Starting phenix.real_space_refine on Fri Jul 3 09:30:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7cq6_30437/07_2026/7cq6_30437.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cq6_30437/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/7cq6_30437/07_2026/7cq6_30437.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cq6_30437/07_2026/7cq6_30437.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7cq6_30437/07_2026/7cq6_30437.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7cq6_30437/07_2026/7cq6_30437.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7cq6_30437/07_2026/7cq6_30437.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cq6_30437/07_2026/7cq6_30437.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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 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 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: 3.15, per 1000 atoms: 0.24 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: 1.05 Conformation dependent library (CDL) restraints added in 592.6 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: 0.37 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: 2.00 Time building geometry restraints manager: 1.42 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: 7642 15.81 - 31.62: 376 31.62 - 47.44: 50 47.44 - 63.25: 3 63.25 - 79.06: 6 Dihedral angle restraints: 8077 sinusoidal: 3124 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 8074 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: 1.840 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.850 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.020 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:6.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 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 : 9.793 79.060 4836 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/Z covalent geometry : bond 0.01037 / 0.42 (13679) covalent geometry : angle 1.12084 / 0.60 (18569) SS BOND : bond 0.01367 / 0.74 ( 11) SS BOND : angle 2.29439 / 1.17 ( 22) hydrogen bonds : bond 0.21883 / 14.39 ( 739) hydrogen bonds : angle 7.80621 / 5.54 ( 2190) Misc. bond : bond 0.00173 / 0.09 ( 1) link_BETA1-4 : bond 0.00353 / 0.17 ( 2) link_BETA1-4 : angle 3.10193 / 1.46 ( 6) link_NAG-ASN : bond 0.00440 / 0.21 ( 2) link_NAG-ASN : angle 5.53224 / 2.93 ( 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 : 0.528 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: 0.7532 time to fit residues: 191.3330 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 : 0.498 ------------------------------------------------------------------------------- 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... 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 623 HIS 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.140006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.107648 restraints weight = 17214.791| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.62 r_work: 0.3077 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13695 Z= 0.140 Angle : 0.647 12.676 18603 Z= 0.335 Chirality : 0.041 0.162 2179 Planarity : 0.005 0.051 2324 Dihedral : 5.262 37.560 1832 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 1.85 % Allowed : 7.49 % Favored : 90.66 % 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: -2.01 (0.19), residues: 1672 helix: -0.38 (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 0.004 0.001 ARG B 110 TYR 0.012 0.001 TYR B 188 PHE 0.018 0.001 PHE D 392 TRP 0.030 0.002 TRP D 179 HIS 0.004 0.001 HIS C 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (13679) covalent geometry : angle 0.64323 / 0.33 (18569) SS BOND : bond 0.00397 / 0.20 ( 11) SS BOND : angle 1.14651 / 0.69 ( 22) hydrogen bonds : bond 0.05392 / 3.54 ( 739) hydrogen bonds : angle 4.45803 / 3.14 ( 2190) Misc. bond : bond 0.00250 / 0.13 ( 1) link_BETA1-4 : bond 0.00449 / 0.23 ( 2) link_BETA1-4 : angle 1.31925 / 0.68 ( 6) link_NAG-ASN : bond 0.00239 / 0.12 ( 2) link_NAG-ASN : angle 3.21906 / 1.68 ( 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 209 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 182 time to evaluate : 0.542 Fit side-chains REVERT: A 160 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8236 (mt-10) REVERT: A 173 ASN cc_start: 0.6984 (m110) cc_final: 0.6776 (m110) REVERT: A 195 HIS cc_start: 0.8301 (OUTLIER) cc_final: 0.7853 (t-90) REVERT: A 237 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7838 (tm-30) REVERT: B 167 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.8105 (mp10) REVERT: B 229 LYS cc_start: 0.8617 (mmpt) cc_final: 0.8087 (mtmt) REVERT: C 99 TYR cc_start: 0.8116 (t80) cc_final: 0.7755 (t80) REVERT: C 111 GLU cc_start: 0.6410 (tt0) cc_final: 0.5720 (mt-10) REVERT: C 572 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8222 (mt-10) REVERT: C 648 VAL cc_start: 0.7370 (t) cc_final: 0.7110 (p) REVERT: C 674 ARG cc_start: 0.6721 (mtm-85) cc_final: 0.6392 (ttm110) REVERT: D 107 PHE cc_start: 0.7191 (t80) cc_final: 0.6832 (t80) REVERT: D 217 LYS cc_start: 0.8274 (mtpp) cc_final: 0.7897 (mtpt) REVERT: D 439 GLN cc_start: 0.8504 (tt0) cc_final: 0.8266 (mt0) REVERT: D 459 TYR cc_start: 0.8470 (m-80) cc_final: 0.8191 (m-80) REVERT: D 584 MET cc_start: 0.9142 (ptm) cc_final: 0.8906 (ttp) REVERT: D 617 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.5547 (mm-30) REVERT: D 658 HIS cc_start: 0.6196 (m-70) cc_final: 0.5965 (m-70) REVERT: D 730 GLU cc_start: 0.6030 (mt-10) cc_final: 0.5646 (mt-10) REVERT: D 731 ARG cc_start: 0.5666 (mtt90) cc_final: 0.5024 (mmp-170) REVERT: D 759 LYS cc_start: 0.6927 (ttpt) cc_final: 0.6337 (ttpt) outliers start: 27 outliers final: 6 residues processed: 197 average time/residue: 0.6649 time to fit residues: 142.1062 Evaluate side-chains 172 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 163 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 283 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: 1.9990 chunk 148 optimal weight: 7.9990 chunk 6 optimal weight: 0.4980 chunk 43 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 123 optimal weight: 0.6980 chunk 78 optimal weight: 0.0030 chunk 74 optimal weight: 6.9990 chunk 140 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 160 optimal weight: 0.9980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 HIS B 113 GLN B 242 ASN ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 GLN C 439 GLN ** 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 = 0.3658 r_free = 0.3658 target = 0.141902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.109624 restraints weight = 17410.761| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.64 r_work: 0.3109 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13695 Z= 0.119 Angle : 0.580 10.558 18603 Z= 0.299 Chirality : 0.040 0.142 2179 Planarity : 0.004 0.050 2324 Dihedral : 4.692 28.012 1831 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 1.92 % Allowed : 9.00 % Favored : 89.08 % 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: -0.78 (0.20), residues: 1672 helix: 0.69 (0.16), residues: 1065 sheet: None (None), residues: 0 loop : -2.81 (0.23), 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 0.014 0.001 PHE C 329 TRP 0.018 0.001 TRP C 524 HIS 0.004 0.001 HIS C 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (13679) covalent geometry : angle 0.57640 / 0.30 (18569) SS BOND : bond 0.00307 / 0.16 ( 11) SS BOND : angle 1.21443 / 0.72 ( 22) hydrogen bonds : bond 0.04390 / 2.89 ( 739) hydrogen bonds : angle 3.96892 / 2.79 ( 2190) Misc. bond : bond 0.00011 / 0.01 ( 1) link_BETA1-4 : bond 0.00550 / 0.28 ( 2) link_BETA1-4 : angle 1.14099 / 0.63 ( 6) link_NAG-ASN : bond 0.00314 / 0.16 ( 2) link_NAG-ASN : angle 2.63620 / 1.38 ( 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 203 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 175 time to evaluate : 0.527 Fit side-chains REVERT: A 144 ARG cc_start: 0.7729 (pmt-80) cc_final: 0.7253 (pmm150) REVERT: A 160 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8205 (mt-10) REVERT: A 195 HIS cc_start: 0.8278 (OUTLIER) cc_final: 0.7852 (t-90) REVERT: A 201 GLU cc_start: 0.7143 (tt0) cc_final: 0.6761 (mm-30) REVERT: A 237 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7965 (tm-30) REVERT: B 152 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7335 (ttt) REVERT: B 167 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.8104 (mp10) REVERT: B 168 GLU cc_start: 0.8625 (tp30) cc_final: 0.7968 (tp30) REVERT: B 229 LYS cc_start: 0.8547 (mmpt) cc_final: 0.8008 (mtpt) REVERT: C 99 TYR cc_start: 0.8128 (t80) cc_final: 0.7882 (t80) REVERT: C 111 GLU cc_start: 0.6472 (tt0) cc_final: 0.5711 (mt-10) REVERT: C 232 SER cc_start: 0.8984 (OUTLIER) cc_final: 0.8765 (m) REVERT: C 648 VAL cc_start: 0.7272 (t) cc_final: 0.7042 (p) REVERT: C 674 ARG cc_start: 0.6674 (mtm-85) cc_final: 0.6306 (ttm110) REVERT: D 107 PHE cc_start: 0.7168 (t80) cc_final: 0.6882 (t80) REVERT: D 217 LYS cc_start: 0.8341 (mtpp) cc_final: 0.8007 (mtpt) REVERT: D 584 MET cc_start: 0.9171 (ptm) cc_final: 0.8929 (ttp) REVERT: D 617 GLU cc_start: 0.6738 (OUTLIER) cc_final: 0.5518 (mm-30) REVERT: D 658 HIS cc_start: 0.6178 (m-70) cc_final: 0.5970 (m-70) REVERT: D 730 GLU cc_start: 0.5894 (mt-10) cc_final: 0.5456 (mt-10) REVERT: D 731 ARG cc_start: 0.5600 (mtt90) cc_final: 0.5076 (mmp-170) REVERT: D 759 LYS cc_start: 0.6882 (ttpt) cc_final: 0.6391 (ttpt) outliers start: 28 outliers final: 9 residues processed: 190 average time/residue: 0.6852 time to fit residues: 141.2660 Evaluate side-chains 175 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 161 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain B residue 152 MET 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 221 VAL Chi-restraints excluded: chain C residue 232 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: 1.9990 chunk 148 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 147 optimal weight: 0.8980 chunk 32 optimal weight: 0.0470 chunk 62 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 67 optimal weight: 0.0050 chunk 160 optimal weight: 7.9990 chunk 155 optimal weight: 0.1980 overall best weight: 0.4092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3676 r_free = 0.3676 target = 0.143371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.111053 restraints weight = 17387.267| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.66 r_work: 0.3133 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 13695 Z= 0.108 Angle : 0.557 9.450 18603 Z= 0.285 Chirality : 0.039 0.136 2179 Planarity : 0.004 0.049 2324 Dihedral : 4.380 24.877 1831 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 1.92 % Allowed : 10.03 % Favored : 88.05 % 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: -0.09 (0.21), residues: 1672 helix: 1.26 (0.16), residues: 1067 sheet: None (None), residues: 0 loop : -2.61 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 110 TYR 0.015 0.001 TYR A 116 PHE 0.012 0.001 PHE D 392 TRP 0.019 0.001 TRP C 524 HIS 0.004 0.001 HIS C 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (13679) covalent geometry : angle 0.55316 / 0.28 (18569) SS BOND : bond 0.00283 / 0.15 ( 11) SS BOND : angle 1.13848 / 0.74 ( 22) hydrogen bonds : bond 0.03817 / 2.51 ( 739) hydrogen bonds : angle 3.73424 / 2.61 ( 2190) Misc. bond : bond 0.00615 / 0.32 ( 1) link_BETA1-4 : bond 0.00632 / 0.33 ( 2) link_BETA1-4 : angle 1.34166 / 0.62 ( 6) link_NAG-ASN : bond 0.00502 / 0.26 ( 2) link_NAG-ASN : angle 2.58816 / 1.38 ( 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 195 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 167 time to evaluate : 0.497 Fit side-chains REVERT: A 110 ARG cc_start: 0.8655 (mtt-85) cc_final: 0.8411 (mmt90) REVERT: A 195 HIS cc_start: 0.8234 (OUTLIER) cc_final: 0.7834 (t-90) REVERT: A 201 GLU cc_start: 0.7083 (tt0) cc_final: 0.6774 (mm-30) REVERT: B 79 ASP cc_start: 0.6366 (p0) cc_final: 0.5597 (m-30) REVERT: B 167 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7970 (mp10) REVERT: B 168 GLU cc_start: 0.8674 (tp30) cc_final: 0.8038 (tp30) REVERT: B 229 LYS cc_start: 0.8598 (mmpt) cc_final: 0.8080 (mtpt) REVERT: C 99 TYR cc_start: 0.7999 (t80) cc_final: 0.7515 (t80) REVERT: C 111 GLU cc_start: 0.6391 (tt0) cc_final: 0.5607 (mt-10) REVERT: C 439 GLN cc_start: 0.7826 (mt0) cc_final: 0.7600 (mt0) REVERT: C 648 VAL cc_start: 0.7163 (t) cc_final: 0.6943 (p) REVERT: D 107 PHE cc_start: 0.7038 (t80) cc_final: 0.6822 (t80) REVERT: D 217 LYS cc_start: 0.8343 (mtpp) cc_final: 0.8004 (mtpt) REVERT: D 566 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9100 (tt) REVERT: D 584 MET cc_start: 0.9198 (ptm) cc_final: 0.8977 (ttp) REVERT: D 658 HIS cc_start: 0.6033 (m-70) cc_final: 0.5818 (m-70) REVERT: D 759 LYS cc_start: 0.6859 (ttpt) cc_final: 0.6322 (ttpt) outliers start: 28 outliers final: 8 residues processed: 184 average time/residue: 0.5959 time to fit residues: 119.7597 Evaluate side-chains 161 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 150 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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 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 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 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: 7.9990 chunk 152 optimal weight: 2.9990 chunk 121 optimal weight: 7.9990 chunk 116 optimal weight: 0.8980 chunk 139 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 167 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 113 GLN ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 768 HIS ** D 