : -2.12 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 669 HIS 0.003 0.000 HIS G 190 PHE 0.017 0.001 PHE G 185 TYR 0.007 0.001 TYR F 211 ARG 0.002 0.000 ARG G 224 Details of bonding type rmsd hydrogen bonds : bond 0.14005 ( 1105) hydrogen bonds : angle 5.54526 ( 3121) covalent geometry : bond 0.00208 (21806) covalent geometry : angle 0.53009 (29659) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 644 time to evaluate : 2.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 LYS cc_start: 0.7833 (mttt) cc_final: 0.7267 (mtmt) REVERT: A 388 LEU cc_start: 0.8396 (mt) cc_final: 0.8159 (mt) REVERT: A 594 GLU cc_start: 0.8111 (tp30) cc_final: 0.7849 (tp30) REVERT: A 604 LEU cc_start: 0.8376 (mt) cc_final: 0.8082 (mt) REVERT: A 630 LYS cc_start: 0.8191 (mttt) cc_final: 0.7979 (mttm) REVERT: A 691 ARG cc_start: 0.7755 (tpt170) cc_final: 0.7552 (tpt-90) REVERT: B 77 GLU cc_start: 0.6885 (tt0) cc_final: 0.6668 (tt0) REVERT: B 202 MET cc_start: 0.8970 (tpp) cc_final: 0.8640 (tpp) REVERT: B 237 LYS cc_start: 0.8678 (ttmt) cc_final: 0.8404 (ttmm) REVERT: C 19 TYR cc_start: 0.8862 (m-80) cc_final: 0.8508 (m-80) REVERT: C 249 LYS cc_start: 0.8507 (tttt) cc_final: 0.8277 (ttmm) REVERT: C 333 ASN cc_start: 0.8024 (t0) cc_final: 0.7790 (t0) REVERT: D 80 LYS cc_start: 0.8349 (mttt) cc_final: 0.8121 (ttpp) REVERT: D 115 ARG cc_start: 0.7963 (ttp-110) cc_final: 0.7018 (mtm-85) REVERT: D 204 ILE cc_start: 0.9408 (mm) cc_final: 0.9076 (mt) REVERT: D 208 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8559 (mm-30) REVERT: E 24 ASN cc_start: 0.7470 (m-40) cc_final: 0.7224 (m-40) REVERT: E 160 LYS cc_start: 0.8275 (tptt) cc_final: 0.7988 (ttpt) REVERT: E 265 LYS cc_start: 0.8556 (mtmt) cc_final: 0.8192 (mttm) REVERT: F 42 ASP cc_start: 0.7119 (t0) cc_final: 0.6847 (t0) REVERT: F 188 MET cc_start: 0.7329 (mmt) cc_final: 0.6323 (mpp) REVERT: G 38 GLN cc_start: 0.8112 (pt0) cc_final: 0.7850 (pt0) REVERT: G 64 HIS cc_start: 0.6877 (p-80) cc_final: 0.6632 (p-80) REVERT: G 124 ASP cc_start: 0.5915 (p0) cc_final: 0.5449 (p0) REVERT: G 247 GLN cc_start: 0.7831 (mt0) cc_final: 0.7505 (mt0) REVERT: H 72 LEU cc_start: 0.5728 (mm) cc_final: 0.5392 (mm) REVERT: H 116 LEU cc_start: 0.6040 (OUTLIER) cc_final: 0.5772 (tp) REVERT: H 131 LEU cc_start: 0.6085 (mt) cc_final: 0.5777 (mp) outliers start: 25 outliers final: 17 residues processed: 664 average time/residue: 0.3896 time to fit residues: 376.8965 Evaluate side-chains 530 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 512 time to evaluate : 2.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 PHE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 256 TRP Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 203 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 217 optimal weight: 8.9990 chunk 195 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 202 optimal weight: 3.9990 chunk 78 optimal weight: 0.0980 chunk 122 optimal weight: 5.9990 chunk 150 optimal weight: 0.0980 chunk 234 optimal weight: 5.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN A 322 ASN A 364 HIS A 413 ASN A 501 ASN A 537 ASN A 672 GLN A 775 ASN A 779 HIS B 18 GLN B 26 ASN B 92 GLN B 108 HIS B 177 GLN B 279 GLN B 317 HIS B 320 ASN C 12 ASN C 221 ASN C 292 ASN C 317 GLN C 333 ASN D 128 ASN D 236 GLN D 303 GLN D 340 HIS D 352 GLN E 18 HIS E 19 ASN E 86 ASN E 103 ASN E 133 HIS F 27 ASN F 38 GLN F 58 GLN ** F 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** G 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 ASN H 153 GLN H 247 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.167384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.120608 restraints weight = 24532.657| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.00 r_work: 0.2957 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 21806 Z= 0.242 Angle : 0.647 10.087 29659 Z= 0.332 Chirality : 0.045 0.188 3451 Planarity : 0.005 0.055 3618 Dihedral : 15.009 125.477 3327 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.36 % Allowed : 16.43 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.86 (0.16), residues: 2555 helix: 0.30 (0.15), residues: 1201 sheet: -0.90 (0.21), residues: 520 loop : -1.45 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 638 HIS 0.006 0.001 HIS B 44 PHE 0.015 0.002 PHE B 142 TYR 0.019 0.002 TYR F 211 ARG 0.011 0.001 ARG C 142 Details of bonding type rmsd hydrogen bonds : bond 0.04545 ( 1105) hydrogen bonds : angle 4.55961 ( 3121) covalent geometry : bond 0.00577 (21806) covalent geometry : angle 0.64668 (29659) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 532 time to evaluate : 2.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 LYS cc_start: 0.8096 (mttt) cc_final: 0.7407 (mtmm) REVERT: A 318 MET cc_start: 0.7791 (mmm) cc_final: 0.7375 (mmm) REVERT: A 350 MET cc_start: 0.7579 (tpp) cc_final: 0.7221 (tpp) REVERT: A 352 TYR cc_start: 0.8125 (p90) cc_final: 0.7828 (p90) REVERT: A 399 MET cc_start: 0.7319 (ptp) cc_final: 0.6982 (ptm) REVERT: A 474 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7098 (tm-30) REVERT: A 600 ARG cc_start: 0.7596 (ptp-110) cc_final: 0.7289 (ptp-110) REVERT: A 604 LEU cc_start: 0.8560 (mt) cc_final: 0.8305 (mt) REVERT: A 711 LYS cc_start: 0.7055 (mtpp) cc_final: 0.6841 (mtpp) REVERT: B 35 GLN cc_start: 0.7945 (tp40) cc_final: 0.7230 (tp40) REVERT: B 115 GLU cc_start: 0.9125 (mp0) cc_final: 0.8218 (mp0) REVERT: B 160 ILE cc_start: 0.9243 (mm) cc_final: 0.8940 (mm) REVERT: B 181 LEU cc_start: 0.8758 (mt) cc_final: 0.8387 (mm) REVERT: B 237 LYS cc_start: 0.8995 (ttmt) cc_final: 0.8732 (ttmm) REVERT: C 75 TYR cc_start: 0.7700 (OUTLIER) cc_final: 0.7036 (t80) REVERT: C 78 MET cc_start: 0.8631 (mpp) cc_final: 0.8373 (mpp) REVERT: C 207 ARG cc_start: 0.8716 (tpt-90) cc_final: 0.8376 (tpt90) REVERT: C 223 ASP cc_start: 0.7228 (m-30) cc_final: 0.6803 (m-30) REVERT: C 249 LYS cc_start: 0.8900 (tttt) cc_final: 0.8693 (ttmm) REVERT: C 333 ASN cc_start: 0.8526 (t0) cc_final: 0.8132 (t0) REVERT: D 35 ASN cc_start: 0.8186 (OUTLIER) cc_final: 0.7909 (p0) REVERT: D 54 LYS cc_start: 0.8759 (mmmt) cc_final: 0.8517 (tptp) REVERT: D 57 ASN cc_start: 0.8802 (p0) cc_final: 0.8584 (p0) REVERT: D 80 LYS cc_start: 0.8687 (mttt) cc_final: 0.8036 (tttm) REVERT: D 249 LYS cc_start: 0.8313 (mmtm) cc_final: 0.8041 (mmtm) REVERT: D 285 LYS cc_start: 0.8639 (tttt) cc_final: 0.8061 (ttmm) REVERT: E 24 ASN cc_start: 0.7618 (m-40) cc_final: 0.7362 (m-40) REVERT: E 52 ARG cc_start: 0.7786 (mtt90) cc_final: 0.7289 (mtt90) REVERT: E 160 LYS cc_start: 0.8477 (tptt) cc_final: 0.8096 (ttpt) REVERT: E 265 LYS cc_start: 0.8673 (mtmt) cc_final: 0.8309 (mttm) REVERT: E 280 ILE cc_start: 0.8670 (mt) cc_final: 0.8440 (tp) REVERT: F 64 HIS cc_start: 0.8251 (p90) cc_final: 0.8045 (p90) REVERT: F 149 ARG cc_start: 0.8408 (ptp-170) cc_final: 0.8111 (ptt180) REVERT: F 188 MET cc_start: 0.7638 (mmt) cc_final: 0.6261 (mpp) REVERT: G 1 MET cc_start: 0.7075 (tmm) cc_final: 0.6746 (tpp) REVERT: G 38 GLN cc_start: 0.8487 (pt0) cc_final: 0.8273 (pt0) REVERT: G 64 HIS cc_start: 0.7764 (p-80) cc_final: 0.7357 (p-80) REVERT: G 146 LYS cc_start: 0.7610 (tptp) cc_final: 0.7128 (mmmt) REVERT: G 158 ILE cc_start: 0.7096 (mm) cc_final: 0.6766 (pt) REVERT: G 245 PHE cc_start: 0.7885 (p90) cc_final: 0.7406 (p90) REVERT: H 72 LEU cc_start: 0.5945 (mm) cc_final: 0.5566 (mm) outliers start: 77 outliers final: 58 residues processed: 576 average time/residue: 0.4072 time to fit residues: 362.5306 Evaluate side-chains 546 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 485 time to evaluate : 2.