Starting phenix.real_space_refine on Thu Jul 31 11:11:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cq6_30437/07_2025/7cq6_30437.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cq6_30437/07_2025/7cq6_30437.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cq6_30437/07_2025/7cq6_30437.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cq6_30437/07_2025/7cq6_30437.map" model { file = "/net/cci-nas-00/data/ceres_data/7cq6_30437/07_2025/7cq6_30437.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cq6_30437/07_2025/7cq6_30437.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLU:plan': 2, 'ASN:plan1': 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: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2} 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: {'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 5046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 5046 Classifications: {'peptide': 650} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 621} Chain breaks: 6 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.03, per 1000 atoms: 0.60 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: 3.26 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.29 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: 3.71 Time building geometry restraints manager: 3.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3823 1.33 - 1.46: 2746 1.46 - 1.58: 6973 1.58 - 1.70: 0 1.70 - 1.82: 137 Bond restraints: 13679 Sorted by residual: bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.58e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.22e+00 bond pdb=" CB PRO C 582 " pdb=" CG PRO C 582 " ideal model delta sigma weight residual 1.492 1.381 0.111 5.00e-02 4.00e+02 4.94e+00 bond pdb=" CG1 ILE D 229 " pdb=" CD1 ILE D 229 " ideal model delta sigma weight residual 1.513 1.430 0.083 3.90e-02 6.57e+02 4.48e+00 bond pdb=" CB VAL C 586 " pdb=" CG1 VAL C 586 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.35e+00 ... (remaining 13674 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 17384 2.03 - 4.05: 958 4.05 - 6.08: 156 6.08 - 8.11: 51 8.11 - 10.14: 20 Bond angle restraints: 18569 Sorted by residual: angle pdb=" C GLY D 205 " pdb=" N ILE D 206 " pdb=" CA ILE D 206 " ideal model delta sigma weight residual 120.24 124.67 -4.43 6.30e-01 2.52e+00 4.94e+01 angle pdb=" N ILE D 114 " pdb=" CA ILE D 114 " pdb=" C ILE D 114 " ideal model delta sigma weight residual 113.53 107.51 6.02 9.80e-01 1.04e+00 3.77e+01 angle pdb=" N THR D 633 " pdb=" CA THR D 633 " pdb=" C THR D 633 " ideal model delta sigma weight residual 109.81 119.95 -10.14 2.21e+00 2.05e-01 2.10e+01 angle pdb=" C ARG B 271 " pdb=" N THR B 272 " pdb=" CA THR B 272 " ideal model delta sigma weight residual 121.54 129.99 -8.45 1.91e+00 2.74e-01 1.96e+01 angle pdb=" C ARG A 271 " pdb=" N THR A 272 " pdb=" CA THR A 272 " ideal model delta sigma weight residual 121.54 129.89 -8.35 1.91e+00 2.74e-01 1.91e+01 ... (remaining 18564 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.81: 7716 15.81 - 31.62: 380 31.62 - 47.44: 54 47.44 - 63.25: 5 63.25 - 79.06: 6 Dihedral angle restraints: 8161 sinusoidal: 3208 harmonic: 4953 Sorted by residual: dihedral pdb=" CA CYS B 115 " pdb=" C CYS B 115 " pdb=" N TYR B 116 " pdb=" CA TYR B 116 " ideal model delta harmonic sigma weight residual 180.00 144.48 35.52 0 5.00e+00 4.00e-02 5.05e+01 dihedral pdb=" CA ILE D 218 " pdb=" C ILE D 218 " pdb=" N PRO D 219 " pdb=" CA PRO D 219 " ideal model delta harmonic sigma weight residual -180.00 -151.09 -28.91 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA PRO A 108 " pdb=" C PRO A 108 " pdb=" N VAL A 109 " pdb=" CA VAL A 109 " ideal model delta harmonic sigma weight residual -180.00 -152.46 -27.54 0 5.00e+00 4.00e-02 3.03e+01 ... (remaining 8158 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1521 0.061 - 0.122: 538 0.122 - 0.183: 100 0.183 - 0.244: 18 0.244 - 0.305: 2 Chirality restraints: 2179 Sorted by residual: chirality pdb=" CB VAL C 513 " pdb=" CA VAL C 513 " pdb=" CG1 VAL C 513 " pdb=" CG2 VAL C 513 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CA