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 768 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.141270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.108565 restraints weight = 17423.340| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.65 r_work: 0.3089 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 13695 Z= 0.130 Angle : 0.581 10.040 18603 Z= 0.297 Chirality : 0.040 0.159 2179 Planarity : 0.004 0.049 2324 Dihedral : 4.383 26.440 1831 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 1.92 % Allowed : 10.99 % Favored : 87.09 % 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: 0.15 (0.21), residues: 1672 helix: 1.48 (0.16), residues: 1066 sheet: None (None), residues: 0 loop : -2.56 (0.23), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 674 TYR 0.013 0.001 TYR A 116 PHE 0.015 0.001 PHE D 392 TRP 0.018 0.001 TRP C 524 HIS 0.007 0.001 HIS D 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (13679) covalent geometry : angle 0.57795 / 0.30 (18569) SS BOND : bond 0.00279 / 0.14 ( 11) SS BOND : angle 1.20681 / 0.71 ( 22) hydrogen bonds : bond 0.04096 / 2.70 ( 739) hydrogen bonds : angle 3.71666 / 2.60 ( 2190) Misc. bond : bond 0.00171 / 0.09 ( 1) link_BETA1-4 : bond 0.00469 / 0.24 ( 2) link_BETA1-4 : angle 1.57066 / 0.72 ( 6) link_NAG-ASN : bond 0.00579 / 0.30 ( 2) link_NAG-ASN : angle 2.57910 / 1.38 ( 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 198 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 170 time to evaluate : 0.501 Fit side-chains REVERT: A 144 ARG cc_start: 0.7603 (pmt-80) cc_final: 0.7216 (pmm150) REVERT: A 160 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8206 (mt-10) REVERT: A 195 HIS cc_start: 0.8260 (OUTLIER) cc_final: 0.7865 (t-90) REVERT: A 201 GLU cc_start: 0.7087 (tt0) cc_final: 0.6803 (mm-30) REVERT: A 223 ASN cc_start: 0.8356 (t0) cc_final: 0.8108 (t0) REVERT: A 237 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7907 (tm-30) REVERT: B 168 GLU cc_start: 0.8616 (tp30) cc_final: 0.8035 (tp30) REVERT: B 192 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8681 (tp) REVERT: B 229 LYS cc_start: 0.8590 (mmpt) cc_final: 0.8087 (mtpt) REVERT: C 99 TYR cc_start: 0.7971 (t80) cc_final: 0.7660 (t80) REVERT: C 103 GLU cc_start: 0.6007 (mt-10) cc_final: 0.5462 (tm-30) REVERT: C 111 GLU cc_start: 0.6437 (tt0) cc_final: 0.5649 (mt-10) REVERT: C 232 SER cc_start: 0.8975 (OUTLIER) cc_final: 0.8763 (m) REVERT: C 439 GLN cc_start: 0.7870 (mt0) cc_final: 0.7632 (mt0) REVERT: C 648 VAL cc_start: 0.7189 (t) cc_final: 0.6970 (p) REVERT: D 107 PHE cc_start: 0.7066 (t80) cc_final: 0.6787 (t80) REVERT: D 217 LYS cc_start: 0.8316 (mtpp) cc_final: 0.7987 (mtpt) REVERT: D 566 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9094 (tt) REVERT: D 617 GLU cc_start: 0.6693 (OUTLIER) cc_final: 0.5465 (mm-30) REVERT: D 658 HIS cc_start: 0.6215 (m-70) cc_final: 0.6010 (m-70) REVERT: D 759 LYS cc_start: 0.6992 (ttpt) cc_final: 0.6458 (ttpt) outliers start: 28 outliers final: 9 residues processed: 185 average time/residue: 0.5956 time to fit residues: 120.0836 Evaluate side-chains 174 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 160 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 HIS 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 232 SER Chi-restraints excluded: chain C residue 401 MET 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 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: 2.9990 chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 146 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 24 optimal weight: 0.4980 chunk 10 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.140850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.108085 restraints weight = 17320.582| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.65 r_work: 0.3093 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 13695 Z= 0.135 Angle : 0.587 10.119 18603 Z= 0.300 Chirality : 0.041 0.140 2179 Planarity : 0.004 0.049 2324 Dihedral : 4.394 27.904 1831 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 1.92 % Allowed : 11.47 % Favored : 86.61 % 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: 0.26 (0.21), residues: 1672 helix: 1.59 (0.16), residues: 1067 sheet: None (None), residues: 0 loop : -2.57 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 110 TYR 0.014 0.001 TYR A 116 PHE 0.015 0.001 PHE D 392 TRP 0.019 0.001 TRP C 524 HIS 0.005 0.001 HIS C 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 (13679) covalent geometry : angle 0.58366 / 0.30 (18569) SS BOND : bond 0.00667 / 0.34 ( 11) SS BOND : angle 1.20239 / 0.67 ( 22) hydrogen bonds : bond 0.04130 / 2.72 ( 739) hydrogen bonds : angle 3.70872 / 2.59 ( 2190) Misc. bond : bond 0.00246 / 0.13 ( 1) link_BETA1-4 : bond 0.00620 / 0.32 ( 2) link_BETA1-4 : angle 1.62209 / 0.75 ( 6) link_NAG-ASN : bond 0.00668 / 0.35 ( 2) link_NAG-ASN : angle 2.58619 / 1.36 ( 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 193 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 0.537 Fit side-chains REVERT: A 144 ARG cc_start: 0.7666 (pmt-80) cc_final: 0.7239 (pmm150) REVERT: A 195 HIS cc_start: 0.8248 (OUTLIER) cc_final: 0.7893 (t-90) REVERT: A 201 GLU cc_start: 0.7025 (tt0) cc_final: 0.6749 (mm-30) REVERT: A 237 GLU cc_start: 0.8289 (tm-30) cc_final: 0.8039 (tm-30) REVERT: B 229 LYS cc_start: 0.8598 (mmpt) cc_final: 0.8131 (mtmt) REVERT: C 99 TYR cc_start: 0.7967 (t80) cc_final: 0.7643 (t80) REVERT: C 103 GLU cc_start: 0.6003 (mt-10) cc_final: 0.5531 (tm-30) REVERT: C 111 GLU cc_start: 0.6479 (tt0) cc_final: 0.5687 (mt-10) REVERT: C 232 SER cc_start: 0.8978 (OUTLIER) cc_final: 0.8766 (m) REVERT: C 439 GLN cc_start: 0.7885 (mt0) cc_final: 0.7644 (mt0) REVERT: C 648 VAL cc_start: 0.7228 (t) cc_final: 0.7025 (p) REVERT: D 97 LEU cc_start: 0.6730 (OUTLIER) cc_final: 0.6323 (pp) REVERT: D 107 PHE cc_start: 0.7058 (t80) cc_final: 0.6823 (t80) REVERT: D 217 LYS cc_start: 0.8312 (mtpp) cc_final: 0.7994 (mtpt) REVERT: D 566 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9100 (tt) REVERT: D 617 GLU cc_start: 0.6700 (OUTLIER) cc_final: 0.5474 (mm-30) REVERT: D 658 HIS cc_start: 0.6235 (m-70) cc_final: 0.6024 (m-70) REVERT: D 759 LYS cc_start: 0.7036 (ttpt) cc_final: 0.6499 (ttpt) outliers start: 28 outliers final: 14 residues processed: 181 average time/residue: 0.5891 time to fit residues: 116.4633 Evaluate side-chains 176 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 157 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain B residue 192 LEU 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 232 SER Chi-restraints excluded: chain C residue 401 MET Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 496 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 441 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 97 optimal weight: 3.9990 chunk 71 optimal weight: 0.2980 chunk 92 optimal weight: 9.9990 chunk 165 optimal weight: 0.9980 chunk 150 optimal weight: 0.0000 chunk 159 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 121 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 223 ASN ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3657 r_free = 0.3657 target = 0.141860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.109291 restraints weight = 17214.666| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.64 r_work: 0.3110 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 13695 Z= 0.118 Angle : 0.566 9.441 18603 Z= 0.290 Chirality : 0.040 0.135 2179 Planarity : 0.004 0.049 2324 Dihedral : 4.288 26.174 1831 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.61 % Allowed : 11.68 % Favored : 85.71 % 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: 0.52 (0.21), residues: 1672 helix: 1.83 (0.16), residues: 1064 sheet: None (None), residues: 0 loop : -2.54 (0.23), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 144 TYR 0.013 0.001 TYR A 116 PHE 0.013 0.001 PHE D 392 TRP 0.020 0.001 TRP C 524 HIS 0.004 0.001 HIS C 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (13679) covalent geometry : angle 0.56349 / 0.29 (18569) SS BOND : bond 0.00384 / 0.20 ( 11) SS BOND : angle 0.94823 / 0.57 ( 22) hydrogen bonds : bond 0.03851 / 2.53 ( 739) hydrogen bonds : angle 3.64440 / 2.54 ( 2190) Misc. bond : bond 0.00075 / 0.04 ( 1) link_BETA1-4 : bond 0.00297 / 0.15 ( 2) link_BETA1-4 : angle 1.42973 / 0.68 ( 6) link_NAG-ASN : bond 0.00417 / 0.22 ( 2) link_NAG-ASN : angle 2.40295 / 1.29 ( 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 206 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 168 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 ARG cc_start: 0.7636 (pmt-80) cc_final: 0.7197 (pmm150) REVERT: A 195 HIS cc_start: 0.8264 (OUTLIER) cc_final: 0.7898 (t-90) REVERT: A 201 GLU cc_start: 0.7040 (tt0) cc_final: 0.6784 (mm-30) REVERT: A 237 GLU cc_start: 0.8312 (tm-30) cc_final: 0.8012 (tm-30) REVERT: B 229 LYS cc_start: 0.8620 (mmpt) cc_final: 0.8152 (mtmt) REVERT: C 99 TYR cc_start: 0.7917 (t80) cc_final: 0.7660 (t80) REVERT: C 103 GLU cc_start: 0.5997 (mt-10) cc_final: 0.5567 (tm-30) REVERT: C 111 GLU cc_start: 