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 75 TYR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 256 TRP Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 227 ASN Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain E residue 311 GLU Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain F residue 33 ASP Chi-restraints excluded: chain F residue 70 MET Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 113 GLU Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 246 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 60 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 194 optimal weight: 0.6980 chunk 180 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 158 optimal weight: 0.0970 chunk 89 optimal weight: 2.9990 chunk 235 optimal weight: 40.0000 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 171 GLN F 27 ASN G 190 HIS ** H 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.169676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.122446 restraints weight = 24340.915| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.89 r_work: 0.3013 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21806 Z= 0.130 Angle : 0.537 11.486 29659 Z= 0.274 Chirality : 0.041 0.161 3451 Planarity : 0.004 0.050 3618 Dihedral : 14.717 129.427 3321 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.62 % Allowed : 18.00 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.26 (0.17), residues: 2555 helix: 0.75 (0.15), residues: 1201 sheet: -0.52 (0.22), residues: 517 loop : -1.16 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 638 HIS 0.007 0.001 HIS B 60 PHE 0.009 0.001 PHE H 28 TYR 0.022 0.001 TYR G 211 ARG 0.009 0.000 ARG A 681 Details of bonding type rmsd hydrogen bonds : bond 0.03622 ( 1105) hydrogen bonds : angle 4.39680 ( 3121) covalent geometry : bond 0.00298 (21806) covalent geometry : angle 0.53721 (29659) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 525 time to evaluate : 2.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 LYS cc_start: 0.8132 (mttt) cc_final: 0.7415 (mtmm) REVERT: A 318 MET cc_start: 0.7849 (mmm) cc_final: 0.7414 (mmm) REVERT: A 399 MET cc_start: 0.7583 (ptp) cc_final: 0.7199 (ptm) REVERT: A 457 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7776 (mm-30) REVERT: A 474 GLN cc_start: 0.7879 (tt0) cc_final: 0.7328 (tm-30) REVERT: A 540 SER cc_start: 0.8183 (t) cc_final: 0.7608 (m) REVERT: A 580 LEU cc_start: 0.9172 (tt) cc_final: 0.8632 (tp) REVERT: A 600 ARG cc_start: 0.7492 (ptp-110) cc_final: 0.7197 (ptp-110) REVERT: A 604 LEU cc_start: 0.8576 (mt) cc_final: 0.8324 (mt) REVERT: B 35 GLN cc_start: 0.7970 (tp40) cc_final: 0.7397 (tp40) REVERT: B 160 ILE cc_start: 0.9276 (mm) cc_final: 0.8994 (mm) REVERT: B 182 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7614 (mm-30) REVERT: B 237 LYS cc_start: 0.8991 (ttmt) cc_final: 0.8743 (ttmm) REVERT: B 238 LYS cc_start: 0.8734 (ttpt) cc_final: 0.8366 (tttp) REVERT: C 19 TYR cc_start: 0.9287 (m-80) cc_final: 0.8964 (m-80) REVERT: C 75 TYR cc_start: 0.7724 (OUTLIER) cc_final: 0.7218 (t80) REVERT: C 184 HIS cc_start: 0.7429 (m-70) cc_final: 0.6518 (t-170) REVERT: C 207 ARG cc_start: 0.8730 (tpt-90) cc_final: 0.8378 (tpt90) REVERT: C 223 ASP cc_start: 0.7261 (m-30) cc_final: 0.6848 (m-30) REVERT: C 249 LYS cc_start: 0.8830 (tttt) cc_final: 0.8629 (ttmm) REVERT: C 333 ASN cc_start: 0.8660 (t0) cc_final: 0.8285 (t0) REVERT: D 54 LYS cc_start: 0.8676 (mmmt) cc_final: 0.8447 (tptp) REVERT: D 57 ASN cc_start: 0.8855 (p0) cc_final: 0.8326 (p0) REVERT: D 80 LYS cc_start: 0.8732 (mttt) cc_final: 0.8005 (tttm) REVERT: D 88 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7928 (tmm) REVERT: D 96 ASN cc_start: 0.8111 (OUTLIER) cc_final: 0.7791 (m-40) REVERT: D 285 LYS cc_start: 0.8613 (tttt) cc_final: 0.8010 (ttmm) REVERT: E 50 LYS cc_start: 0.8512 (mttt) cc_final: 0.8231 (mttp) REVERT: E 118 GLN cc_start: 0.6964 (mp10) cc_final: 0.6577 (mm-40) REVERT: E 160 LYS cc_start: 0.8305 (tptt) cc_final: 0.7883 (ttpt) REVERT: E 265 LYS cc_start: 0.8705 (mtmt) cc_final: 0.8365 (mttm) REVERT: E 280 ILE cc_start: 0.8672 (mt) cc_final: 0.8417 (tp) REVERT: F 64 HIS cc_start: 0.8225 (p90) cc_final: 0.8005 (p90) REVERT: F 91 ILE cc_start: 0.8803 (mt) cc_final: 0.8567 (mt) REVERT: F 129 GLU cc_start: 0.6204 (OUTLIER) cc_final: 0.5884 (pp20) REVERT: F 188 MET cc_start: 0.7637 (mmt) cc_final: 0.6234 (mpp) REVERT: G 1 MET cc_start: 0.7143 (tmm) cc_final: 0.6794 (tpp) REVERT: G 24 GLN cc_start: 0.7310 (mm110) cc_final: 0.7037 (mm-40) REVERT: G 38 GLN cc_start: 0.8590 (pt0) cc_final: 0.8311 (pt0) REVERT: G 64 HIS cc_start: 0.7839 (p-80) cc_final: 0.7415 (p-80) REVERT: G 146 LYS cc_start: 0.7594 (tptp) cc_final: 0.7182 (mmmt) REVERT: G 158 ILE cc_start: 0.7154 (mm) cc_final: 0.6883 (pt) REVERT: G 245 PHE cc_start: 0.8083 (p90) cc_final: 0.7721 (p90) REVERT: H 72 LEU cc_start: 0.5930 (mm) cc_final: 0.5542 (mm) REVERT: H 161 MET cc_start: 0.5752 (mtp) cc_final: 0.5521 (mtp) REVERT: H 181 ILE cc_start: 0.7485 (mt) cc_final: 0.7042 (tp) REVERT: H 204 ASP cc_start: 0.5812 (OUTLIER) cc_final: 0.5300 (m-30) outliers start: 83 outliers final: 47 residues processed: 573 average time/residue: 0.3511 time to fit residues: 303.9845 Evaluate side-chains 537 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 485 time to evaluate : 2.