Starting phenix.real_space_refine on Wed Mar 4 11:52:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cq6_30437/03_2026/7cq6_30437.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cq6_30437/03_2026/7cq6_30437.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cq6_30437/03_2026/7cq6_30437.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cq6_30437/03_2026/7cq6_30437.map" model { file = "/net/cci-nas-00/data/ceres_data/7cq6_30437/03_2026/7cq6_30437.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cq6_30437/03_2026/7cq6_30437.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 90 5.16 5 Cl 4 4.86 5 C 8674 2.51 5 N 2228 2.21 5 O 2396 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13392 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1648 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 199} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1642 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 198} Chain breaks: 3 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 4996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 4996 Classifications: {'peptide': 647} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 26, 'TRANS': 620} Chain breaks: 5 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 5046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 5046 Classifications: {'peptide': 650} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 621} Chain breaks: 6 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.08, per 1000 atoms: 0.23 Number of scatterers: 13392 At special positions: 0 Unit cell: (134.193, 113.464, 127.647, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 90 16.00 O 2396 8.00 N 2228 7.00 C 8674 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS A 112 " - pdb=" SG CYS A 171 " distance=2.02 Simple disulfide: pdb=" SG CYS A 174 " - pdb=" SG CYS A 255 " distance=2.06 Simple disulfide: pdb=" SG CYS A 221 " - pdb=" SG CYS A 275 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 142 " distance=2.03 Simple disulfide: pdb=" SG CYS B 101 " - pdb=" SG CYS B 115 " distance=2.06 Simple disulfide: pdb=" SG CYS B 112 " - pdb=" SG CYS B 171 " distance=2.03 Simple disulfide: pdb=" SG CYS B 174 " - pdb=" SG CYS B 255 " distance=2.02 Simple disulfide: pdb=" SG CYS B 221 " - pdb=" SG CYS B 275 " distance=2.03 Simple disulfide: pdb=" SG CYS C 438 " - pdb=" SG CYS C 454 " distance=2.04 Simple disulfide: pdb=" SG CYS D 438 " - pdb=" SG CYS D 454 " distance=2.03 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=1, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG E 1 " - " ASN A 263 " " NAG F 1 " - " ASN B 263 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 542.8 milliseconds 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3208 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 8 sheets defined 63.7% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 83 through 105 removed outlier: 3.858A pdb=" N LEU A 87 " --> pdb=" O GLU A 83 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 88 " --> pdb=" O CYS A 84 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER A 94 " --> pdb=" O ASP A 90 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 129 removed outlier: 3.547A pdb=" N GLN A 120 " --> pdb=" O TYR A 116 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN A 121 " --> pdb=" O PRO A 117 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 167 Processing helix chain 'A' and resid 186 through 203 Processing helix chain 'A' and resid 217 through 222 removed outlier: 3.795A pdb=" N CYS A 221 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 217 through 222' Processing helix chain 'A' and resid 224 through 244 removed outlier: 3.685A pdb=" N TYR A 228 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU A 243 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU A 244 " --> pdb=" O LYS A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 271 Processing helix chain 'A' and resid 282 through 306 removed outlier: 3.524A pdb=" N PHE A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) Proline residue: A 296 - end of helix Processing helix chain 'B' and resid 81 through 87 Processing helix chain 'B' and resid 90 through 105 removed outlier: 3.518A pdb=" N GLU B 97 " --> pdb=" O ASN B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 115 removed outlier: 3.693A pdb=" N CYS B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 131 removed outlier: 3.780A pdb=" N ASP B 127 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE B 129 " --> pdb=" O LYS B 125 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG B 131 " --> pdb=" O ASP B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 169 removed outlier: 3.695A pdb=" N SER B 159 " --> pdb=" O VAL B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 201 removed outlier: 3.548A pdb=" N ASN B 191 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU B 201 " --> pdb=" O LEU B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 244 removed outlier: 3.604A pdb=" N TYR B 228 " --> pdb=" O CYS B 224 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS B 240 " --> pdb=" O SER B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 270 removed outlier: 3.854A pdb=" N ALA B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 293 removed outlier: 3.827A pdb=" N VAL B 285 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE B 286 " --> pdb=" O THR B 282 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE B 291 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU B 293 " --> pdb=" O SER B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 306 removed outlier: 3.801A pdb=" N LEU B 301 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE B 304 " --> pdb=" O TYR B 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 115 removed outlier: 3.585A pdb=" N ARG C 113 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE C 114 " --> pdb=" O GLU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 170 removed outlier: 4.708A pdb=" N ARG C 126 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TRP C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG C 157 " --> pdb=" O GLY C 153 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL C 158 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS C 165 " --> pdb=" O GLY C 161 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N GLU C 168 " --> pdb=" O ASP C 164 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LYS C 169 " --> pdb=" O LYS C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 196 removed outlier: 3.975A pdb=" N VAL C 189 " --> pdb=" O ALA C 185 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE C 193 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL C 194 " --> pdb=" O GLY C 190 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE C 196 " --> pdb=" O VAL