0.6585 (tt0) cc_final: 0.5797 (mt-10) REVERT: C 439 GLN cc_start: 0.7887 (mt0) cc_final: 0.7640 (mt0) REVERT: C 741 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.6668 (pmm) REVERT: D 97 LEU cc_start: 0.6414 (OUTLIER) cc_final: 0.6040 (pp) REVERT: D 103 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7128 (tm-30) REVERT: D 107 PHE cc_start: 0.7057 (t80) cc_final: 0.6765 (t80) REVERT: D 217 LYS cc_start: 0.8308 (mtpp) cc_final: 0.8031 (mtmt) REVERT: D 566 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9099 (tt) REVERT: D 604 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.8051 (ptp) REVERT: D 658 HIS cc_start: 0.6192 (m-70) cc_final: 0.5982 (m-70) REVERT: D 759 LYS cc_start: 0.7232 (ttpt) cc_final: 0.6732 (ttpt) outliers start: 38 outliers final: 12 residues processed: 189 average time/residue: 0.6057 time to fit residues: 125.1045 Evaluate side-chains 175 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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 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 496 VAL Chi-restraints excluded: chain C residue 639 ARG Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 103 GLU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 23 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 143 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 223 ASN ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3650 r_free = 0.3650 target = 0.141295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.108646 restraints weight = 17176.661| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.65 r_work: 0.3094 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2883 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 : 0.578 9.596 18603 Z= 0.296 Chirality : 0.040 0.136 2179 Planarity : 0.004 0.049 2324 Dihedral : 4.278 26.353 1831 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.27 % Allowed : 12.29 % Favored : 85.44 % 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: 0.63 (0.21), residues: 1672 helix: 1.92 (0.16), residues: 1064 sheet: None (None), residues: 0 loop : -2.49 (0.24), residues: 608 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 0.019 0.001 TRP C 524 HIS 0.004 0.001 HIS C 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (13679) covalent geometry : angle 0.57586 / 0.30 (18569) SS BOND : bond 0.00323 / 0.17 ( 11) SS BOND : angle 0.92214 / 0.53 ( 22) hydrogen bonds : bond 0.03930 / 2.58 ( 739) hydrogen bonds : angle 3.63556 / 2.54 ( 2190) Misc. bond : bond 0.00192 / 0.10 ( 1) link_BETA1-4 : bond 0.00435 / 0.23 ( 2) link_BETA1-4 : angle 1.53729 / 0.71 ( 6) link_NAG-ASN : bond 0.00586 / 0.31 ( 2) link_NAG-ASN : angle 2.35624 / 1.26 ( 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 198 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 165 time to evaluate : 0.504 Fit side-chains REVERT: A 144 ARG cc_start: 0.7632 (pmt-80) cc_final: 0.7192 (pmm150) REVERT: A 195 HIS cc_start: 0.8270 (OUTLIER) cc_final: 0.7914 (t-90) REVERT: A 237 GLU cc_start: 0.8309 (tm-30) cc_final: 0.8106 (tm-30) REVERT: B 168 GLU cc_start: 0.8525 (tp30) cc_final: 0.7834 (tp30) REVERT: B 229 LYS cc_start: 0.8588 (mmpt) cc_final: 0.8148 (mtmt) REVERT: C 99 TYR cc_start: 0.7885 (t80) cc_final: 0.7654 (t80) REVERT: C 103 GLU cc_start: 0.5970 (mt-10) cc_final: 0.5566 (tm-30) REVERT: C 111 GLU cc_start: 0.6570 (tt0) cc_final: 0.5726 (mt-10) REVERT: C 439 GLN cc_start: 0.7909 (mt0) cc_final: 0.7659 (mt0) REVERT: C 741 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.6642 (pmm) REVERT: D 97 LEU cc_start: 0.6419 (OUTLIER) cc_final: 0.6071 (pp) REVERT: D 103 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7172 (tm-30) REVERT: D 107 PHE cc_start: 0.7122 (t80) cc_final: 0.6806 (t80) REVERT: D 217 LYS cc_start: 0.8293 (mtpp) cc_final: 0.8029 (mtmt) REVERT: D 566 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9075 (tt) REVERT: D 604 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.8077 (ptp) REVERT: D 617 GLU cc_start: 0.6724 (OUTLIER) cc_final: 0.5480 (mm-30) REVERT: D 658 HIS cc_start: 0.6199 (m-70) cc_final: 0.5993 (m-70) REVERT: D 759 LYS cc_start: 0.7236 (ttpt) cc_final: 0.6700 (ttpt) outliers start: 33 outliers final: 14 residues processed: 181 average time/residue: 0.5119 time to fit residues: 101.5213 Evaluate side-chains 176 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 195 HIS 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 401 MET Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 480 ASP Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 