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain C residue 75 TYR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 256 TRP Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 227 ASN Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 70 MET Chi-restraints excluded: chain F residue 117 LYS Chi-restraints excluded: chain F residue 129 GLU Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 113 GLU Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 199 MET Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 204 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 246 optimal weight: 8.9990 chunk 219 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 153 optimal weight: 0.1980 chunk 166 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 144 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 296 HIS B 317 HIS F 27 ASN G 58 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.164681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.118229 restraints weight = 24613.918| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.01 r_work: 0.2936 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 21806 Z= 0.231 Angle : 0.613 13.467 29659 Z= 0.309 Chirality : 0.043 0.163 3451 Planarity : 0.004 0.052 3618 Dihedral : 14.859 129.343 3319 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.23 % Allowed : 19.92 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.15 (0.17), residues: 2555 helix: 0.69 (0.15), residues: 1217 sheet: -0.42 (0.22), residues: 525 loop : -0.91 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 295 HIS 0.005 0.001 HIS E 18 PHE 0.013 0.002 PHE H 248 TYR 0.026 0.002 TYR E 42 ARG 0.008 0.001 ARG A 681 Details of bonding type rmsd hydrogen bonds : bond 0.04185 ( 1105) hydrogen bonds : angle 4.52642 ( 3121) covalent geometry : bond 0.00547 (21806) covalent geometry : angle 0.61306 (29659) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 515 time to evaluate : 2.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 LYS cc_start: 0.8228 (mttt) cc_final: 0.7444 (mtmm) REVERT: A 318 MET cc_start: 0.8037 (mmm) cc_final: 0.7522 (mmm) REVERT: A 347 ARG cc_start: 0.7505 (ptm160) cc_final: 0.7001 (ptp-170) REVERT: A 352 TYR cc_start: 0.8166 (p90) cc_final: 0.7898 (p90) REVERT: A 388 LEU cc_start: 0.8706 (mt) cc_final: 0.8251 (mt) REVERT: A 399 MET cc_start: 0.7571 (ptp) cc_final: 0.7145 (ptm) REVERT: A 457 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7840 (mm-30) REVERT: A 474 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7272 (tm-30) REVERT: A 540 SER cc_start: 0.8107 (t) cc_final: 0.7886 (m) REVERT: A 600 ARG cc_start: 0.7656 (ptp-110) cc_final: 0.7452 (ptp-110) REVERT: A 604 LEU cc_start: 0.8660 (mt) cc_final: 0.8412 (mt) REVERT: A 679 TYR cc_start: 0.7713 (m-80) cc_final: 0.7256 (m-80) REVERT: A 767 LYS cc_start: 0.5868 (mtmm) cc_final: 0.5661 (mtmm) REVERT: B 35 GLN cc_start: 0.8069 (tp40) cc_final: 0.7287 (tp40) REVERT: B 160 ILE cc_start: 0.9342 (mm) cc_final: 0.9044 (mm) REVERT: B 182 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7750 (mm-30) REVERT: B 246 GLU cc_start: 0.8662 (mp0) cc_final: 0.7991 (mp0) REVERT: C 19 TYR cc_start: 0.9354 (m-80) cc_final: 0.9095 (m-80) REVERT: C 68 ARG cc_start: 0.8670 (ttm-80) cc_final: 0.8352 (mtm-85) REVERT: C 88 ARG cc_start: 0.8825 (mtm180) cc_final: 0.8586 (mtm180) REVERT: C 184 HIS cc_start: 0.7541 (m-70) cc_final: 0.6519 (t-170) REVERT: C 223 ASP cc_start: 0.7500 (m-30) cc_final: 0.7116 (m-30) REVERT: C 256 TRP cc_start: 0.9352 (OUTLIER) cc_final: 0.7688 (t60) REVERT: C 333 ASN cc_start: 0.8762 (t0) cc_final: 0.8332 (t0) REVERT: D 54 LYS cc_start: 0.8683 (mmmt) cc_final: 0.8473 (tptp) REVERT: D 80 LYS cc_start: 0.8788 (mttt) cc_final: 0.8058 (tttm) REVERT: D 96 ASN cc_start: 0.8231 (OUTLIER) cc_final: 0.7944 (m-40) REVERT: D 285 LYS cc_start: 0.8628 (tttt) cc_final: 0.8036 (ttmm) REVERT: E 118 GLN cc_start: 0.6990 (mp10) cc_final: 0.6607 (mm-40) REVERT: E 160 LYS cc_start: 0.8442 (tptt) cc_final: 0.8086 (ttpt) REVERT: E 163 LYS cc_start: 0.8413 (mttt) cc_final: 0.7833 (tptt) REVERT: E 265 LYS cc_start: 0.8681 (mtmt) cc_final: 0.8428 (mttm) REVERT: E 280 ILE cc_start: 0.8727 (mt) cc_final: 0.8431 (tp) REVERT: F 8 GLU cc_start: 0.7524 (pm20) cc_final: 0.7272 (pm20) REVERT: F 91 ILE cc_start: 0.8825 (OUTLIER) cc_final: 0.8613 (mt) REVERT: F 129 GLU cc_start: 0.6217 (OUTLIER) cc_final: 0.5899 (pp20) REVERT: F 188 MET cc_start: 0.7699 (mmt) cc_final: 0.6279 (mpp) REVERT: F 242 LYS cc_start: 0.8390 (mtmm) cc_final: 0.7933 (mmmm) REVERT: G 1 MET cc_start: 0.7243 (tmm) cc_final: 0.6968 (tpp) REVERT: G 38 GLN cc_start: 0.8662 (pt0) cc_final: 0.8406 (pt0) REVERT: G 64 HIS cc_start: 0.8035 (p-80) cc_final: 0.7670 (p-80) REVERT: G 146 LYS cc_start: 0.7561 (tptp) cc_final: 0.7116 (mmmt) REVERT: G 158 ILE cc_start: 0.7278 (mm) cc_final: 0.6963 (pt) REVERT: G 238 GLN cc_start: 0.8013 (tt0) cc_final: 0.7789 (tt0) REVERT: G 245 PHE cc_start: 0.8119 (p90) cc_final: 0.7765 (p90) REVERT: G 254 PHE cc_start: 0.6458 (m-80) cc_final: 0.6086 (m-80) REVERT: H 161 MET cc_start: 0.5991 (mtp) cc_final: 0.5621 (mtp) outliers start: 97 outliers final: 72 residues processed: 567 average time/residue: 0.4364 time to fit residues: 377.0648 Evaluate side-chains 569 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 492 time to evaluate : 2.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 75 TYR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 256 TRP Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 227 ASN Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 70 MET Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 117 LYS Chi-restraints excluded: chain F residue 129 GLU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 113 GLU Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 163 THR Chi-restraints excluded: chain H residue 199 MET Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 256 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 19 optimal weight: 0.2980 chunk 231 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 175 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 chunk 251 optimal weight: 7.9990 chunk 248 optimal weight: 10.0000 chunk 199 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 317 HIS C 171 GLN F 27 ASN G 58 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.165543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.118525 restraints weight = 24653.012| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.99 r_work: 0.2948 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21806 Z= 0.164 Angle : 0.559 14.715 29659 Z= 0.283 Chirality : 0.041 0.148 3451 Planarity : 0.004 0.050 3618 Dihedral : 14.802 130.098 3319 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.84 % Allowed : 20.79 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.07 (0.17), residues: 2555 helix: 0.85 (0.15), residues: 1216 sheet: -0.28 (0.22), residues: 521 loop : -0.80 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 295 HIS 0.018 0.001 HIS B 317 PHE 0.012 0.001 PHE D 290 TYR 0.028 0.002 TYR E 42 ARG 0.006 0.000 ARG E 184 Details of bonding type rmsd hydrogen bonds : bond 0.03764 ( 1105) hydrogen bonds : angle 4.45376 ( 3121) covalent geometry : bond 0.00385 (21806) covalent geometry : angle 0.55891 (29659) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 505 time to evaluate : 2.