C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 202 removed outlier: 3.618A pdb=" N ALA C 202 " --> pdb=" O PRO C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 214 Processing helix chain 'C' and resid 223 through 240 Processing helix chain 'C' and resid 247 through 249 No H-bonds generated for 'chain 'C' and resid 247 through 249' Processing helix chain 'C' and resid 250 through 262 removed outlier: 3.744A pdb=" N SER C 262 " --> pdb=" O ALA C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 280 removed outlier: 3.754A pdb=" N ARG C 280 " --> pdb=" O GLU C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 302 removed outlier: 4.018A pdb=" N ARG C 286 " --> pdb=" O ASP C 282 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP C 287 " --> pdb=" O THR C 283 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA C 291 " --> pdb=" O ASP C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 314 Processing helix chain 'C' and resid 320 through 347 Processing helix chain 'C' and resid 374 through 405 removed outlier: 3.692A pdb=" N PHE C 378 " --> pdb=" O GLU C 374 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA C 380 " --> pdb=" O PRO C 376 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ARG C 405 " --> pdb=" O MET C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 434 removed outlier: 3.527A pdb=" N ALA C 421 " --> pdb=" O ALA C 417 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA C 425 " --> pdb=" O ALA C 421 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA C 428 " --> pdb=" O THR C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 465 Processing helix chain 'C' and resid 469 through 478 Processing helix chain 'C' and resid 486 through 503 removed outlier: 3.955A pdb=" N PHE C 499 " --> pdb=" O LEU C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 536 Processing helix chain 'C' and resid 543 through 560 removed outlier: 3.812A pdb=" N TYR C 547 " --> pdb=" O ASP C 543 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU C 549 " --> pdb=" O GLY C 545 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET C 550 " --> pdb=" O LYS C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 575 Processing helix chain 'C' and resid 579 through 595 Processing helix chain 'C' and resid 600 through 609 removed outlier: 4.029A pdb=" N GLN C 609 " --> pdb=" O HIS C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 630 removed outlier: 3.551A pdb=" N GLU C 629 " --> pdb=" O THR C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 652 Processing helix chain 'C' and resid 681 through 688 Processing helix chain 'C' and resid 753 through 764 removed outlier: 3.567A pdb=" N LEU C 760 " --> pdb=" O ARG C 756 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA C 763 " --> pdb=" O LYS C 759 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU C 764 " --> pdb=" O LEU C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 784 through 789 removed outlier: 3.665A pdb=" N ALA C 788 " --> pdb=" O ARG C 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 110 Processing helix chain 'D' and resid 121 through 170 removed outlier: 3.504A pdb=" N TRP D 127 " --> pdb=" O GLU D 123 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS D 165 " --> pdb=" O GLY D 161 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N GLU D 168 " --> pdb=" O ASP D 164 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS D 169 " --> pdb=" O LYS D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 196 removed outlier: 3.510A pdb=" N LEU D 177 " --> pdb=" O SER D 173 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU D 178 " --> pdb=" O PHE D 174 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TRP D 179 " --> pdb=" O SER D 175 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA D 184 " --> pdb=" O ALA D 180 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE D 193 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N VAL D 194 " --> pdb=" O GLY D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 202 removed outlier: 3.659A pdb=" N ALA D 202 " --> pdb=" O PRO D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 215 removed outlier: 3.641A pdb=" N ASN D 214 " --> pdb=" O LYS D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 240 removed outlier: 3.509A pdb=" N LEU D 227 " --> pdb=" O ARG D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 264 removed outlier: 4.215A pdb=" N GLN D 263 " --> pdb=" O ALA D 259 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLY D 264 " --> pdb=" O GLY D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 302 removed outlier: 3.628A pdb=" N ARG D 286 " --> pdb=" O ASP D 282 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASP D 287 " --> pdb=" O THR D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 314 Processing helix chain 'D' and resid 320 through 346 removed outlier: 3.594A pdb=" N HIS D 346 " --> pdb=" O LEU D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 373 No H-bonds generated for 'chain 'D' and resid 371 through 373' Processing helix chain 'D' and resid 374 through 407 removed outlier: 3.709A pdb=" N PHE D 402 " --> pdb=" O TRP D 398 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG D 405 " --> pdb=" O MET D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 434 removed outlier: 3.816A pdb=" N ALA D 425 " --> pdb=" O ALA D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 478 Processing helix chain 'D' and resid 486 through 505 removed outlier: 3.516A pdb=" N LEU D 495 " --> pdb=" O GLY D 491 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL D 496 " --> pdb=" O LEU D 492 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE D 499 " --> pdb=" O LEU D 495 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR D 505 " --> pdb=" O ALA D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 536 removed outlier: 3.568A pdb=" N SER D 517 " --> pdb=" O VAL D 513 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TRP D 524 " --> pdb=" O ILE D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 560 removed outlier: 3.567A pdb=" N TYR D 547 " --> pdb=" O ASP D 543 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU D 549 " --> pdb=" O GLY D 545 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET D 550 " --> pdb=" O LYS D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 574 removed outlier: 3.804A pdb=" N VAL D 568 " --> pdb=" O LEU D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 596 Processing helix chain 'D' and resid 600 through 608 Processing helix chain 'D' and resid 646 through 651 Processing helix chain 'D' and resid 681 through 688 Processing helix chain 'D' and resid 709 through 714 Processing helix chain 'D' and resid 753 through 764 Processing helix chain 'D' and resid 784 through 788 Processing sheet with id=AA1, first strand: chain 'C' and resid 265 through 266 Processing sheet with id=AA2, first strand: chain 'C' and resid 438 through 439 Processing sheet with id=AA3, first strand: chain 'C' and resid 638 through 639 removed outlier: 6.614A pdb=" N LEU C 638 " --> pdb=" O VAL C 664 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 747 through 749 removed outlier: 6.711A pdb=" N VAL C 748 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY C 780 " --> pdb=" O VAL C 771 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 438 through 439 Processing sheet with id=AA6, first strand: chain 'D' and resid 638 through 639 removed outlier: 5.502A pdb=" N LEU D 638 " --> pdb=" O VAL D 664 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 641 through 643 Processing sheet with id=AA8, first strand: chain 'D' and resid 747 through 749 removed outlier: 4.431A pdb=" N GLY D 780 " --> pdb=" O VAL D 771 " (cutoff:3.500A) 739 hydrogen bonds defined for protein. 