ARG B 107 " pdb=" N ARG B 107 " pdb=" C ARG B 107 " pdb=" CB ARG B 107 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CA ARG A 107 " pdb=" N ARG A 107 " pdb=" C ARG A 107 " pdb=" CB ARG A 107 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 2176 not shown) Planarity restraints: 2326 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 179 " 0.035 2.00e-02 2.50e+03 2.68e-02 1.79e+01 pdb=" CG TRP C 179 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 TRP C 179 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP C 179 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 179 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP C 179 " -0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP C 179 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 179 " 0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 179 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP C 179 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 179 " 0.034 2.00e-02 2.50e+03 2.60e-02 1.68e+01 pdb=" CG TRP D 179 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 TRP D 179 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP D 179 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 179 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 179 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP D 179 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 179 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 179 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP D 179 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 272 " -0.016 2.00e-02 2.50e+03 3.14e-02 9.84e+00 pdb=" C THR B 272 " 0.054 2.00e-02 2.50e+03 pdb=" O THR B 272 " -0.020 2.00e-02 2.50e+03 pdb=" N PHE B 273 " -0.018 2.00e-02 2.50e+03 ... (remaining 2323 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2604 2.77 - 3.30: 12417 3.30 - 3.83: 21284 3.83 - 4.37: 25495 4.37 - 4.90: 44859 Nonbonded interactions: 106659 Sorted by model distance: nonbonded pdb=" O MET C 368 " pdb=" OH TYR C 579 " model vdw 2.233 3.040 nonbonded pdb=" O MET D 368 " pdb=" OH TYR D 579 " model vdw 2.270 3.040 nonbonded pdb=" O LEU D 500 " pdb=" OG1 THR D 504 " model vdw 2.274 3.040 nonbonded pdb=" OG SER D 298 " pdb=" OG1 THR D 335 " model vdw 2.287 3.040 nonbonded pdb=" OD1 ASP A 76 " pdb=" OG SER A 145 " model vdw 2.301 3.040 ... (remaining 106654 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 73 through 245 or resid 253 through 306)) selection = (chain 'B' and (resid 73 through 204 or resid 216 through 245 or resid 253 throu \ gh 306)) } ncs_group { reference = (chain 'C' and (resid 94 through 617 or resid 625 through 652 or resid 657 throu \ gh 688 or resid 708 through 790 or resid 901 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 790 or resid 901 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: 1.120 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: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 31.230 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:12.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.111 13695 Z= 0.420 Angle : 1.128 10.136 18603 Z= 0.606 Chirality : 0.062 0.305 2179 Planarity : 0.008 0.067 2324 Dihedral : 9.887 79.060 4920 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 0.27 % Allowed : 2.06 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.069 0.006 TRP D 179 HIS 0.010 0.002 HIS C 479 PHE 0.031 0.004 PHE C 329 TYR 0.029 0.003 TYR C 406 ARG 0.020 0.002 ARG C 526 Details of bonding type rmsd link_NAG-ASN : bond 0.00440 ( 2) link_NAG-ASN : angle 5.53224 ( 6) link_BETA1-4 : bond 0.00353 ( 2) link_BETA1-4 : angle 3.10193 ( 6) hydrogen bonds : bond 0.21883 ( 739) hydrogen bonds : angle 7.80621 ( 2190) SS BOND : bond 0.01367 ( 11) SS BOND : angle 2.29439 ( 22) covalent geometry : bond 0.01037 (13679) covalent geometry : angle 1.12084 (18569) Misc. bond : bond 0.00173 ( 1) *********************** 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 : 1.622 Fit side-chains REVERT: A 160 GLU cc_start: 0.7587 (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: 0.8087 (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: 1.7091 time to fit residues: 433.8722 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 : 1.443 ------------------------------------------------------------------------------- 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 142 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 132 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 98 optimal weight: 0.0170 chunk 153 optimal weight: 0.7980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 ASN ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN ** C 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 GLN C 479 HIS C 555 GLN C 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 = 0.3644 r_free = 0.3644 target = 0.140721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.108427 restraints weight = 17127.918| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.62 r_work: 0.3075 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13695 Z= 0.136 Angle : 0.643 12.459 18603 Z= 0.334 Chirality : 0.041 0.162 2179 Planarity : 0.005 0.052 2324 Dihedral : 5.681 42.785 1916 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 1.85 % Allowed : 7.28 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.19), residues: 1672 helix: -0.28 (0.15), residues: 1063 sheet: None (None), residues: 0 loop : -3.05 (0.22), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 179 HIS 0.004 0.001 HIS C 605 PHE 0.016 0.001 PHE C 329 TYR 0.014 0.001 TYR B 188 ARG 0.005 0.001 ARG D 362 Details of bonding type rmsd link_NAG-ASN : bond 0.00246 ( 2) link_NAG-ASN : angle 3.19502 ( 6) link_BETA1-4 : bond 0.00482 ( 2) link_BETA1-4 : angle 1.41017 ( 6) hydrogen bonds : bond 0.05221 ( 739) hydrogen bonds : angle 4.43206 ( 2190) SS BOND : bond 0.00346 ( 11) SS BOND : angle 1.15529 ( 22) covalent geometry : bond 0.00290 (13679) covalent geometry : angle 0.63943 (18569) Misc. bond : bond 0.00151 ( 1) *********************** 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 211 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 184 time to evaluate : 1.973 Fit side-chains REVERT: A 144 ARG cc_start: 0.7679 (pmt-80) cc_final: 0.7256 (pmm150) REVERT: A 160 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8224 (mt-10) REVERT: A 195 HIS cc_start: 0.8238 (OUTLIER) cc_final: 0.7820 (t-90) REVERT: A 237 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7883 (tm-30) REVERT: B 167 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.8095 (mp10) REVERT: B 229 LYS cc_start: 0.8614 (mmpt) cc_final: 0.8086 (mtmt) REVERT: C 99 TYR cc_start: 0.8083 (t80) cc_final: 0.7648 (t80) REVERT: C 111 GLU cc_start: 0.6431 (tt0) cc_final: 0.5740 (mt-10) REVERT: C 572 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8218 (mt-10) REVERT: C 674 ARG cc_start: 0.6773 (mtm-85) cc_final: 0.6457 (ttm110) REVERT: D 107 PHE cc_start: 0.7256 (t80) cc_final: 0.6895 (t80) REVERT: D 217 LYS cc_start: 0.8267 (mtpp) cc_final: 0.7907 (mtpt) REVERT: D 439 GLN cc_start: 0.8506 (tt0) cc_final: 0.8272 (mt0) REVERT: D 459 TYR cc_start: 0.8464 (m-80) cc_final: 0.8179 (m-80) REVERT: D 584 MET cc_start: 0.9145 (ptm) cc_final: 0.8904 (ttp) REVERT: D 617 GLU cc_start: 0.6786 (OUTLIER) cc_final: 0.5558 (mm-30) REVERT: D 658 HIS cc_start: 0.6192 (m-70) cc_final: 0.5955 (m-70) REVERT: D 759 LYS cc_start: 0.6907 (ttpt) cc_final: 0.6340 (ttpt) outliers start: 27 outliers final: 6 residues processed: 199 average time/residue: 1.8078 time to fit residues: 389.9084 Evaluate side-chains 171 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 162 time to evaluate : 1.321 ------------------------------------------------------------------------------- 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 167 GLN Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 617 GLU Chi-restraints excluded: chain D residue 754 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 33 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 92 optimal weight: 0.0170 overall best weight: 1.7624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 ASN ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 