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 LYS cc_start: 0.8169 (mttt) cc_final: 0.7444 (mtmm) REVERT: A 347 ARG cc_start: 0.7553 (ptm160) cc_final: 0.7034 (ptp-170) REVERT: A 350 MET cc_start: 0.7760 (tpp) cc_final: 0.7318 (tpp) REVERT: A 365 LEU cc_start: 0.8387 (mm) cc_final: 0.8143 (mp) REVERT: A 388 LEU cc_start: 0.8731 (mt) cc_final: 0.8268 (mt) REVERT: A 399 MET cc_start: 0.7531 (ptp) cc_final: 0.7131 (ptm) REVERT: A 457 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7866 (mm-30) REVERT: A 474 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7306 (tm-30) REVERT: A 580 LEU cc_start: 0.9224 (tp) cc_final: 0.8808 (tp) REVERT: A 604 LEU cc_start: 0.8636 (mt) cc_final: 0.8396 (mt) REVERT: A 679 TYR cc_start: 0.7712 (m-80) cc_final: 0.7260 (m-80) REVERT: B 35 GLN cc_start: 0.8004 (tp40) cc_final: 0.7302 (tp40) REVERT: B 77 GLU cc_start: 0.8067 (tt0) cc_final: 0.7761 (tt0) REVERT: B 160 ILE cc_start: 0.9341 (mm) cc_final: 0.9023 (mm) REVERT: B 182 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7771 (mm-30) REVERT: B 238 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8286 (tttp) REVERT: C 19 TYR cc_start: 0.9324 (m-80) cc_final: 0.9036 (m-80) REVERT: C 88 ARG cc_start: 0.8766 (mtm180) cc_final: 0.8551 (mtm180) REVERT: C 223 ASP cc_start: 0.7378 (m-30) cc_final: 0.6992 (m-30) REVERT: C 256 TRP cc_start: 0.9288 (OUTLIER) cc_final: 0.7785 (t60) REVERT: C 333 ASN cc_start: 0.8799 (t0) cc_final: 0.8395 (t0) REVERT: D 51 LYS cc_start: 0.8516 (mmmm) cc_final: 0.8311 (mmmm) REVERT: D 80 LYS cc_start: 0.8735 (mttt) cc_final: 0.8063 (tttm) REVERT: D 88 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.8067 (tmm) REVERT: D 96 ASN cc_start: 0.8261 (OUTLIER) cc_final: 0.7957 (m-40) REVERT: D 285 LYS cc_start: 0.8596 (tttt) cc_final: 0.8005 (ttmm) REVERT: E 54 MET cc_start: 0.8064 (mmt) cc_final: 0.7827 (mmt) REVERT: E 118 GLN cc_start: 0.6915 (mp10) cc_final: 0.6539 (mm-40) REVERT: E 160 LYS cc_start: 0.8385 (tptt) cc_final: 0.8023 (ttpt) REVERT: E 163 LYS cc_start: 0.8394 (mttt) cc_final: 0.7729 (tptt) REVERT: E 265 LYS cc_start: 0.8701 (mtmt) cc_final: 0.8446 (mttm) REVERT: F 91 ILE cc_start: 0.8852 (mt) cc_final: 0.8644 (mt) REVERT: F 129 GLU cc_start: 0.6190 (OUTLIER) cc_final: 0.5866 (pp20) REVERT: F 149 ARG cc_start: 0.8668 (ptp-170) cc_final: 0.8386 (ptt180) REVERT: F 188 MET cc_start: 0.7684 (mmt) cc_final: 0.6283 (mpp) REVERT: F 242 LYS cc_start: 0.8349 (mtmm) cc_final: 0.7929 (mmmm) REVERT: G 1 MET cc_start: 0.7295 (tmm) cc_final: 0.7029 (tpp) REVERT: G 24 GLN cc_start: 0.7495 (mm110) cc_final: 0.7284 (mm-40) REVERT: G 38 GLN cc_start: 0.8647 (pt0) cc_final: 0.8380 (pt0) REVERT: G 64 HIS cc_start: 0.8166 (p-80) cc_final: 0.7816 (p-80) REVERT: G 120 ASP cc_start: 0.7640 (OUTLIER) cc_final: 0.7151 (m-30) REVERT: G 146 LYS cc_start: 0.7584 (tptp) cc_final: 0.7123 (mmmt) REVERT: G 158 ILE cc_start: 0.7254 (mm) cc_final: 0.6965 (pt) REVERT: G 245 PHE cc_start: 0.8058 (p90) cc_final: 0.7839 (p90) REVERT: H 161 MET cc_start: 0.5933 (mtp) cc_final: 0.5540 (mtp) outliers start: 88 outliers final: 69 residues processed: 560 average time/residue: 0.3420 time to fit residues: 289.6157 Evaluate side-chains 566 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 490 time to evaluate : 2.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 75 TYR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 256 TRP Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 227 ASN Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 117 LYS Chi-restraints excluded: chain F residue 129 GLU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 113 GLU Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 163 THR Chi-restraints excluded: chain H residue 199 MET Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 256 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 96 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 220 optimal weight: 8.9990 chunk 134 optimal weight: 4.9990 chunk 171 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 121 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 251 optimal weight: 0.9990 chunk 135 optimal weight: 0.1980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 171 GLN F 27 ASN G 58 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.167419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.120882 restraints weight = 24506.116| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.01 r_work: 0.2975 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21806 Z= 0.120 Angle : 0.533 15.322 29659 Z= 0.269 Chirality : 0.040 0.151 3451 Planarity : 0.004 0.051 3618 Dihedral : 14.697 130.061 3319 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.62 % Allowed : 21.45 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.33 (0.17), residues: 2555 helix: 1.05 (0.15), residues: 1215 sheet: -0.10 (0.23), residues: 520 loop : -0.68 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 295 HIS 0.016 0.001 HIS B 317 PHE 0.011 0.001 PHE G 6 TYR 0.022 0.001 TYR E 42 ARG 0.010 0.000 ARG A 600 Details of bonding type rmsd hydrogen bonds : bond 0.03404 ( 1105) hydrogen bonds : angle 4.35596 ( 3121) covalent geometry : bond 0.00272 (21806) covalent geometry : angle 0.53252 (29659) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 509 time to evaluate : 2.