639 ARG Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 103 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 38 optimal weight: 0.0170 chunk 21 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 141 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 65 optimal weight: 0.0870 chunk 103 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 223 ASN ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 373 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 = 0.3662 r_free = 0.3662 target = 0.142622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.109816 restraints weight = 17336.314| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.72 r_work: 0.3111 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 13695 Z= 0.112 Angle : 0.557 8.720 18603 Z= 0.285 Chirality : 0.039 0.135 2179 Planarity : 0.004 0.048 2324 Dihedral : 4.164 24.839 1831 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 2.06 % Allowed : 12.64 % 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: 0.83 (0.22), residues: 1672 helix: 2.12 (0.16), residues: 1061 sheet: None (None), residues: 0 loop : -2.48 (0.23), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 144 TYR 0.013 0.001 TYR A 116 PHE 0.012 0.001 PHE D 392 TRP 0.022 0.001 TRP C 524 HIS 0.005 0.001 HIS D 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (13679) covalent geometry : angle 0.55470 / 0.28 (18569) SS BOND : bond 0.00297 / 0.16 ( 11) SS BOND : angle 0.85178 / 0.55 ( 22) hydrogen bonds : bond 0.03645 / 2.39 ( 739) hydrogen bonds : angle 3.57279 / 2.49 ( 2190) Misc. bond : bond 0.00191 / 0.10 ( 1) link_BETA1-4 : bond 0.00409 / 0.21 ( 2) link_BETA1-4 : angle 1.28378 / 0.64 ( 6) link_NAG-ASN : bond 0.00491 / 0.26 ( 2) link_NAG-ASN : angle 2.06831 / 1.13 ( 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 201 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 0.416 Fit side-chains REVERT: A 144 ARG cc_start: 0.7524 (pmt-80) cc_final: 0.7031 (pmm150) REVERT: A 195 HIS cc_start: 0.8252 (OUTLIER) cc_final: 0.7903 (t-90) REVERT: A 237 GLU cc_start: 0.8282 (tm-30) cc_final: 0.8016 (tm-30) REVERT: B 79 ASP cc_start: 0.6390 (p0) cc_final: 0.5522 (m-30) REVERT: B 168 GLU cc_start: 0.8520 (tp30) cc_final: 0.7762 (tp30) REVERT: B 229 LYS cc_start: 0.8450 (mmpt) cc_final: 0.7870 (mtmt) REVERT: C 99 TYR cc_start: 0.7757 (t80) cc_final: 0.7509 (t80) REVERT: C 103 GLU cc_start: 0.5798 (mt-10) cc_final: 0.5416 (tm-30) REVERT: C 111 GLU cc_start: 0.6332 (tt0) cc_final: 0.5498 (mt-10) REVERT: C 439 GLN cc_start: 0.7842 (mt0) cc_final: 0.7593 (mt0) REVERT: C 741 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.6374 (pmm) REVERT: D 97 LEU cc_start: 0.6133 (OUTLIER) cc_final: 0.5762 (pp) REVERT: D 103 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.6971 (tm-30) REVERT: D 107 PHE cc_start: 0.6658 (t80) cc_final: 0.6346 (t80) REVERT: D 217 LYS cc_start: 0.8213 (mtpp) cc_final: 0.7902 (mtmt) REVERT: D 566 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8992 (tt) REVERT: D 604 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7832 (ptp) REVERT: D 617 GLU cc_start: 0.6621 (OUTLIER) cc_final: 0.5382 (mm-30) REVERT: D 658 HIS cc_start: 0.5874 (m-70) cc_final: 0.5661 (m-70) REVERT: D 759 LYS cc_start: 0.6948 (ttpt) cc_final: 0.6427 (ttpt) outliers start: 30 outliers final: 11 residues processed: 188 average time/residue: 0.4999 time to fit residues: 103.3513 Evaluate side-chains 174 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 HIS 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 496 VAL Chi-restraints excluded: chain C residue 639 ARG Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 103 GLU 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: 0.0470 chunk 154 optimal weight: 0.5980 chunk 110 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 138 optimal weight: 0.0060 chunk 47 optimal weight: 0.4980 chunk 29 optimal weight: 0.0770 chunk 58 optimal weight: 7.9990 chunk 57 optimal weight: 0.0470 chunk 62 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.1350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 223 ASN ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3702 r_free = 0.3702 target = 0.145874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.113307 restraints weight = 17244.430| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.72 r_work: 0.3166 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.083 13695 Z= 0.108 Angle : 0.552 9.497 18603 Z= 0.283 Chirality : 0.039 0.148 2179 Planarity : 0.004 0.049 2324 Dihedral : 3.982 