HIS 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.137231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.104656 restraints weight = 17421.948| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.63 r_work: 0.2984 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13695 Z= 0.191 Angle : 0.668 13.132 18603 Z= 0.343 Chirality : 0.043 0.161 2179 Planarity : 0.005 0.049 2324 Dihedral : 5.242 32.254 1915 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 2.40 % Allowed : 9.20 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.20), residues: 1672 helix: 0.48 (0.16), residues: 1066 sheet: -2.74 (2.04), residues: 5 loop : -2.85 (0.23), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 179 HIS 0.007 0.001 HIS C 479 PHE 0.019 0.002 PHE D 392 TYR 0.013 0.002 TYR A 116 ARG 0.006 0.001 ARG D 326 Details of bonding type rmsd link_NAG-ASN : bond 0.00450 ( 2) link_NAG-ASN : angle 3.03449 ( 6) link_BETA1-4 : bond 0.00173 ( 2) link_BETA1-4 : angle 1.65838 ( 6) hydrogen bonds : bond 0.05405 ( 739) hydrogen bonds : angle 4.16132 ( 2190) SS BOND : bond 0.00437 ( 11) SS BOND : angle 1.45705 ( 22) covalent geometry : bond 0.00462 (13679) covalent geometry : angle 0.66427 (18569) Misc. bond : bond 0.00039 ( 1) *********************** 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 205 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 170 time to evaluate : 1.660 Fit side-chains REVERT: A 160 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8200 (mt-10) REVERT: A 195 HIS cc_start: 0.8361 (OUTLIER) cc_final: 0.7941 (t-90) REVERT: B 152 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7514 (ttt) REVERT: B 167 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.8032 (mp10) REVERT: B 168 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8429 (tp30) REVERT: B 229 LYS cc_start: 0.8524 (mmpt) cc_final: 0.7955 (mtpt) REVERT: C 99 TYR cc_start: 0.8080 (t80) cc_final: 0.7832 (t80) REVERT: C 111 GLU cc_start: 0.6313 (tt0) cc_final: 0.5565 (mt-10) REVERT: C 263 GLN cc_start: 0.8016 (mp-120) cc_final: 0.7791 (mp10) REVERT: C 674 ARG cc_start: 0.6592 (mtm-85) cc_final: 0.6164 (ttm110) REVERT: D 107 PHE cc_start: 0.7035 (t80) cc_final: 0.6719 (t80) REVERT: D 217 LYS cc_start: 0.8223 (mtpp) cc_final: 0.7831 (mtmt) REVERT: D 459 TYR cc_start: 0.8428 (m-80) cc_final: 0.8191 (m-80) REVERT: D 571 MET cc_start: 0.9113 (ttm) cc_final: 0.8876 (ttp) REVERT: D 584 MET cc_start: 0.9120 (ptm) cc_final: 0.8910 (ttp) REVERT: D 617 GLU cc_start: 0.6518 (OUTLIER) cc_final: 0.5314 (mm-30) REVERT: D 658 HIS cc_start: 0.6362 (m-70) cc_final: 0.6122 (m-70) REVERT: D 731 ARG cc_start: 0.5716 (mtt90) cc_final: 0.5085 (mmp-170) REVERT: D 759 LYS cc_start: 0.6750 (ttpt) cc_final: 0.6259 (ttmt) outliers start: 35 outliers final: 12 residues processed: 188 average time/residue: 1.7385 time to fit residues: 353.9563 Evaluate side-chains 176 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 639 ARG Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 325 TRP Chi-restraints excluded: chain D residue 617 GLU Chi-restraints excluded: chain D residue 754 LEU Chi-restraints excluded: chain D residue 757 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 121 optimal weight: 6.9990 chunk 144 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 88 optimal weight: 0.2980 chunk 26 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 161 optimal weight: 0.0020 chunk 155 optimal weight: 0.8980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 GLN ** C 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.140860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.108281 restraints weight = 17151.655| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.64 r_work: 0.3091 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 13695 Z= 0.116 Angle : 0.583 11.274 18603 Z= 0.300 Chirality : 0.040 0.139 2179 Planarity : 0.004 0.050 2324 Dihedral : 4.735 26.303 1915 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 1.65 % Allowed : 10.58 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.21), residues: 1672 helix: 1.07 (0.16), residues: 