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 LYS cc_start: 0.8103 (mttt) cc_final: 0.7370 (mtmm) REVERT: A 347 ARG cc_start: 0.7534 (ptm160) cc_final: 0.7071 (ptp-170) REVERT: A 350 MET cc_start: 0.7698 (tpp) cc_final: 0.7248 (tpp) REVERT: A 365 LEU cc_start: 0.8386 (mm) cc_final: 0.8111 (mp) REVERT: A 399 MET cc_start: 0.7537 (ptp) cc_final: 0.7178 (ptm) REVERT: A 474 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.7277 (tm-30) REVERT: A 544 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7646 (mt-10) REVERT: A 580 LEU cc_start: 0.9241 (tp) cc_final: 0.8855 (tp) REVERT: A 630 LYS cc_start: 0.8948 (ttmt) cc_final: 0.8566 (mttm) REVERT: A 679 TYR cc_start: 0.7687 (m-80) cc_final: 0.7247 (m-80) REVERT: B 35 GLN cc_start: 0.7945 (tp40) cc_final: 0.7287 (tp40) REVERT: B 160 ILE cc_start: 0.9355 (mm) cc_final: 0.9035 (mm) REVERT: B 182 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7762 (mm-30) REVERT: B 238 LYS cc_start: 0.8821 (ttpt) cc_final: 0.8290 (tttp) REVERT: C 19 TYR cc_start: 0.9284 (m-80) cc_final: 0.8997 (m-80) REVERT: C 68 ARG cc_start: 0.8580 (ttm-80) cc_final: 0.8315 (mtm-85) REVERT: C 88 ARG cc_start: 0.8744 (mtm180) cc_final: 0.8542 (mtm180) REVERT: C 207 ARG cc_start: 0.8644 (tpt-90) cc_final: 0.8409 (tpt90) REVERT: C 223 ASP cc_start: 0.7376 (m-30) cc_final: 0.7013 (m-30) REVERT: C 256 TRP cc_start: 0.9275 (OUTLIER) cc_final: 0.7865 (t60) REVERT: C 333 ASN cc_start: 0.8757 (t0) cc_final: 0.8399 (t0) REVERT: D 35 ASN cc_start: 0.8415 (OUTLIER) cc_final: 0.8151 (p0) REVERT: D 51 LYS cc_start: 0.8435 (mmmm) cc_final: 0.8227 (mmmm) REVERT: D 57 ASN cc_start: 0.9012 (p0) cc_final: 0.8655 (p0) REVERT: D 80 LYS cc_start: 0.8718 (mttt) cc_final: 0.8052 (tttm) REVERT: D 88 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.8027 (tmm) REVERT: D 96 ASN cc_start: 0.8257 (OUTLIER) cc_final: 0.7942 (m-40) REVERT: D 285 LYS cc_start: 0.8565 (tttt) cc_final: 0.7973 (ttmm) REVERT: E 118 GLN cc_start: 0.6899 (mp10) cc_final: 0.6519 (mm-40) REVERT: E 160 LYS cc_start: 0.8359 (tptt) cc_final: 0.7994 (ttpt) REVERT: E 163 LYS cc_start: 0.8379 (mttt) cc_final: 0.7709 (tptt) REVERT: E 256 LYS cc_start: 0.8386 (mmmt) cc_final: 0.7666 (mmtp) REVERT: E 265 LYS cc_start: 0.8720 (mtmt) cc_final: 0.8469 (mttm) REVERT: F 8 GLU cc_start: 0.7419 (pm20) cc_final: 0.7154 (pm20) REVERT: F 129 GLU cc_start: 0.6213 (OUTLIER) cc_final: 0.5890 (pp20) REVERT: F 188 MET cc_start: 0.7663 (mmt) cc_final: 0.6294 (mpp) REVERT: F 242 LYS cc_start: 0.8366 (mtmm) cc_final: 0.7934 (mmmm) REVERT: G 38 GLN cc_start: 0.8652 (pt0) cc_final: 0.8303 (pt0) REVERT: G 64 HIS cc_start: 0.8121 (p-80) cc_final: 0.7746 (p-80) REVERT: G 120 ASP cc_start: 0.7558 (OUTLIER) cc_final: 0.7113 (m-30) REVERT: G 146 LYS cc_start: 0.7595 (tptp) cc_final: 0.7132 (mmmt) REVERT: G 245 PHE cc_start: 0.8008 (p90) cc_final: 0.7780 (p90) REVERT: H 161 MET cc_start: 0.5912 (mtp) cc_final: 0.5499 (mtp) REVERT: H 250 LEU cc_start: 0.3924 (OUTLIER) cc_final: 0.3317 (mt) outliers start: 83 outliers final: 65 residues processed: 563 average time/residue: 0.3460 time to fit residues: 294.1506 Evaluate side-chains 559 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 486 time to evaluate : 2.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 75 TYR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 256 TRP Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 70 MET Chi-restraints excluded: chain F residue 129 GLU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 113 GLU Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 163 THR Chi-restraints excluded: chain H residue 199 MET Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 256 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 214 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 224 optimal weight: 9.9990 chunk 201 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 49 optimal weight: 0.1980 chunk 6 optimal weight: 2.9990 chunk 169 optimal weight: 7.9990 chunk 128 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 138 optimal weight: 0.0670 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 317 HIS C 171 GLN D 303 GLN F 27 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.168516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.121912 restraints weight = 24432.369| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.98 r_work: 0.2996 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21806 Z= 0.113 Angle : 0.526 15.727 29659 Z= 0.265 Chirality : 0.040 0.148 3451 Planarity : 0.004 0.050 3618 Dihedral : 14.609 129.973 3319 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.57 % Allowed : 21.67 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.53 (0.17), residues: 2555 helix: 1.21 (0.15), residues: 1214 sheet: 0.02 (0.23), residues: 522 loop : -0.59 (0.23), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 324 HIS 0.005 0.001 HIS B 317 PHE 0.011 0.001 PHE D 290 TYR 0.033 0.001 TYR E 42 ARG 0.008 0.000 ARG A 600 Details of bonding type rmsd hydrogen bonds : bond 0.03235 ( 1105) hydrogen bonds : angle 4.28412 ( 3121) covalent geometry : bond 0.00258 (21806) covalent geometry : angle 0.52563 (29659) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 510 time to evaluate : 2.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 LYS cc_start: 0.8029 (mttt) cc_final: 0.7384 (mtmm) REVERT: A 318 MET cc_start: 0.7827 (mmm) cc_final: 0.7563 (mmm) REVERT: A 347 ARG cc_start: 0.7485 (ptm160) cc_final: 0.7069 (ptp-170) REVERT: A 350 MET cc_start: 0.7722 (tpp) cc_final: 0.7260 (tpp) REVERT: A 399 MET cc_start: 0.7503 (ptp) cc_final: 0.7160 (ptm) REVERT: A 474 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7249 (tm-30) REVERT: A 487 LEU cc_start: 0.8483 (mt) cc_final: 0.8068 (mt) REVERT: A 489 THR cc_start: 0.8691 (m) cc_final: 0.8367 (p) REVERT: A 544 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7391 (mt-10) REVERT: A 580 LEU cc_start: 0.9232 (tp) cc_final: 0.8861 (tp) REVERT: A 593 GLN cc_start: 0.9046 (tm-30) cc_final: 0.8434 (tm-30) REVERT: A 630 LYS cc_start: 0.8930 (ttmt) cc_final: 0.8568 (mttm) REVERT: A 679 TYR cc_start: 0.7664 (m-80) cc_final: 0.7223 (m-80) REVERT: A 691 ARG cc_start: 0.7689 (tpt-90) cc_final: 0.7423 (tpt-90) REVERT: A 767 LYS cc_start: 0.5835 (mtmm) cc_final: 0.5606 (mtmm) REVERT: B 35 GLN cc_start: 0.7891 (tp40) cc_final: 0.7293 (tp40) REVERT: B 160 ILE cc_start: 0.9361 (mm) cc_final: 0.9040 (mm) REVERT: B 182 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7800 (mm-30) REVERT: B 237 LYS cc_start: 0.9037 (ttmt) cc_final: 0.8806 (ttmm) REVERT: B 238 LYS cc_start: 0.8794 (ttpt) cc_final: 0.8247 (tttp) REVERT: C 19 TYR cc_start: 0.9274 (m-80) cc_final: 0.8979 (m-80) REVERT: C 68 ARG cc_start: 0.8512 (ttm-80) cc_final: 0.8262 (mtm-85) REVERT: C 88 ARG cc_start: 0.8713 (mtm180) cc_final: 0.8482 (mtm180) REVERT: C 207 ARG cc_start: 0.8607 (tpt-90) cc_final: 0.8366 (tpt90) REVERT: C 223 ASP cc_start: 0.7272 (m-30) cc_final: 0.6926 (m-30) REVERT: C 256 TRP cc_start: 0.9272 (OUTLIER) cc_final: 0.7909 (t60) REVERT: C 333 ASN cc_start: 0.8758 (t0) cc_final: 0.8435 (t0) REVERT: D 35 ASN cc_start: 0.8390 (OUTLIER) cc_final: 0.8167 (p0) REVERT: D 51 LYS cc_start: 0.8386 (mmmm) cc_final: 0.8176 (mmmm) REVERT: D 57 ASN cc_start: 0.9022 (p0) cc_final: 0.8616 (p0) REVERT: D 80 LYS cc_start: 0.8706 (mttt) cc_final: 0.8027 (tttm) REVERT: D 88 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.8007 (tmm) REVERT: D 96 ASN cc_start: 0.8232 (OUTLIER) cc_final: 0.7944 (m-40) REVERT: D 285 LYS cc_start: 0.8548 (tttt) cc_final: 0.7938 (ttmm) REVERT: E 118 GLN cc_start: 0.6921 (mp10) cc_final: 0.6544 (mm-40) REVERT: E 160 LYS cc_start: 0.8413 (tptt) cc_final: 0.7977 (ttpt) REVERT: E 163 LYS cc_start: 0.8384 (mttt) cc_final: 0.7705 (tptt) REVERT: E 236 MET cc_start: 0.6843 (ttm) cc_final: 0.6495 (tmm) REVERT: E 256 LYS cc_start: 0.8370 (mmmt) cc_final: 0.7653 (mmtp) REVERT: E 265 LYS cc_start: 0.8720 (mtmt) cc_final: 0.8472 (mttm) REVERT: F 8 GLU cc_start: 0.7394 (pm20) cc_final: 0.7135 (pm20) REVERT: F 129 GLU cc_start: 0.6205 (OUTLIER) cc_final: 0.5879 (pp20) REVERT: F 188 MET cc_start: 0.7734 (mmt) cc_final: 0.6307 (mpp) REVERT: F 242 LYS cc_start: 0.8366 (mtmm) cc_final: 0.7940 (mmmm) REVERT: G 38 GLN cc_start: 0.8584 (pt0) cc_final: 0.8273 (pt0) REVERT: G 64 HIS cc_start: 0.7995 (p-80) cc_final: 0.7651 (p-80) REVERT: G 120 ASP cc_start: 0.7542 (OUTLIER) cc_final: 0.7129 (m-30) REVERT: G 143 GLU cc_start: 0.7402 (pm20) cc_final: 0.6839 (pm20) REVERT: G 146 LYS cc_start: 0.7608 (tptp) cc_final: 0.7148 (mmmt) REVERT: G 245 PHE cc_start: 0.7998 (p90) cc_final: 0.7758 (p90) REVERT: H 126 LEU cc_start: 0.6914 (OUTLIER) cc_final: 0.6606 (mm) REVERT: H 161 MET cc_start: 0.5896 (mtp) cc_final: 0.5427 (mtp) outliers start: 82 outliers final: 62 residues processed: 562 average time/residue: 0.3480 time to fit residues: 295.8340 Evaluate side-chains 559 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 489 time to evaluate : 2.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 75 TYR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 256 TRP Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 70 MET Chi-restraints excluded: chain F residue 129 GLU Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 113 GLU Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 163 THR Chi-restraints excluded: chain H residue 199 MET Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 256 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 48 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 chunk 237 optimal weight: 9.9990 chunk 113 optimal weight: 0.9980 chunk 200 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 131 optimal weight: 0.9980 chunk 96 optimal weight: 0.1980 chunk 16 optimal weight: 3.9990 chunk 170 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 171 GLN F 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.168321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.121912 restraints weight = 24636.246| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.01 r_work: 0.2992 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21806 Z= 0.118 Angle : 0.528 15.838 29659 Z= 0.265 Chirality : 0.040 0.150 3451 Planarity : 0.004 0.050 3618 Dihedral : 14.578 129.584 3319 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.62 % Allowed : 21.75 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.63 (0.17), residues: 2555 helix: 1.26 (0.15), residues: 1216 sheet: 0.09 (0.23), residues: 517 loop : -0.48 (0.23), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 543 HIS 0.003 0.001 HIS E 18 PHE 0.011 0.001 PHE D 290 TYR 0.036 0.001 TYR E 42 ARG 0.010 0.000 ARG E 184 Details of bonding type rmsd hydrogen bonds : bond 0.03262 ( 1105) hydrogen bonds : angle 4.26014 ( 3121) covalent geometry : bond 0.00272 (21806) covalent geometry : angle 0.52809 (29659) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 492 time to evaluate : 2.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 LYS cc_start: 0.8012 (mttt) cc_final: 0.7298 (mtmm) REVERT: A 318 MET cc_start: 0.7806 (mmm) cc_final: 0.7559 (mmm) REVERT: A 347 ARG cc_start: 0.7520 (ptm160) cc_final: 0.7102 (ptp-170) REVERT: A 350 MET cc_start: 0.7745 (tpp) cc_final: 0.7279 (tpp) REVERT: A 365 LEU cc_start: 0.8304 (mm) cc_final: 0.8100 (mp) REVERT: A 399 MET cc_start: 0.7379 (ptp) cc_final: 0.7062 (ptm) REVERT: A 474 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7246 (tm-30) REVERT: A 544 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7214 (mt-10) REVERT: A 580 LEU cc_start: 0.9207 (tp) cc_final: 0.8844 (tp) REVERT: A 593 GLN cc_start: 0.9056 (tm-30) cc_final: 0.8445 (tm-30) REVERT: A 630 LYS cc_start: 0.8926 (ttmt) cc_final: 0.8549 (mttm) REVERT: A 679 TYR cc_start: 0.7660 (m-80) cc_final: 0.7221 (m-80) REVERT: B 9 LEU cc_start: 0.8804 (mt) cc_final: 0.8595 (mt) REVERT: B 129 ARG cc_start: 0.8256 (mmm160) cc_final: 0.7899 (mmm160) REVERT: B 160 ILE cc_start: 0.9326 (mm) cc_final: 0.8998 (mm) REVERT: B 182 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7817 (mm-30) REVERT: B 237 LYS cc_start: 0.9047 (ttmt) cc_final: 0.8825 (ttmm) REVERT: B 238 LYS cc_start: 0.8847 (ttpt) cc_final: 0.8310 (tttp) REVERT: C 19 TYR cc_start: 0.9278 (m-80) cc_final: 0.8965 (m-80) REVERT: C 68 ARG cc_start: 0.8490 (ttm-80) cc_final: 0.8236 (mtm-85) REVERT: C 88 ARG cc_start: 0.8700 (mtm180) cc_final: 0.8460 (mtm180) REVERT: C 207 ARG cc_start: 0.8611 (tpt-90) cc_final: 0.8353 (tpt90) REVERT: C 223 ASP cc_start: 0.7365 (m-30) cc_final: 0.6992 (m-30) REVERT: C 256 TRP cc_start: 0.9266 (OUTLIER) cc_final: 0.7960 (t60) REVERT: C 333 ASN cc_start: 0.8772 (t0) cc_final: 0.8445 (t0) REVERT: D 35 ASN cc_start: 0.8375 (OUTLIER) cc_final: 0.8167 (p0) REVERT: D 51 LYS cc_start: 0.8388 (mmmm) cc_final: 0.8043 (mmmm) REVERT: D 57 ASN cc_start: 0.9030 (p0) cc_final: 0.8640 (p0) REVERT: D 80 LYS cc_start: 0.8705 (mttt) cc_final: 0.8035 (tttm) REVERT: D 88 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.7997 (tmm) REVERT: D 96 ASN cc_start: 0.8227 (OUTLIER) cc_final: 0.7945 (m-40) REVERT: D 208 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8595 (mm-30) REVERT: D 285 LYS cc_start: 0.8546 (tttt) cc_final: 0.7938 (ttmm) REVERT: E 118 GLN cc_start: 0.6903 (mp10) cc_final: 0.6520 (mm-40) REVERT: E 160 LYS cc_start: 0.8418 (tptt) cc_final: 0.7988 (ttpt) REVERT: E 163 LYS cc_start: 0.8423 (mttt) cc_final: 0.7745 (tptt) REVERT: E 236 MET cc_start: 0.6878 (ttm) cc_final: 0.6507 (tmm) REVERT: E 256 LYS cc_start: 0.8379 (mmmt) cc_final: 0.7660 (mmtp) REVERT: E 265 LYS cc_start: 0.8690 (mtmt) cc_final: 0.8440 (mttm) REVERT: F 55 GLU cc_start: 0.7947 (mp0) cc_final: 0.7745 (mp0) REVERT: F 129 GLU cc_start: 0.6198 (OUTLIER) cc_final: 0.5879 (pp20) REVERT: F 188 MET cc_start: 0.7720 (mmt) cc_final: 0.6304 (mpp) REVERT: F 242 LYS cc_start: 0.8374 (mtmm) cc_final: 0.7960 (mmmm) REVERT: G 38 GLN cc_start: 0.8539 (pt0) cc_final: 0.8335 (pt0) REVERT: G 64 HIS cc_start: 0.7989 (p-80) cc_final: 0.7654 (p-80) REVERT: G 120 ASP cc_start: 0.7472 (OUTLIER) cc_final: 0.7102 (m-30) REVERT: G 146 LYS cc_start: 0.7597 (tptp) cc_final: 0.7147 (mmmt) REVERT: G 245 PHE cc_start: 0.8008 (p90) cc_final: 0.7791 (p90) REVERT: H 126 LEU cc_start: 0.6872 (OUTLIER) cc_final: 0.6567 (mm) REVERT: H 161 MET cc_start: 0.5916 (mtp) cc_final: 0.5469 (mtp) outliers start: 83 outliers final: 65 residues processed: 547 average time/residue: 0.3429 time to fit residues: 284.6272 Evaluate side-chains 555 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 482 time to evaluate : 2.