24.309 1831 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 1.30 % Allowed : 13.94 % Favored : 84.75 % 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: 1.06 (0.22), residues: 1672 helix: 2.31 (0.16), residues: 1066 sheet: None (None), residues: 0 loop : -2.46 (0.23), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 110 TYR 0.013 0.001 TYR A 116 PHE 0.017 0.001 PHE C 276 TRP 0.024 0.001 TRP C 524 HIS 0.005 0.001 HIS D 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (13679) covalent geometry : angle 0.54973 / 0.28 (18569) SS BOND : bond 0.00234 / 0.13 ( 11) SS BOND : angle 0.78878 / 0.60 ( 22) hydrogen bonds : bond 0.03186 / 2.09 ( 739) hydrogen bonds : angle 3.45789 / 2.41 ( 2190) Misc. bond : bond 0.00052 / 0.03 ( 1) link_BETA1-4 : bond 0.00646 / 0.33 ( 2) link_BETA1-4 : angle 1.01467 / 0.58 ( 6) link_NAG-ASN : bond 0.00611 / 0.32 ( 2) link_NAG-ASN : angle 2.24473 / 1.21 ( 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 188 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 0.382 Fit side-chains REVERT: A 144 ARG cc_start: 0.7382 (pmt-80) cc_final: 0.7012 (pmm150) REVERT: A 195 HIS cc_start: 0.8254 (OUTLIER) cc_final: 0.7863 (t-90) REVERT: A 237 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7987 (tm-30) REVERT: B 79 ASP cc_start: 0.6472 (p0) cc_final: 0.5539 (m-30) REVERT: B 168 GLU cc_start: 0.8536 (tp30) cc_final: 0.7797 (tp30) REVERT: B 229 LYS cc_start: 0.8447 (mmpt) cc_final: 0.7865 (mtmt) REVERT: C 99 TYR cc_start: 0.7685 (t80) cc_final: 0.7469 (t80) REVERT: C 103 GLU cc_start: 0.5565 (mt-10) cc_final: 0.5193 (tm-30) REVERT: C 111 GLU cc_start: 0.6314 (tt0) cc_final: 0.5827 (mt-10) REVERT: C 439 GLN cc_start: 0.7782 (mt0) cc_final: 0.7504 (mm110) REVERT: C 737 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.6153 (pp) REVERT: C 741 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.6365 (pmm) REVERT: D 103 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.6984 (tm-30) REVERT: D 107 PHE cc_start: 0.6705 (t80) cc_final: 0.6425 (t80) REVERT: D 217 LYS cc_start: 0.8194 (mtpp) cc_final: 0.7885 (mtmt) REVERT: D 373 HIS cc_start: 0.7850 (p90) cc_final: 0.7610 (p90) REVERT: D 604 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.8073 (ptp) REVERT: D 617 GLU cc_start: 0.6496 (OUTLIER) cc_final: 0.5274 (mm-30) REVERT: D 658 HIS cc_start: 0.5783 (m-70) cc_final: 0.5577 (m-70) REVERT: D 759 LYS cc_start: 0.6824 (ttpt) cc_final: 0.6285 (ttpt) outliers start: 19 outliers final: 8 residues processed: 180 average time/residue: 0.4960 time to fit residues: 98.2758 Evaluate side-chains 174 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 160 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 HIS 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 639 ARG Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 441 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: 0.7980 chunk 51 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 103 optimal weight: 0.0980 chunk 57 optimal weight: 0.2980 chunk 61 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 223 ASN ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3685 r_free = 0.3685 target = 0.144353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.111615 restraints weight = 17335.879| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.72 r_work: 0.3148 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.083 13695 Z= 0.110 Angle : 0.551 8.053 18603 Z= 0.281 Chirality : 0.039 0.147 2179 Planarity : 0.004 0.048 2324 Dihedral : 3.975 23.784 1831 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 1.51 % Allowed : 13.87 % Favored : 84.62 % 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: 1.11 (0.22), residues: 1672 helix: 2.36 (0.16), residues: 1062 sheet: None (None), residues: 0 loop : -2.42 (0.24), residues: 610 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 0.012 0.001 PHE D 392 TRP 0.020 0.001 TRP C 524 HIS 0.003 0.001 HIS C 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (13679) covalent geometry : angle 0.54873 / 0.28 (18569) SS BOND : bond 0.00255 / 0.14 ( 11) SS BOND : angle 0.84614 / 0.55 ( 22) hydrogen bonds : bond 0.03418 / 2.24 ( 739) hydrogen bonds : angle 3.44874 / 2.41 ( 2190) Misc. bond : bond 0.00219 / 0.12 ( 1) link_BETA1-4 : bond 0.00595 / 0.31 ( 2) link_BETA1-4 : angle 1.38896 / 0.66 ( 6) link_NAG-ASN : bond 0.00579 / 0.30 ( 2) link_NAG-ASN : angle 1.98546 / 1.09 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4578.73 seconds wall clock time: 78 minutes 40.97 seconds (4720.97 seconds total)