1069 sheet: None (None), residues: 0 loop : -2.72 (0.23), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 524 HIS 0.005 0.001 HIS C 605 PHE 0.011 0.001 PHE C 329 TYR 0.014 0.001 TYR A 116 ARG 0.005 0.000 ARG A 110 Details of bonding type rmsd link_NAG-ASN : bond 0.00698 ( 2) link_NAG-ASN : angle 2.75573 ( 6) link_BETA1-4 : bond 0.00481 ( 2) link_BETA1-4 : angle 1.15692 ( 6) hydrogen bonds : bond 0.04214 ( 739) hydrogen bonds : angle 3.90607 ( 2190) SS BOND : bond 0.00839 ( 11) SS BOND : angle 1.00001 ( 22) covalent geometry : bond 0.00244 (13679) covalent geometry : angle 0.57963 (18569) Misc. bond : bond 0.00484 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 169 time to evaluate : 1.831 Fit side-chains REVERT: A 110 ARG cc_start: 0.8752 (mtt-85) cc_final: 0.8497 (mmt90) REVERT: A 144 ARG cc_start: 0.7737 (pmt-80) cc_final: 0.7291 (pmm150) REVERT: A 160 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8220 (mt-10) REVERT: A 195 HIS cc_start: 0.8263 (OUTLIER) cc_final: 0.7871 (t-90) REVERT: A 201 GLU cc_start: 0.7047 (tt0) cc_final: 0.6698 (mm-30) REVERT: A 237 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7870 (tm-30) REVERT: B 229 LYS cc_start: 0.8592 (mmpt) cc_final: 0.8075 (mtpt) REVERT: C 99 TYR cc_start: 0.8058 (t80) cc_final: 0.7716 (t80) REVERT: C 111 GLU cc_start: 0.6480 (tt0) cc_final: 0.5721 (mt-10) REVERT: D 107 PHE cc_start: 0.7143 (t80) cc_final: 0.6844 (t80) REVERT: D 217 LYS cc_start: 0.8289 (mtpp) cc_final: 0.7985 (mtpt) REVERT: D 566 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9094 (tt) REVERT: D 571 MET cc_start: 0.9054 (ttm) cc_final: 0.8851 (ttp) REVERT: D 584 MET cc_start: 0.9197 (ptm) cc_final: 0.8994 (ttp) REVERT: D 617 GLU cc_start: 0.6748 (OUTLIER) cc_final: 0.5497 (mm-30) REVERT: D 658 HIS cc_start: 0.6103 (m-70) cc_final: 0.5876 (m-70) REVERT: D 759 LYS cc_start: 0.6972 (ttpt) cc_final: 0.6392 (ttmt) outliers start: 24 outliers final: 7 residues processed: 182 average time/residue: 1.5594 time to fit residues: 306.4669 Evaluate side-chains 168 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 158 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 HIS 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 D residue 267 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 325 TRP Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 617 GLU Chi-restraints excluded: chain D residue 754 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 162 optimal weight: 0.9990 chunk 148 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 159 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 165 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 768 HIS ** D 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 768 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.136456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.103845 restraints weight = 17254.514| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.62 r_work: 0.2987 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 13695 Z= 0.207 Angle : 0.662 13.511 18603 Z= 0.338 Chirality : 0.044 0.160 2179 Planarity : 0.005 0.049 2324 Dihedral : 4.839 28.964 1915 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 1.99 % Allowed : 11.54 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.21), residues: 1672 helix: 1.11 (0.16), residues: 1068 sheet: -2.39 (2.24), residues: 5 loop : -2.69 (0.23), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 524 HIS 0.007 0.001 HIS C 479 PHE 0.018 0.002 PHE D 392 TYR 0.013 0.002 TYR A 116 ARG 0.006 0.001 ARG D 526 Details of bonding type rmsd link_NAG-ASN : bond 0.00953 ( 2) link_NAG-ASN : angle 2.83910 ( 6) link_BETA1-4 : bond 0.00132 ( 2) link_BETA1-4 : angle 1.91367 ( 6) hydrogen bonds : bond 0.05115 ( 739) hydrogen bonds : angle 4.01586 ( 2190) SS BOND : bond 0.00469 ( 11) SS BOND : angle 1.13616 ( 22) covalent geometry : bond 0.00508 (13679) covalent geometry : angle 0.65874 (18569) Misc. bond : bond 0.00301 ( 1) *********************** 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 189 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 