2190 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.91 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3823 1.33 - 1.46: 2746 1.46 - 1.58: 6973 1.58 - 1.70: 0 1.70 - 1.82: 137 Bond restraints: 13679 Sorted by residual: bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.58e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.22e+00 bond pdb=" CB PRO C 582 " pdb=" CG PRO C 582 " ideal model delta sigma weight residual 1.492 1.381 0.111 5.00e-02 4.00e+02 4.94e+00 bond pdb=" CG1 ILE D 229 " pdb=" CD1 ILE D 229 " ideal model delta sigma weight residual 1.513 1.430 0.083 3.90e-02 6.57e+02 4.48e+00 bond pdb=" CB VAL C 586 " pdb=" CG1 VAL C 586 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.35e+00 ... (remaining 13674 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 17384 2.03 - 4.05: 958 4.05 - 6.08: 156 6.08 - 8.11: 51 8.11 - 10.14: 20 Bond angle restraints: 18569 Sorted by residual: angle pdb=" C GLY D 205 " pdb=" N ILE D 206 " pdb=" CA ILE D 206 " ideal model delta sigma weight residual 120.24 124.67 -4.43 6.30e-01 2.52e+00 4.94e+01 angle pdb=" N ILE D 114 " pdb=" CA ILE D 114 " pdb=" C ILE D 114 " ideal model delta sigma weight residual 113.53 107.51 6.02 9.80e-01 1.04e+00 3.77e+01 angle pdb=" N THR D 633 " pdb=" CA THR D 633 " pdb=" C THR D 633 " ideal model delta sigma weight residual 109.81 119.95 -10.14 2.21e+00 2.05e-01 2.10e+01 angle pdb=" C ARG B 271 " pdb=" N THR B 272 " pdb=" CA THR B 272 " ideal model delta sigma weight residual 121.54 129.99 -8.45 1.91e+00 2.74e-01 1.96e+01 angle pdb=" C ARG A 271 " pdb=" N THR A 272 " pdb=" CA THR A 272 " ideal model delta sigma weight residual 121.54 129.89 -8.35 1.91e+00 2.74e-01 1.91e+01 ... (remaining 18564 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.81: 7716 15.81 - 31.62: 380 31.62 - 47.44: 54 47.44 - 63.25: 5 63.25 - 79.06: 6 Dihedral angle restraints: 8161 sinusoidal: 3208 harmonic: 4953 Sorted by residual: dihedral pdb=" CA CYS B 115 " pdb=" C CYS B 115 " pdb=" N TYR B 116 " pdb=" CA TYR B 116 " ideal model delta harmonic sigma weight residual 180.00 144.48 35.52 0 5.00e+00 4.00e-02 5.05e+01 dihedral pdb=" CA ILE D 218 " pdb=" C ILE D 218 " pdb=" N PRO D 219 " pdb=" CA PRO D 219 " ideal model delta harmonic sigma weight residual -180.00 -151.09 -28.91 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA PRO A 108 " pdb=" C PRO A 108 " pdb=" N VAL A 109 " pdb=" CA VAL A 109 " ideal model delta harmonic sigma weight residual -180.00 -152.46 -27.54 0 5.00e+00 4.00e-02 3.03e+01 ... (remaining 8158 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1521 0.061 - 0.122: 538 0.122 - 0.183: 100 0.183 - 0.244: 18 0.244 - 0.305: 2 Chirality restraints: 2179 Sorted by residual: chirality pdb=" CB VAL C 513 " pdb=" CA VAL C 513 " pdb=" CG1 VAL C 513 " pdb=" CG2 VAL C 513 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CA ARG B 107 " pdb=" N ARG B 107 " pdb=" C ARG B 107 " pdb=" CB ARG B 107 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CA ARG A 107 " pdb=" N ARG A 107 " pdb=" C ARG A 107 " pdb=" CB ARG A 107 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 2176 not shown) Planarity restraints: 2326 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 179 " 0.035 2.00e-02 2.50e+03 2.68e-02 1.79e+01 pdb=" CG TRP C 179 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 TRP C 179 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP C 179 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 179 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP C 179 " -0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP C 179 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 179 " 0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 179 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP C 179 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 179 " 0.034 2.00e-02 2.50e+03 2.60e-02 1.68e+01 pdb=" CG TRP D 179 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 TRP D 179 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP D 179 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 179 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 179 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP D 179 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 179 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 179 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP D 179 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 272 " -0.016 2.00e-02 2.50e+03 3.14e-02 9.84e+00 pdb=" C THR B 272 " 0.054 2.00e-02 2.50e+03 pdb=" O THR B 272 " -0.020 2.00e-02 2.50e+03 pdb=" N PHE B 273 " -0.018 2.00e-02 2.50e+03 ... (remaining 2323 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2604 2.77 - 3.30: 12417 3.30 - 3.83: 21284 3.83 - 4.37: 25495 4.37 - 4.90: 44859 Nonbonded interactions: 106659 Sorted by model distance: nonbonded pdb=" O MET C 368 " pdb=" OH TYR C 579 " model vdw 2.233 3.040 nonbonded pdb=" O MET D 368 " pdb=" OH TYR D 579 " model vdw 2.270 3.040 nonbonded pdb=" O LEU D 500 " pdb=" OG1 THR D 504 " model vdw 2.274 3.040 nonbonded pdb=" OG SER D 298 " pdb=" OG1 THR D 335 " model vdw 2.287 3.040 nonbonded pdb=" OD1 ASP A 76 " pdb=" OG SER A 145 " model vdw 2.301 3.040 ... (remaining 106654 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 73 through 245 or resid 253 through 306)) selection = (chain 'B' and (resid 73 through 204 or resid 216 through 245 or resid 253 throu \ gh 306)) } ncs_group { reference = (chain 'C' and (resid 94 through 617 or resid 625 through 652 or resid 657 throu \ gh 688 or resid 708 through 902)) selection = (chain 'D' and (resid 94 through 366 or (resid 367 and (name N or name CA or nam \ e C or name O or name CB )) or resid 368 through 617 or resid 625 through 688 or \ (resid 708 through 710 and (name N or name CA or name C or name O or name CB )) \ or resid 711 through 716 or resid 736 through 902)) } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 1.