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 75 TYR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 256 TRP Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 70 MET Chi-restraints excluded: chain F residue 129 GLU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 113 GLU Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 163 THR Chi-restraints excluded: chain H residue 199 MET Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 256 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 11 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 92 optimal weight: 0.6980 chunk 133 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 128 optimal weight: 0.7980 chunk 203 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 171 GLN F 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.168201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.121780 restraints weight = 24554.247| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.98 r_work: 0.2987 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21806 Z= 0.122 Angle : 0.535 15.657 29659 Z= 0.268 Chirality : 0.040 0.151 3451 Planarity : 0.004 0.050 3618 Dihedral : 14.526 129.245 3319 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.62 % Allowed : 22.14 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.73 (0.17), residues: 2555 helix: 1.32 (0.15), residues: 1213 sheet: 0.13 (0.23), residues: 518 loop : -0.40 (0.23), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 295 HIS 0.003 0.001 HIS B 60 PHE 0.011 0.001 PHE D 290 TYR 0.034 0.001 TYR E 42 ARG 0.009 0.000 ARG E 184 Details of bonding type rmsd hydrogen bonds : bond 0.03292 ( 1105) hydrogen bonds : angle 4.24539 ( 3121) covalent geometry : bond 0.00283 (21806) covalent geometry : angle 0.53539 (29659) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 484 time to evaluate : 2.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 LYS cc_start: 0.7953 (mttt) cc_final: 0.7253 (mtmm) REVERT: A 318 MET cc_start: 0.7654 (mmm) cc_final: 0.7414 (mmm) REVERT: A 347 ARG cc_start: 0.7496 (ptm160) cc_final: 0.7076 (ptp-170) REVERT: A 350 MET cc_start: 0.7425 (tpp) cc_final: 0.6924 (tpp) REVERT: A 365 LEU cc_start: 0.8237 (mm) cc_final: 0.8006 (mp) REVERT: A 399 MET cc_start: 0.7167 (ptp) cc_final: 0.6838 (ptm) REVERT: A 474 GLN cc_start: 0.7811 (OUTLIER) cc_final: 0.7037 (tm-30) REVERT: A 476 ARG cc_start: 0.8122 (ttm110) cc_final: 0.7689 (mtm-85) REVERT: A 544 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7118 (mt-10) REVERT: A 580 LEU cc_start: 0.9170 (tp) cc_final: 0.8813 (tp) REVERT: A 630 LYS cc_start: 0.8852 (ttmt) cc_final: 0.8473 (mttm) REVERT: A 679 TYR cc_start: 0.7571 (m-80) cc_final: 0.7177 (m-80) REVERT: B 129 ARG cc_start: 0.8081 (mmm160) cc_final: 0.7665 (mmm160) REVERT: B 182 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7755 (mm-30) REVERT: B 237 LYS cc_start: 0.8982 (ttmt) cc_final: 0.8746 (ttmm) REVERT: B 238 LYS cc_start: 0.8717 (ttpt) cc_final: 0.8177 (tttp) REVERT: C 19 TYR cc_start: 0.9214 (m-80) cc_final: 0.8897 (m-80) REVERT: C 68 ARG cc_start: 0.8323 (ttm-80) cc_final: 0.8049 (mtm-85) REVERT: C 88 ARG cc_start: 0.8691 (mtm180) cc_final: 0.8454 (mtm180) REVERT: C 207 ARG cc_start: 0.8470 (tpt-90) cc_final: 0.8223 (tpt90) REVERT: C 223 ASP cc_start: 0.7103 (m-30) cc_final: 0.6781 (m-30) REVERT: C 256 TRP cc_start: 0.9245 (OUTLIER) cc_final: 0.8039 (t60) REVERT: C 333 ASN cc_start: 0.8685 (t0) cc_final: 0.8353 (t0) REVERT: D 51 LYS cc_start: 0.8330 (mmmm) cc_final: 0.8011 (mmmm) REVERT: D 57 ASN cc_start: 0.8931 (p0) cc_final: 0.8543 (p0) REVERT: D 80 LYS cc_start: 0.8637 (mttt) cc_final: 0.7999 (tttm) REVERT: D 88 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.7845 (tmm) REVERT: D 96 ASN cc_start: 0.7983 (OUTLIER) cc_final: 0.7690 (m-40) REVERT: D 285 LYS cc_start: 0.8492 (tttt) cc_final: 0.7896 (ttmm) REVERT: E 118 GLN cc_start: 0.6847 (mp10) cc_final: 0.6467 (mm-40) REVERT: E 160 LYS cc_start: 0.8389 (tptt) cc_final: 0.7962 (ttpt) REVERT: E 163 LYS cc_start: 0.8359 (mttt) cc_final: 0.7684 (tptt) REVERT: E 256 LYS cc_start: 0.8345 (mmmt) cc_final: 0.7626 (mmtp) REVERT: E 265 LYS cc_start: 0.8654 (mtmt) cc_final: 0.8427 (mttm) REVERT: F 129 GLU cc_start: 0.6185 (OUTLIER) cc_final: 0.5869 (pp20) REVERT: F 188 MET cc_start: 0.7634 (mmt) cc_final: 0.6269 (mpp) REVERT: F 242 LYS cc_start: 0.8233 (mtmm) cc_final: 0.7875 (mmmm) REVERT: G 8 GLU cc_start: 0.8535 (pm20) cc_final: 0.8307 (pm20) REVERT: G 38 GLN cc_start: 0.8471 (pt0) cc_final: 0.8237 (pt0) REVERT: G 64 HIS cc_start: 0.7845 (p-80) cc_final: 0.7544 (p-80) REVERT: G 120 ASP cc_start: 0.7271 (OUTLIER) cc_final: 0.7040 (m-30) REVERT: G 146 LYS cc_start: 0.7590 (tptp) cc_final: 0.7143 (mmmt) REVERT: G 245 PHE cc_start: 0.7840 (p90) cc_final: 0.7627 (p90) REVERT: H 7 GLU cc_start: 0.7121 (mp0) cc_final: 0.6875 (mp0) REVERT: H 126 LEU cc_start: 0.6820 (OUTLIER) cc_final: 0.6500 (mm) REVERT: H 161 MET cc_start: 0.5887 (mtp) cc_final: 0.5410 (mtp) outliers start: 83 outliers final: 64 residues processed: 539 average time/residue: 0.3626 time to fit residues: 296.3012 Evaluate side-chains 548 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 477 time to evaluate : 2.