1.579 Fit side-chains revert: symmetry clash REVERT: A 195 HIS cc_start: 0.8300 (OUTLIER) cc_final: 0.7917 (t-90) REVERT: A 201 GLU cc_start: 0.7320 (tt0) cc_final: 0.6979 (mm-30) REVERT: B 229 LYS cc_start: 0.8488 (mmpt) cc_final: 0.7939 (mtpt) REVERT: C 99 TYR cc_start: 0.8051 (t80) cc_final: 0.7792 (t80) REVERT: C 111 GLU cc_start: 0.6060 (tt0) cc_final: 0.5273 (mt-10) REVERT: C 480 ASP cc_start: 0.8553 (OUTLIER) cc_final: 0.8291 (m-30) REVERT: C 599 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7697 (pm20) REVERT: D 97 LEU cc_start: 0.6819 (OUTLIER) cc_final: 0.6480 (pp) REVERT: D 217 LYS cc_start: 0.8268 (mtpp) cc_final: 0.7903 (mtmt) REVERT: D 439 GLN cc_start: 0.8359 (tt0) cc_final: 0.8125 (mt0) REVERT: D 566 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9052 (tt) REVERT: D 617 GLU cc_start: 0.6376 (OUTLIER) cc_final: 0.5185 (mm-30) REVERT: D 658 HIS cc_start: 0.6733 (m-70) cc_final: 0.6533 (m-70) REVERT: D 731 ARG cc_start: 0.5806 (OUTLIER) cc_final: 0.4933 (mmp-170) REVERT: D 759 LYS cc_start: 0.7052 (ttpt) cc_final: 0.6492 (ttpt) outliers start: 29 outliers final: 13 residues processed: 176 average time/residue: 1.4433 time to fit residues: 275.6625 Evaluate side-chains 174 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 154 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 MET 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 222 LYS Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 480 ASP Chi-restraints excluded: chain C residue 599 GLU Chi-restraints excluded: chain C residue 639 ARG Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 325 TRP Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 617 GLU Chi-restraints excluded: chain D residue 731 ARG 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 116 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 164 optimal weight: 0.0980 chunk 38 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 37 optimal weight: 0.4980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3619 r_free = 0.3619 target = 0.138903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.106278 restraints weight = 17427.882| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.64 r_work: 0.3055 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 13695 Z= 0.128 Angle : 0.592 12.080 18603 Z= 0.303 Chirality : 0.040 0.142 2179 Planarity : 0.004 0.049 2324 Dihedral : 4.593 26.969 1915 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 1.99 % Allowed : 12.64 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.21), residues: 1672 helix: 1.42 (0.16), residues: 1068 sheet: None (None), residues: 0 loop : -2.60 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 524 HIS 0.009 0.001 HIS D 373 PHE 0.013 0.001 PHE D 392 TYR 0.013 0.001 TYR A 116 ARG 0.004 0.000 ARG B 144 Details of bonding type rmsd link_NAG-ASN : bond 0.00561 ( 2) link_NAG-ASN : angle 2.62030 ( 6) link_BETA1-4 : bond 0.00476 ( 2) link_BETA1-4 : angle 1.60172 ( 6) hydrogen bonds : bond 0.04291 ( 739) hydrogen bonds : angle 3.86553 ( 2190) SS BOND : bond 0.00324 ( 11) SS BOND : angle 0.97654 ( 22) covalent geometry : bond 0.00293 (13679) covalent geometry : angle 0.58894 (18569) Misc. bond : bond 0.00206 ( 1) *********************** 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 196 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 167 time to evaluate : 1.594 Fit side-chains revert: symmetry clash REVERT: A 144 ARG cc_start: 0.7641 (pmt-80) cc_final: 0.7269 (pmm150) REVERT: A 160 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8233 (mt-10) REVERT: A 195 HIS cc_start: 0.8252 (OUTLIER) cc_final: 0.7899 (t-90) REVERT: A 201 GLU cc_start: 0.7287 (tt0) cc_final: 0.7013 (mm-30) REVERT: A 223 ASN cc_start: 0.8384 (t0) cc_final: 0.8183 (t0) REVERT: A 237 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7802 (tm-30) REVERT: B 229 LYS cc_start: 0.8576 (mmpt) cc_final: 0.8085 (mtpt) REVERT: C 99 TYR cc_start: 0.8028 (t80) cc_final: 0.7777 (t80) REVERT: C 111 GLU cc_start: 0.6327 (tt0) cc_final: 0.5528 (mt-10) REVERT: D 97 LEU cc_start: 0.6824 (OUTLIER) cc_final: 0.6496 (pp) REVERT: D 103 GLU cc_start: 0.8081 (tp30) cc_final: 0.7064 (tm-30) REVERT: D 217 LYS cc_start: 0.8336 (mtpp) cc_final: 0.8078 (mtmt) REVERT: D 566 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9076 (tt) REVERT: D 584 MET cc_start: 0.8994 (ttp) cc_final: 0.8672 (ttm) REVERT: D 617 GLU cc_start: 0.6692 (OUTLIER) cc_final: 0.5469 (mm-30) REVERT: D 658 HIS cc_start: 0.6161 (m-70) cc_final: 0.5957 (m-70) REVERT: D 731 ARG cc_start: 0.5586 (OUTLIER) cc_final: 0.4872 (mmp-170) REVERT: D 759 LYS cc_start: 0.7191 (ttpt) cc_final: 0.6590 (ttmt) REVERT: D 785 LYS cc_start: 0.7763 (mtpt) cc_final: 0.7309 (mtpp) outliers start: 29 outliers final: 14 residues processed: 180 average time/residue: 1.4541 time to fit residues: 283.8589 Evaluate side-chains 177 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 148 MET 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 439 GLN Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 480 ASP Chi-restraints excluded: chain C residue 639 ARG Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 325 TRP Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 617 GLU Chi-restraints excluded: chain D residue 731 ARG 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 76 optimal weight: 2.9990 chunk 160 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 12 optimal weight: 8.9990 chunk 136 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3588 r_free = 0.3588 target = 0.136401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.103687 restraints weight = 17345.941| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.63 r_work: 0.3032 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 13695 Z= 0.189 Angle : 0.644 13.227 18603 Z= 0.330 Chirality : 0.043 0.165 2179 Planarity : 0.005 0.048 2324 Dihedral : 4.732 27.495 1915 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 2.47 % Allowed : 12.71 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.21), residues: 1672 helix: 1.39 (0.16), residues: 1067 sheet: -2.26 (2.20), residues: 5 loop : -2.61 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 524 HIS 0.007 0.001 HIS C 479 PHE 0.018 0.002 PHE C 392 TYR 0.014 0.001 TYR A 116 ARG 0.005 0.001 ARG C 526 Details of bonding type rmsd link_NAG-ASN : bond 0.00786 ( 2) link_NAG-ASN : angle 2.80093 ( 6) link_BETA1-4 : bond 0.00544 ( 2) link_BETA1-4 : angle 1.71636 ( 6) hydrogen bonds : bond 0.04937 ( 739) hydrogen bonds : angle 3.95812 ( 2190) SS BOND : bond 0.00360 ( 11) SS BOND : angle 1.15501 ( 22) covalent geometry : bond 0.00465 (13679) covalent geometry : angle 0.64105 (18569) Misc. bond : bond 0.00323 ( 1) *********************** 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 195 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 159 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 ARG cc_start: 0.7603 (pmt-80) cc_final: 0.7208 (pmm150) REVERT: A 160 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8264 (mt-10) REVERT: A 195 HIS cc_start: 0.8320 (OUTLIER) cc_final: 0.7980 (t-90) REVERT: A 201 GLU cc_start: 0.7410 (tt0) cc_final: 0.7151 (mm-30) REVERT: A 237 GLU cc_start: 0.8311 (tm-30) cc_final: 0.7944 (tm-30) REVERT: B 229 LYS cc_start: 0.8585 (mmpt) cc_final: 0.8138 (mtmt) REVERT: C 99 TYR cc_start: 0.8051 (t80) cc_final: 0.7843 (t80) REVERT: C 111 GLU cc_start: 0.6429 (tt0) cc_final: 0.5629 (mt-10) REVERT: C 480 ASP cc_start: 0.8552 (OUTLIER) cc_final: 0.8309 (m-30) REVERT: C 599 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7704 (pm20) REVERT: C 676 GLN cc_start: 0.7234 (OUTLIER) cc_final: 0.5303 (mp10) REVERT: C 741 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.6721 (pmm) REVERT: D 97 LEU cc_start: 0.6784 (OUTLIER) cc_final: 0.6432 (pp) REVERT: D 103 GLU cc_start: 0.8085 (tp30) cc_final: 0.7082 (tm-30) REVERT: D 217 LYS cc_start: 0.8350 (mtpp) cc_final: 0.8049 (mtmt) REVERT: D 566 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9075 (tt) REVERT: D 617 GLU cc_start: 0.6593 (OUTLIER) cc_final: 0.5342 (mm-30) REVERT: D 731 ARG cc_start: 0.5634 (OUTLIER) cc_final: 0.4881 (mmp-170) REVERT: D 735 MET cc_start: 0.6858 (OUTLIER) cc_final: 0.6630 (ptm) REVERT: D 759 LYS cc_start: 0.7227 (ttpt) cc_final: 0.6623 (ttpt) REVERT: D 785 LYS cc_start: 0.7633 (mtpt) cc_final: 0.6775 (mptt) outliers start: 36 outliers final: 17 residues processed: 178 average time/residue: 1.4689 time to fit residues: 283.3375 Evaluate side-chains 182 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 1.