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.520 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 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:8.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 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 : 0.010 0.111 13695 Z= 0.420 Angle : 1.128 10.136 18603 Z= 0.606 Chirality : 0.062 0.305 2179 Planarity : 0.008 0.067 2324 Dihedral : 9.887 79.060 4920 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 0.27 % Allowed : 2.06 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.47 (0.15), residues: 1672 helix: -2.65 (0.11), residues: 1051 sheet: -3.33 (1.71), residues: 5 loop : -3.32 (0.21), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG C 526 TYR 0.029 0.003 TYR C 406 PHE 0.031 0.004 PHE C 329 TRP 0.069 0.006 TRP D 179 HIS 0.010 0.002 HIS C 479 Details of bonding type rmsd covalent geometry : bond 0.01037 (13679) covalent geometry : angle 1.12084 (18569) SS BOND : bond 0.01367 ( 11) SS BOND : angle 2.29439 ( 22) hydrogen bonds : bond 0.21883 ( 739) hydrogen bonds : angle 7.80621 ( 2190) Misc. bond : bond 0.00173 ( 1) link_BETA1-4 : bond 0.00353 ( 2) link_BETA1-4 : angle 3.10193 ( 6) link_NAG-ASN : bond 0.00440 ( 2) link_NAG-ASN : angle 5.53224 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 234 time to evaluate : 0.476 Fit side-chains REVERT: A 160 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7378 (mt-10) REVERT: A 244 LEU cc_start: 0.7406 (pp) cc_final: 0.7206 (pp) REVERT: B 229 LYS cc_start: 0.8415 (mmpt) cc_final: 0.8152 (mtmt) REVERT: B 238 MET cc_start: 0.7698 (mtt) cc_final: 0.7485 (mtm) REVERT: B 286 ILE cc_start: 0.8480 (mm) cc_final: 0.8159 (mt) REVERT: C 111 GLU cc_start: 0.6681 (tt0) cc_final: 0.6045 (mt-10) REVERT: C 287 ASP cc_start: 0.8207 (m-30) cc_final: 0.7889 (m-30) REVERT: C 562 MET cc_start: 0.8086 (ptp) cc_final: 0.7754 (ptm) REVERT: C 648 VAL cc_start: 0.7876 (t) cc_final: 0.7648 (p) REVERT: C 674 ARG cc_start: 0.7046 (mtm-85) cc_final: 0.6572 (ttm110) REVERT: D 107 PHE cc_start: 0.7666 (t80) cc_final: 0.7385 (t80) REVERT: D 217 LYS cc_start: 0.8034 (mtpp) cc_final: 0.7731 (mtpt) REVERT: D 274 LYS cc_start: 0.5830 (mttt) cc_final: 0.5611 (pttt) REVERT: D 584 MET cc_start: 0.8682 (ptm) cc_final: 0.8299 (ttp) REVERT: D 658 HIS cc_start: 0.6323 (m-70) cc_final: 0.6106 (m-70) REVERT: D 759 LYS cc_start: 0.7535 (ttpt) cc_final: 0.7040 (ttpt) REVERT: D 760 LEU cc_start: 0.7549 (mt) cc_final: 0.7345 (mm) outliers start: 4 outliers final: 1 residues processed: 237 average time/residue: 0.7851 time to fit residues: 198.5844 Evaluate side-chains 167 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 166 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 ASN ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN ** C 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 GLN C 479 HIS C 555 GLN C 657 ASN C 777 GLN D 162 ASN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 HIS D 263 GLN ** D 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 555 GLN D 657 ASN D 683 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.140130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.107777 restraints weight = 17179.918| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.62 r_work: 0.3085 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13695 Z= 0.142 Angle : 0.655 12.546 18603 Z= 0.340 Chirality : 0.041 0.163 2179 Planarity : 0.005 0.053 2324 Dihedral : 5.729 43.235 1916 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 1.85 % Allowed : 7.35 % Favored : 90.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.19), residues: 1672 helix: -0.34 (0.15), residues: 1063 sheet: -2.88 (2.04), residues: 5 loop : -3.06 (0.22), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 326 TYR 0.014 0.001 TYR B 188 PHE 0.017 0.001 PHE D 392 TRP 0.032 0.002 TRP D 179 HIS 0.004 0.001 HIS C 605 Details of bonding type rmsd covalent geometry : bond 0.00308 (13679) covalent geometry : angle 0.65145 (18569) SS BOND : bond 0.00396 ( 11) SS BOND : angle 1.19406 ( 22) hydrogen bonds : bond 0.05420 ( 739) hydrogen bonds : angle 4.46586 ( 2190) Misc. bond : bond 0.00140 ( 1) link_BETA1-4 : bond 0.00507 ( 2) link_BETA1-4 : angle 1.25932 ( 6) link_NAG-ASN : bond 0.00245 ( 2) link_NAG-ASN : angle 3.25335 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 180 time to evaluate : 0.358 Fit side-chains REVERT: A 144 ARG cc_start: 0.7690 (pmt-80) cc_final: 0.7274 (pmm150) REVERT: A 160 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8224 (mt-10) REVERT: A 195 HIS cc_start: 0.8261 (OUTLIER) cc_final: 0.7810 (t-90) REVERT: A 237 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7834 (tm-30) REVERT: B 167 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.8084 (mp10) REVERT: B 229 LYS cc_start: 0.8619 (mmpt) cc_final: 0.8097 (mtmt) REVERT: C 99 TYR cc_start: 0.8110 (t80) cc_final: 0.7722 (t80) REVERT: C 111 GLU cc_start: 0.6357 (tt0) cc_final: 0.5651 (mt-10) REVERT: C 572 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8217 (mt-10) REVERT: C 674 ARG cc_start: 0.6751 (mtm-85) cc_final: 0.6426 (ttm110) REVERT: D 107 PHE cc_start: 0.7251 (t80) cc_final: 0.6897 (t80) REVERT: D 217 LYS cc_start: 0.8276 (mtpp) cc_final: 0.7901 (mtpt) REVERT: D 439 GLN cc_start: 0.8516 (tt0) cc_final: 0.8279 (mt0) REVERT: D 459 TYR cc_start: 0.8475 (m-80) cc_final: 0.8227 (m-80) REVERT: D 584 MET cc_start: 0.9124 (ptm) cc_final: 0.8875 (ttp) REVERT: D 617 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.5578 (mm-30) REVERT: D 658 HIS cc_start: 0.6214 (m-70) cc_final: 0.5985 (m-70) REVERT: D 759 LYS cc_start: 0.6936 (ttpt) cc_final: 0.6355 (ttpt) outliers start: 27 outliers final: 5 residues processed: 195 average time/residue: 0.6186 time to fit residues: 130.6099 Evaluate side-chains 169 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 161 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 617 GLU Chi-restraints excluded: chain D residue 754 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 141 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 160 optimal weight: 7.