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 75 TYR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 256 TRP Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 70 MET Chi-restraints excluded: chain F residue 129 GLU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 113 GLU Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 163 THR Chi-restraints excluded: chain H residue 199 MET Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 256 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 58 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 128 optimal weight: 0.7980 chunk 87 optimal weight: 0.4980 chunk 46 optimal weight: 0.6980 chunk 221 optimal weight: 9.9990 chunk 143 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 171 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.168389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.121983 restraints weight = 24681.070| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.99 r_work: 0.2993 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21806 Z= 0.121 Angle : 0.541 15.867 29659 Z= 0.271 Chirality : 0.040 0.147 3451 Planarity : 0.004 0.051 3618 Dihedral : 14.458 129.111 3317 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.05 % Allowed : 23.02 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.77 (0.17), residues: 2555 helix: 1.35 (0.15), residues: 1215 sheet: 0.16 (0.23), residues: 520 loop : -0.38 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 543 HIS 0.003 0.001 HIS B 60 PHE 0.011 0.001 PHE D 290 TYR 0.035 0.001 TYR E 42 ARG 0.010 0.000 ARG A 691 Details of bonding type rmsd hydrogen bonds : bond 0.03240 ( 1105) hydrogen bonds : angle 4.23406 ( 3121) covalent geometry : bond 0.00281 (21806) covalent geometry : angle 0.54082 (29659) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 497 time to evaluate : 2.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 LYS cc_start: 0.7982 (mttt) cc_final: 0.7280 (mtmm) REVERT: A 318 MET cc_start: 0.7785 (mmm) cc_final: 0.7529 (mmm) REVERT: A 347 ARG cc_start: 0.7505 (ptm160) cc_final: 0.7108 (ptp-170) REVERT: A 350 MET cc_start: 0.7776 (tpp) cc_final: 0.7295 (tpp) REVERT: A 365 LEU cc_start: 0.8283 (mm) cc_final: 0.8055 (mp) REVERT: A 399 MET cc_start: 0.7378 (ptp) cc_final: 0.7013 (ptm) REVERT: A 474 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7123 (tm-30) REVERT: A 476 ARG cc_start: 0.8220 (ttm110) cc_final: 0.7795 (mtm-85) REVERT: A 544 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7099 (mt-10) REVERT: A 570 ARG cc_start: 0.7986 (mtp85) cc_final: 0.7761 (mtp85) REVERT: A 580 LEU cc_start: 0.9193 (tp) cc_final: 0.8836 (tp) REVERT: A 630 LYS cc_start: 0.8945 (ttmt) cc_final: 0.8565 (mttm) REVERT: A 679 TYR cc_start: 0.7661 (m-80) cc_final: 0.7207 (m-80) REVERT: B 77 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7597 (tt0) REVERT: B 129 ARG cc_start: 0.8274 (mmm160) cc_final: 0.7870 (mmm160) REVERT: B 182 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7830 (mm-30) REVERT: B 237 LYS cc_start: 0.9065 (ttmt) cc_final: 0.8833 (ttmm) REVERT: B 238 LYS cc_start: 0.8850 (ttpt) cc_final: 0.8306 (tttp) REVERT: C 19 TYR cc_start: 0.9283 (m-80) cc_final: 0.9005 (m-80) REVERT: C 68 ARG cc_start: 0.8471 (ttm-80) cc_final: 0.8204 (mtm-85) REVERT: C 78 MET cc_start: 0.8451 (mpp) cc_final: 0.8144 (mpp) REVERT: C 88 ARG cc_start: 0.8675 (mtm180) cc_final: 0.8450 (mtm180) REVERT: C 184 HIS cc_start: 0.7507 (m-70) cc_final: 0.6569 (t-170) REVERT: C 207 ARG cc_start: 0.8615 (tpt-90) cc_final: 0.8357 (tpt90) REVERT: C 223 ASP cc_start: 0.7334 (m-30) cc_final: 0.6967 (m-30) REVERT: C 256 TRP cc_start: 0.9282 (OUTLIER) cc_final: 0.8122 (t60) REVERT: C 333 ASN cc_start: 0.8736 (t0) cc_final: 0.8412 (t0) REVERT: D 47 THR cc_start: 0.9293 (m) cc_final: 0.8907 (p) REVERT: D 51 LYS cc_start: 0.8374 (mmmm) cc_final: 0.8025 (mmmm) REVERT: D 57 ASN cc_start: 0.9040 (p0) cc_final: 0.8637 (p0) REVERT: D 80 LYS cc_start: 0.8716 (mttt) cc_final: 0.8036 (tttm) REVERT: D 88 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.7951 (tmm) REVERT: D 96 ASN cc_start: 0.8216 (OUTLIER) cc_final: 0.7954 (m-40) REVERT: D 285 LYS cc_start: 0.8527 (tttt) cc_final: 0.7929 (ttmm) REVERT: E 118 GLN cc_start: 0.6899 (mp10) cc_final: 0.6531 (mm-40) REVERT: E 160 LYS cc_start: 0.8385 (tptt) cc_final: 0.7910 (ttpt) REVERT: E 163 LYS cc_start: 0.8469 (mttt) cc_final: 0.7795 (tptt) REVERT: E 236 MET cc_start: 0.6800 (ttm) cc_final: 0.6448 (tmm) REVERT: E 256 LYS cc_start: 0.8363 (mmmt) cc_final: 0.7654 (mmtp) REVERT: E 265 LYS cc_start: 0.8676 (mtmt) cc_final: 0.8456 (mttm) REVERT: F 129 GLU cc_start: 0.6122 (OUTLIER) cc_final: 0.5785 (pp20) REVERT: F 188 MET cc_start: 0.7657 (mmt) cc_final: 0.6237 (mpp) REVERT: F 242 LYS cc_start: 0.8322 (mtmm) cc_final: 0.7950 (mmmm) REVERT: G 8 GLU cc_start: 0.8586 (pm20) cc_final: 0.8350 (pm20) REVERT: G 38 GLN cc_start: 0.8513 (pt0) cc_final: 0.8282 (pt0) REVERT: G 64 HIS cc_start: 0.8018 (p-80) cc_final: 0.7684 (p-80) REVERT: G 146 LYS cc_start: 0.7608 (tptp) cc_final: 0.7168 (mmmt) REVERT: G 245 PHE cc_start: 0.8016 (p90) cc_final: 0.7785 (p90) REVERT: H 7 GLU cc_start: 0.7268 (mp0) cc_final: 0.6979 (mp0) REVERT: H 55 GLU cc_start: 0.7288 (mp0) cc_final: 0.5210 (pm20) REVERT: H 126 LEU cc_start: 0.6827 (OUTLIER) cc_final: 0.6530 (mm) REVERT: H 161 MET cc_start: 0.5930 (mtp) cc_final: 0.5455 (mtp) outliers start: 70 outliers final: 60 residues processed: 544 average time/residue: 0.3553 time to fit residues: 292.0016 Evaluate side-chains 553 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 486 time to evaluate : 2.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 75 TYR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 256 TRP Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 70 MET Chi-restraints excluded: chain F residue 129 GLU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 113 GLU Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 163 THR Chi-restraints excluded: chain H residue 199 MET Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 256 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 109 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 257 optimal weight: 10.0000 chunk 189 optimal weight: 0.9990 chunk 229 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 171 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.166835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.119563 restraints weight = 24549.202| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.85 r_work: 0.2983 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21806 Z= 0.156 Angle : 0.568 15.767 29659 Z= 0.285 Chirality : 0.041 0.151 3451 Planarity : 0.004 0.050 3618 Dihedral : 14.505 130.151 3316 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.14 % Allowed : 23.19 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.71 (0.17), residues: 2555 helix: 1.28 (0.15), residues: 1214 sheet: 0.16 (0.23), residues: 520 loop : -0.40 (0.23), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 638 HIS 0.004 0.001 HIS B 60 PHE 0.012 0.001 PHE D 290 TYR 0.029 0.001 TYR E 42 ARG 0.015 0.001 ARG A 663 Details of bonding type rmsd hydrogen bonds : bond 0.03568 ( 1105) hydrogen bonds : angle 4.30192 ( 3121) covalent geometry : bond 0.00371 (21806) covalent geometry : angle 0.56827 (29659) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13431.83 seconds wall clock time: 233 minutes 24.94 seconds (14004.94 seconds total)