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 ASN ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 HIS C 263 GLN C 439 GLN C 623 HIS ** C 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 768 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.138732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.106181 restraints weight = 17406.408| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.64 r_work: 0.3039 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13695 Z= 0.161 Angle : 0.631 12.339 18603 Z= 0.324 Chirality : 0.042 0.152 2179 Planarity : 0.005 0.050 2324 Dihedral : 5.145 31.642 1915 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 2.20 % Allowed : 8.93 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.20), residues: 1672 helix: 0.52 (0.16), residues: 1069 sheet: -2.80 (2.01), residues: 5 loop : -2.83 (0.23), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 526 TYR 0.012 0.001 TYR A 116 PHE 0.017 0.001 PHE D 392 TRP 0.021 0.002 TRP D 179 HIS 0.006 0.001 HIS C 479 Details of bonding type rmsd covalent geometry : bond 0.00382 (13679) covalent geometry : angle 0.62725 (18569) SS BOND : bond 0.00415 ( 11) SS BOND : angle 1.32011 ( 22) hydrogen bonds : bond 0.05039 ( 739) hydrogen bonds : angle 4.10842 ( 2190) Misc. bond : bond 0.00087 ( 1) link_BETA1-4 : bond 0.00146 ( 2) link_BETA1-4 : angle 1.57295 ( 6) link_NAG-ASN : bond 0.00548 ( 2) link_NAG-ASN : angle 2.87227 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 170 time to evaluate : 0.475 Fit side-chains REVERT: A 160 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8268 (mt-10) REVERT: A 195 HIS cc_start: 0.8291 (OUTLIER) cc_final: 0.7880 (t-90) REVERT: B 152 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.7522 (ttt) REVERT: B 167 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.8138 (mp10) REVERT: B 168 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8457 (tp30) REVERT: B 229 LYS cc_start: 0.8583 (mmpt) cc_final: 0.8053 (mtpt) REVERT: C 99 TYR cc_start: 0.8095 (t80) cc_final: 0.7721 (t80) REVERT: C 111 GLU cc_start: 0.6427 (tt0) cc_final: 0.5679 (mt-10) REVERT: C 674 ARG cc_start: 0.6753 (mtm-85) cc_final: 0.6370 (ttm110) REVERT: D 107 PHE cc_start: 0.7181 (t80) cc_final: 0.6859 (t80) REVERT: D 217 LYS cc_start: 0.8291 (mtpp) cc_final: 0.7945 (mtmt) REVERT: D 459 TYR cc_start: 0.8486 (m-80) cc_final: 0.8210 (m-80) REVERT: D 571 MET cc_start: 0.9102 (ttm) cc_final: 0.8872 (ttp) REVERT: D 584 MET cc_start: 0.9168 (ptm) cc_final: 0.8958 (ttp) REVERT: D 617 GLU cc_start: 0.6588 (OUTLIER) cc_final: 0.5397 (mm-30) REVERT: D 658 HIS cc_start: 0.6227 (m-70) cc_final: 0.6013 (m-70) REVERT: D 731 ARG cc_start: 0.5705 (mtt90) cc_final: 0.5120 (mmp-170) REVERT: D 759 LYS cc_start: 0.6951 (ttpt) cc_final: 0.6445 (ttmt) outliers start: 32 outliers final: 10 residues processed: 186 average time/residue: 0.6314 time to fit residues: 126.7894 Evaluate side-chains 174 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 639 ARG Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 325 TRP Chi-restraints excluded: chain D residue 617 GLU Chi-restraints excluded: chain D residue 754 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 41 optimal weight: 3.9990 chunk 148 optimal weight: 8.9990 chunk 134 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 67 optimal weight: 7.9990 chunk 160 optimal weight: 4.9990 chunk 155 optimal weight: 0.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 GLN ** C 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.138656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.105984 restraints weight = 17365.513| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.64 r_work: 0.3070 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 13695 Z= 0.145 Angle : 0.605 12.040 18603 Z= 0.310 Chirality : 0.041 0.146 2179 Planarity : 0.004 0.049 2324 Dihedral : 4.777 26.389 1915 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 1.92 % Allowed : 10.23 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.21), residues: 1672 helix: 1.02 (0.16), residues: 1067 sheet: -2.45 (2.26), residues: 5 loop : -2.71 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 110 TYR 0.012 0.001 TYR B 116 PHE 0.015 0.001 PHE D 392 TRP 0.019 0.002 TRP C 524 HIS 0.005 0.001 HIS C 605 Details of bonding type rmsd covalent geometry : bond 0.00344 (13679) covalent geometry : angle 0.60117 (18569) SS BOND : bond 0.00332 ( 11) SS BOND : angle 1.31760 ( 22) hydrogen bonds : bond 0.04564 ( 739) hydrogen bonds : angle 3.94411 ( 2190) Misc. bond : bond 0.00250 ( 1) link_BETA1-4 : bond 0.00258 ( 2) link_BETA1-4 : angle 1.41507 ( 6) link_NAG-ASN : bond 0.00998 ( 2) link_NAG-ASN : angle 2.66326 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 0.453 Fit side-chains REVERT: A 144 ARG cc_start: 0.7778 (pmt-80) cc_final: 0.7286 (pmm150) REVERT: A 148 MET cc_start: 0.8712 (ptp) cc_final: 0.8498 (ptm) REVERT: A 160 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8252 (mt-10) REVERT: A 195 HIS cc_start: 0.8275 (OUTLIER) cc_final: 0.7891 (t-90) REVERT: A 201 GLU cc_start: 0.7262 (tt0) cc_final: 0.6887 (mm-30) REVERT: B 168 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8427 (tp30) REVERT: B 229 LYS cc_start: 0.8628 (mmpt) cc_final: 0.8154 (mtmt) REVERT: C 99 TYR cc_start: 0.8105 (t80) cc_final: 0.7666 (t80) REVERT: C 111 GLU cc_start: 0.6457 (tt0) cc_final: 0.5656 (mt-10) REVERT: C 674 ARG cc_start: 0.6702 (mtm-85) cc_final: 0.5758 (ttm110) REVERT: C 676 GLN cc_start: 0.7248 (OUTLIER) cc_final: 0.5322 (mp10) REVERT: C 737 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7215 (pp) REVERT: D 107 PHE cc_start: 0.7201 (t80) cc_final: 0.6869 (t80) REVERT: D 217 LYS cc_start: 0.8302 (mtpp) cc_final: 0.7962 (mtmt) REVERT: D 566 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9088 (tt) REVERT: D 571 MET cc_start: 0.9057 (ttm) cc_final: 0.8839 (ttp) REVERT: D 617 GLU cc_start: 0.6532 (OUTLIER) cc_final: 0.5354 (mm-30) REVERT: D 658 HIS cc_start: 0.6239 (m-70) cc_final: 0.6016 (m-70) REVERT: D 731 ARG cc_start: 0.5584 (mtt90) cc_final: 0.5038 (mmp-170) REVERT: D 759 LYS cc_start: 0.7003 (ttpt) cc_final: 0.6408 (ttmt) outliers start: 28 outliers final: 11 residues processed: 181 average time/residue: 0.6177 time to fit residues: 121.4062 Evaluate side-chains 168 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 480 ASP Chi-restraints excluded: chain C residue 639 ARG Chi-restraints excluded: chain C residue 676 GLN Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 325 TRP Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 617 GLU Chi-restraints excluded: chain D residue 754 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 96 optimal weight: 7.9990 chunk 162 optimal weight: 0.3980 chunk 152 optimal weight: 0.8980 chunk 121 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 139 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 167 optimal weight: 0.3980 chunk 85 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 GLN C 768 HIS ** D 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.140743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.108179 restraints weight = 17420.629| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.65 r_work: 0.3045 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 13695 Z= 0.118 Angle : 0.569 10.942 18603 Z= 0.291 Chirality : 0.039 0.144 2179 Planarity : 0.004 0.049 2324 Dihedral : 4.483 27.843 1915 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 1.51 % Allowed : 11.95 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.21), residues: 1672 helix: 1.37 (0.16), residues: 1069 sheet: None (None), residues: 0 loop : -2.59 (0.23), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 110 TYR 0.014 0.001 TYR A 116 PHE 0.012 0.001 PHE D 392 TRP 0.020 0.001 TRP C 524 HIS 0.005 0.001 HIS C 605 Details of bonding type rmsd covalent geometry : bond 0.00265 (13679) covalent geometry : angle 0.56611 (18569) SS BOND : bond 0.00303 ( 11) SS BOND : angle 1.04534 ( 22) hydrogen bonds : bond 0.04056 ( 739) hydrogen bonds : angle 3.80892 ( 2190) Misc. bond : bond 0.00175 ( 1) link_BETA1-4 : bond 0.00670 ( 2) link_BETA1-4 : angle 1.37524 ( 6) link_NAG-ASN : bond 0.00460 ( 2) link_NAG-ASN : angle 2.46535 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 0.444 Fit side-chains REVERT: A 195 HIS cc_start: 0.8278 (OUTLIER) cc_final: 0.7865 (t-90) REVERT: A 201 GLU cc_start: 0.7273 (tt0) cc_final: 0.6869 (mm-30) REVERT: A 223 ASN cc_start: 0.8360 (t0) cc_final: 0.8051 (t0) REVERT: B 168 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8374 (tp30) REVERT: B 192 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8646 (tp) REVERT: B 229 LYS cc_start: 0.8600 (mmpt) cc_final: 0.8034 (mtpt) REVERT: C 99 TYR cc_start: 0.7944 (t80) cc_final: 0.7602 (t80) REVERT: C 111 GLU cc_start: 0.6347 (tt0) cc_final: 0.5525 (mt-10) REVERT: D 97 LEU cc_start: 0.6665 (OUTLIER) cc_final: 0.6243 (pp) REVERT: D 107 PHE cc_start: 0.6875 (t80) cc_final: 0.6593 (t80) REVERT: D 217 LYS cc_start: 0.8245 (mtpp) cc_final: 0.7951 (mtmt) REVERT: D 439 GLN cc_start: 0.8221 (tt0) cc_final: 0.7954 (mt0) REVERT: D 566 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.9037 (tt) REVERT: D 617 GLU cc_start: 0.6575 (OUTLIER) cc_final: 0.5358 (mm-30) REVERT: D 658 HIS cc_start: 0.6059 (m-70) cc_final: 0.5829 (m-70) REVERT: D 731 ARG cc_start: 0.5486 (mtt90) cc_final: 0.4776 (mmp-170) REVERT: D 759 LYS cc_start: 0.6862 (ttpt) cc_final: 0.6264 (ttmt) outliers start: 22 outliers final: 8 residues processed: 173 average time/residue: 0.5898 time to fit residues: 111.3632 Evaluate side-chains 164 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 639 ARG Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 325 TRP Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 617 GLU Chi-restraints excluded: chain D residue 754 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 57 optimal weight: 9.9990 chunk 16 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 146 optimal weight: 0.5980 chunk 59 optimal weight: 4.9990 chunk 42 optimal weight: 0.0040 chunk 6 optimal weight: 0.0970 chunk 24 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 GLN ** D 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.142412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.110046 restraints weight = 17332.373| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.65 r_work: 0.3113 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.077 13695 Z= 0.110 Angle : 0.552 9.739 18603 Z= 0.283 Chirality : 0.039 0.143 2179 Planarity : 0.004 0.049 2324 Dihedral : 4.275 24.626 1915 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 1.92 % Allowed : 11.68 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.21), residues: 1672 helix: 1.72 (0.16), residues: 1070 sheet: None (None), residues: 0 loop : -2.53 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 674 TYR 0.013 0.001 TYR B 116 PHE 0.011 0.001 PHE D 392 TRP 0.021 0.001 TRP C 524 HIS 0.004 0.001 HIS C 605 Details of bonding type rmsd covalent geometry : bond 0.00237 (13679) covalent geometry : angle 0.54952 (18569) SS BOND : bond 0.00309 ( 11) SS BOND : angle 0.96124 ( 22) hydrogen bonds : bond 0.03683 ( 739) hydrogen bonds : angle 3.66711 ( 2190) Misc. bond : bond 0.00434 ( 1) link_BETA1-4 : bond 0.00319 ( 2) link_BETA1-4 : angle 1.35145 ( 6) link_NAG-ASN : bond 0.00574 ( 2) link_NAG-ASN : angle 2.30974 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 0.554 Fit side-chains REVERT: A 144 ARG cc_start: 0.7623 (pmt-80) cc_final: 0.7226 (pmm150) REVERT: A 201 GLU cc_start: 0.7007 (tt0) cc_final: 0.6745 (mm-30) REVERT: A 242 ASN cc_start: 0.7982 (OUTLIER) cc_final: 0.7476 (t0) REVERT: B 167 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7105 (mp10) REVERT: B 229 LYS cc_start: 0.8582 (mmpt) cc_final: 0.8089 (mtmt) REVERT: C 99 TYR cc_start: 0.7942 (t80) cc_final: 0.7651 (t80) REVERT: C 103 GLU cc_start: 0.6000 (mt-10) cc_final: 0.5579 (tm-30) REVERT: C 111 GLU cc_start: 0.6489 (tt0) cc_final: 0.5695 (mt-10) REVERT: C 439 GLN cc_start: 0.7824 (mt0) cc_final: 0.7598 (mt0) REVERT: D 103 GLU cc_start: 0.8053 (tp30) cc_final: 0.7069 (tm-30) REVERT: D 107 PHE cc_start: 0.7039 (t80) cc_final: 0.6753 (t80) REVERT: D 217 LYS cc_start: 0.8322 (mtpp) cc_final: 0.8064 (mtmt) REVERT: D 439 GLN cc_start: 0.8136 (tt0) cc_final: 0.7909 (mt0) REVERT: D 566 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9089 (tt) REVERT: D 572 GLU cc_start: 0.8212 (tt0) cc_final: 0.8009 (tt0) REVERT: D 604 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.8116 (ptp) REVERT: D 759 LYS cc_start: 0.7150 (ttpt) cc_final: 0.6586 (ttmt) REVERT: D 785 LYS cc_start: 0.7758 (mtpt) cc_final: 0.7301 (mtpp) outliers start: 28 outliers final: 10 residues processed: 190 average time/residue: 0.5556 time to fit residues: 115.2829 Evaluate side-chains 169 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 155 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ASN Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 480 ASP Chi-restraints excluded: chain C residue 639 ARG Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 325 TRP Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 754 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 97 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 92 optimal weight: 10.0000 chunk 165 optimal weight: 6.9990 chunk 150 optimal weight: 0.9990 chunk 159 optimal weight: 0.0570 chunk 109 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 121 optimal weight: 8.9990 chunk 118 optimal weight: 2.9990 overall best weight: 1.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 768 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.139750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.107120 restraints weight = 17210.430| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.64 r_work: 0.3052 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 13695 Z= 0.145 Angle : 0.591 10.981 18603 Z= 0.301 Chirality : 0.041 0.148 2179 Planarity : 0.004 0.049 2324 Dihedral : 4.394 26.892 1915 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 2.27 % Allowed : 12.43 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.21), residues: 1672 helix: 1.75 (0.16), residues: 1067 sheet: None (None), residues: 0 loop : -2.56 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 110 TYR 0.013 0.001 TYR A 116 PHE 0.016 0.001 PHE D 392 TRP 0.017 0.001 TRP C 524 HIS 0.005 0.001 HIS C 479 Details of bonding type rmsd covalent geometry : bond 0.00344 (13679) covalent geometry : angle 0.58719 (18569) SS BOND : bond 0.00290 ( 11) SS BOND : angle 1.05924 ( 22) hydrogen bonds : bond 0.04168 ( 739) hydrogen bonds : angle 3.72231 ( 2190) Misc. bond : bond 0.00232 ( 1) link_BETA1-4 : bond 0.00693 ( 2) link_BETA1-4 : angle 1.71247 ( 6) link_NAG-ASN : bond 0.01296 ( 2) link_NAG-ASN : angle 2.84084 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 155 time to evaluate : 0.458 Fit side-chains REVERT: A 144 ARG cc_start: 0.7600 (pmt-80) cc_final: 0.7180 (pmm150) REVERT: A 195 HIS cc_start: 0.8277 (OUTLIER) cc_final: 0.7975 (t-90) REVERT: A 201 GLU cc_start: 0.7099 (tt0) cc_final: 0.6867 (mm-30) REVERT: B 167 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7157 (mp10) REVERT: B 229 LYS cc_start: 0.8562 (mmpt) cc_final: 0.8027 (mtpt) REVERT: B 267 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8320 (mtmm) REVERT: C 111 GLU cc_start: 0.6588 (tt0) cc_final: 0.5732 (mt-10) REVERT: C 439 GLN cc_start: 0.7877 (mt0) cc_final: 0.7642 (mt0) REVERT: C 676 GLN cc_start: 0.7090 (OUTLIER) cc_final: 0.5141 (mp10) REVERT: C 737 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.6457 (pp) REVERT: C 741 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.6633 (pmm) REVERT: D 97 LEU cc_start: 0.6453 (OUTLIER) cc_final: 0.6127 (pp) REVERT: D 103 GLU cc_start: 0.8052 (tp30) cc_final: 0.7060 (tm-30) REVERT: D 107 PHE cc_start: 0.7080 (t80) cc_final: 0.6789 (t80) REVERT: D 217 LYS cc_start: 0.8301 (mtpp) cc_final: 0.8041 (mtmt) REVERT: D 439 GLN cc_start: 0.8167 (tt0) cc_final: 0.7913 (mt0) REVERT: D 566 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9108 (tt) REVERT: D 617 GLU cc_start: 0.6582 (OUTLIER) cc_final: 0.5371 (mm-30) REVERT: D 759 LYS cc_start: 0.7128 (ttpt) cc_final: 0.6583 (ttpt) outliers start: 33 outliers final: 10 residues processed: 174 average time/residue: 0.5863 time to fit residues: 110.7927 Evaluate side-chains 170 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 480 ASP Chi-restraints excluded: chain C residue 639 ARG Chi-restraints excluded: chain C residue 676 GLN Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 325 TRP Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 617 GLU Chi-restraints excluded: chain D residue 640 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 23 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 143 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 64 optimal weight: 0.0770 chunk 112 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 71 optimal weight: 0.0060 overall best weight: 0.4554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN A 242 ASN ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.142645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.110352 restraints weight = 17153.699| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.64 r_work: 0.3126 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.079 13695 Z= 0.108 Angle : 0.553 9.516 18603 Z= 0.282 Chirality : 0.039 0.138 2179 Planarity : 0.004 0.051 2324 Dihedral : 4.256 24.425 1915 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 1.58 % Allowed : 13.26 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.22), residues: 1672 helix: 2.04 (0.16), residues: 1065 sheet: None (None), residues: 0 loop : -2.44 (0.24), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 110 TYR 0.013 0.001 TYR A 116 PHE 0.011 0.001 PHE D 392 TRP 0.022 0.001 TRP C 524 HIS 0.004 0.001 HIS C 605 Details of bonding type rmsd covalent geometry : bond 0.00236 (13679) covalent geometry : angle 0.55075 (18569) SS BOND : bond 0.00263 ( 11) SS BOND : angle 0.95651 ( 22) hydrogen bonds : bond 0.03602 ( 739) hydrogen bonds : angle 3.61347 ( 2190) Misc. bond : bond 0.00042 ( 1) link_BETA1-4 : bond 0.00316 ( 2) link_BETA1-4 : angle 1.34424 ( 6) link_NAG-ASN : bond 0.00295 ( 2) link_NAG-ASN : angle 2.33705 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 0.397 Fit side-chains REVERT: A 144 ARG cc_start: 0.7604 (pmt-80) cc_final: 0.7158 (pmm150) REVERT: B 229 LYS cc_start: 0.8598 (mmpt) cc_final: 0.8125 (mtmt) REVERT: C 99 TYR cc_start: 0.7466 (t80) cc_final: 0.7185 (t80) REVERT: C 111 GLU cc_start: 0.6630 (tt0) cc_final: 0.5787 (mt-10) REVERT: C 439 GLN cc_start: 0.7852 (mt0) cc_final: 0.7621 (mt0) REVERT: C 741 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.6642 (pmm) REVERT: D 103 GLU cc_start: 0.8012 (tp30) cc_final: 0.7058 (tm-30) REVERT: D 107 PHE cc_start: 0.7048 (t80) cc_final: 0.6757 (t80) REVERT: D 217 LYS cc_start: 0.8306 (mtpp) cc_final: 0.8055 (mtmt) REVERT: D 439 GLN cc_start: 0.8095 (tt0) cc_final: 0.7867 (mt0) REVERT: D 566 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9085 (tt) REVERT: D 604 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.8016 (ptp) REVERT: D 759 LYS cc_start: 0.7239 (ttpt) cc_final: 0.6697 (ttpt) REVERT: D 785 LYS cc_start: 0.7591 (mtpt) cc_final: 0.6754 (mptt) outliers start: 23 outliers final: 10 residues processed: 182 average time/residue: 0.5658 time to fit residues: 112.2607 Evaluate side-chains 169 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 480 ASP Chi-restraints excluded: chain C residue 639 ARG Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 325 TRP Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 754 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 38 optimal weight: 0.0060 chunk 21 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 65 optimal weight: 0.0870 chunk 103 optimal weight: 4.9990 chunk 15 optimal weight: 0.0270 overall best weight: 0.3832 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.142338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.110077 restraints weight = 17325.927| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.64 r_work: 0.3135 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.078 13695 Z= 0.108 Angle : 0.549 9.356 18603 Z= 0.281 Chirality : 0.039 0.135 2179 Planarity : 0.004 0.052 2324 Dihedral : 4.177 24.386 1915 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 1.51 % Allowed : 13.94 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.22), residues: 1672 helix: 2.20 (0.16), residues: 1060 sheet: None (None), residues: 0 loop : -2.44 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 110 TYR 0.013 0.001 TYR A 116 PHE 0.013 0.001 PHE D 322 TRP 0.020 0.001 TRP C 524 HIS 0.009 0.001 HIS D 373 Details of bonding type rmsd covalent geometry : bond 0.00234 (13679) covalent geometry : angle 0.54720 (18569) SS BOND : bond 0.00224 ( 11) SS BOND : angle 0.95763 ( 22) hydrogen bonds : bond 0.03545 ( 739) hydrogen bonds : angle 3.57614 ( 2190) Misc. bond : bond 0.00172 ( 1) link_BETA1-4 : bond 0.00526 ( 2) link_BETA1-4 : angle 1.36801 ( 6) link_NAG-ASN : bond 0.00583 ( 2) link_NAG-ASN : angle 2.05512 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 0.477 Fit side-chains REVERT: A 144 ARG cc_start: 0.7554 (pmt-80) cc_final: 0.7097 (pmm150) REVERT: B 79 ASP cc_start: 0.6373 (p0) cc_final: 0.5542 (m-30) REVERT: B 168 GLU cc_start: 0.8534 (tp30) cc_final: 0.7805 (tp30) REVERT: B 229 LYS cc_start: 0.8523 (mmpt) cc_final: 0.7997 (mtmt) REVERT: C 99 TYR cc_start: 0.7432 (t80) cc_final: 0.7011 (t80) REVERT: C 111 GLU cc_start: 0.6464 (tt0) cc_final: 0.5609 (mt-10) REVERT: C 439 GLN cc_start: 0.7842 (mt0) cc_final: 0.7613 (mt0) REVERT: C 737 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.6431 (pp) REVERT: C 741 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.6478 (pmm) REVERT: D 97 LEU cc_start: 0.6281 (OUTLIER) cc_final: 0.5924 (pp) REVERT: D 103 GLU cc_start: 0.7914 (tp30) cc_final: 0.6958 (tm-30) REVERT: D 107 PHE cc_start: 0.6888 (t80) cc_final: 0.6596 (t80) REVERT: D 217 LYS cc_start: 0.8275 (mtpp) cc_final: 0.8009 (mtmt) REVERT: D 439 GLN cc_start: 0.7991 (tt0) cc_final: 0.7760 (mt0) REVERT: D 566 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.9053 (tt) REVERT: D 604 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.7923 (ptp) REVERT: D 617 GLU cc_start: 0.6665 (OUTLIER) cc_final: 0.5427 (mm-30) REVERT: D 759 LYS cc_start: 0.7099 (ttpt) cc_final: 0.6548 (ttpt) REVERT: D 785 LYS cc_start: 0.7521 (mtpt) cc_final: 0.7206 (mtpp) outliers start: 22 outliers final: 9 residues processed: 171 average time/residue: 0.5826 time to fit residues: 108.5393 Evaluate side-chains 167 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 480 ASP Chi-restraints excluded: chain C residue 639 ARG Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 325 TRP Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 617 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 151 optimal weight: 3.9990 chunk 154 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 138 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 58 optimal weight: 0.9990 chunk 57 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN ** D 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.140945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.108677 restraints weight = 17247.657| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.63 r_work: 0.3070 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 13695 Z= 0.126 Angle : 0.575 10.259 18603 Z= 0.293 Chirality : 0.040 0.138 2179 Planarity : 0.004 0.054 2324 Dihedral : 4.238 25.688 1915 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 1.24 % Allowed : 14.08 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.21), residues: 1672 helix: 2.17 (0.16), residues: 1058 sheet: None (None), residues: 0 loop : -2.51 (0.23), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 110 TYR 0.013 0.001 TYR A 116 PHE 0.014 0.001 PHE D 392 TRP 0.018 0.001 TRP C 524 HIS 0.005 0.001 HIS D 373 Details of bonding type rmsd covalent geometry : bond 0.00292 (13679) covalent geometry : angle 0.57269 (18569) SS BOND : bond 0.00258 ( 11) SS BOND : angle 1.03101 ( 22) hydrogen bonds : bond 0.03888 ( 739) hydrogen bonds : angle 3.62150 ( 2190) Misc. bond : bond 0.00178 ( 1) link_BETA1-4 : bond 0.00446 ( 2) link_BETA1-4 : angle 1.47812 ( 6) link_NAG-ASN : bond 0.00644 ( 2) link_NAG-ASN : angle 2.09598 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 0.455 Fit side-chains REVERT: A 144 ARG cc_start: 0.7532 (pmt-80) cc_final: 0.7050 (pmm150) REVERT: B 79 ASP cc_start: 0.6419 (p0) cc_final: 0.5546 (m-30) REVERT: B 168 GLU cc_start: 0.8518 (tp30) cc_final: 0.7758 (tp30) REVERT: B 229 LYS cc_start: 0.8466 (mmpt) cc_final: 0.7933 (mtmt) REVERT: C 99 TYR cc_start: 0.7456 (t80) cc_final: 0.7057 (t80) REVERT: C 103 GLU cc_start: 0.5828 (tt0) cc_final: 0.5493 (tm-30) REVERT: C 111 GLU cc_start: 0.6373 (tt0) cc_final: 0.5539 (mt-10) REVERT: C 439 GLN cc_start: 0.7864 (mt0) cc_final: 0.7602 (mt0) REVERT: C 737 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.6065 (pp) REVERT: C 741 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.6420 (pmm) REVERT: D 97 LEU cc_start: 0.6212 (OUTLIER) cc_final: 0.5869 (pp) REVERT: D 103 GLU cc_start: 0.7849 (tp30) cc_final: 0.6884 (tm-30) REVERT: D 107 PHE cc_start: 0.6753 (t80) cc_final: 0.6448 (t80) REVERT: D 217 LYS cc_start: 0.8233 (mtpp) cc_final: 0.7962 (mtmt) REVERT: D 439 GLN cc_start: 0.7960 (tt0) cc_final: 0.7721 (mt0) REVERT: D 566 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.9007 (tt) REVERT: D 604 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.7883 (ptp) REVERT: D 617 GLU cc_start: 0.6564 (OUTLIER) cc_final: 0.5293 (mm-30) REVERT: D 759 LYS cc_start: 0.7056 (ttpt) cc_final: 0.6526 (ttpt) outliers start: 18 outliers final: 9 residues processed: 167 average time/residue: 0.5651 time to fit residues: 103.1406 Evaluate side-chains 167 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 480 ASP Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 325 TRP Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 617 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 132 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 19 optimal weight: 0.0570 chunk 5 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 58 optimal weight: 0.0030 overall best weight: 0.4508 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN ** D 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.142033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.109805 restraints weight = 17348.641| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.63 r_work: 0.3092 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.078 13695 Z= 0.110 Angle : 0.557 9.913 18603 Z= 0.285 Chirality : 0.039 0.136 2179 Planarity : 0.004 0.053 2324 Dihedral : 4.174 25.022 1915 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 1.37 % Allowed : 14.22 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.22), residues: 1672 helix: 2.27 (0.16), residues: 1059 sheet: None (None), residues: 0 loop : -2.44 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 110 TYR 0.013 0.001 TYR A 116 PHE 0.013 0.001 PHE D 322 TRP 0.020 0.001 TRP C 524 HIS 0.005 0.001 HIS D 373 Details of bonding type rmsd covalent geometry : bond 0.00243 (13679) covalent geometry : angle 0.55500 (18569) SS BOND : bond 0.00236 ( 11) SS BOND : angle 0.96871 ( 22) hydrogen bonds : bond 0.03664 ( 739) hydrogen bonds : angle 3.58426 ( 2190) Misc. bond : bond 0.00165 ( 1) link_BETA1-4 : bond 0.00486 ( 2) link_BETA1-4 : angle 1.37704 ( 6) link_NAG-ASN : bond 0.00595 ( 2) link_NAG-ASN : angle 2.04728 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4504.84 seconds wall clock time: 77 minutes 15.56 seconds (4635.56 seconds total)