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 192 LEU 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 439 GLN Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 480 ASP Chi-restraints excluded: chain C residue 599 GLU Chi-restraints excluded: chain C residue 639 ARG Chi-restraints excluded: chain C residue 676 GLN Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 325 TRP Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 617 GLU Chi-restraints excluded: chain D residue 708 LEU Chi-restraints excluded: chain D residue 731 ARG Chi-restraints excluded: chain D residue 733 CYS Chi-restraints excluded: chain D residue 735 MET Chi-restraints excluded: chain D residue 754 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 27 optimal weight: 0.6980 chunk 133 optimal weight: 0.9980 chunk 124 optimal weight: 0.7980 chunk 127 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 164 optimal weight: 6.9990 chunk 77 optimal weight: 0.5980 chunk 89 optimal weight: 0.9980 chunk 154 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN ** D 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.138856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.106211 restraints weight = 17337.700| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.65 r_work: 0.3060 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 13695 Z= 0.127 Angle : 0.595 11.998 18603 Z= 0.305 Chirality : 0.040 0.160 2179 Planarity : 0.004 0.049 2324 Dihedral : 4.516 26.529 1915 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 2.06 % Allowed : 13.12 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.21), residues: 1672 helix: 1.67 (0.16), residues: 1067 sheet: -2.27 (2.24), residues: 5 loop : -2.51 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 524 HIS 0.005 0.001 HIS D 373 PHE 0.013 0.001 PHE D 392 TYR 0.014 0.001 TYR A 116 ARG 0.005 0.000 ARG B 144 Details of bonding type rmsd link_NAG-ASN : bond 0.00586 ( 2) link_NAG-ASN : angle 2.44073 ( 6) link_BETA1-4 : bond 0.00610 ( 2) link_BETA1-4 : angle 1.46841 ( 6) hydrogen bonds : bond 0.04230 ( 739) hydrogen bonds : angle 3.83072 ( 2190) SS BOND : bond 0.00288 ( 11) SS BOND : angle 0.97727 ( 22) covalent geometry : bond 0.00292 (13679) covalent geometry : angle 0.59226 (18569) Misc. bond : bond 0.00205 ( 1) *********************** 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 191 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 1.434 Fit side-chains REVERT: A 144 ARG cc_start: 0.7647 (pmt-80) cc_final: 0.7206 (pmm150) REVERT: A 160 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8242 (mt-10) REVERT: A 195 HIS cc_start: 0.8291 (OUTLIER) cc_final: 0.7935 (t-90) REVERT: A 201 GLU cc_start: 0.7352 (tt0) cc_final: 0.7114 (mm-30) REVERT: A 237 GLU cc_start: 0.8322 (tm-30) cc_final: 0.7940 (tm-30) REVERT: B 110 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.8275 (mpt180) REVERT: B 229 LYS cc_start: 0.8605 (mmpt) cc_final: 0.8150 (mtmt) REVERT: C 111 GLU cc_start: 0.6458 (tt0) cc_final: 0.5656 (mt-10) REVERT: C 480 ASP cc_start: 0.8461 (OUTLIER) cc_final: 0.8227 (m-30) REVERT: C 599 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7622 (pm20) REVERT: C 737 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.6555 (pp) REVERT: C 741 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.6730 (pmm) REVERT: D 97 LEU cc_start: 0.6480 (OUTLIER) cc_final: 0.6123 (pp) REVERT: D 103 GLU cc_start: 0.8081 (tp30) cc_final: 0.7105 (tm-30) REVERT: D 217 LYS cc_start: 0.8334 (mtpp) cc_final: 0.8044 (mtmt) REVERT: D 566 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.9063 (tt) REVERT: D 617 GLU cc_start: 0.6611 (OUTLIER) cc_final: 0.5371 (mm-30) REVERT: D 731 ARG cc_start: 0.5522 (OUTLIER) cc_final: 0.4839 (mmp-170) REVERT: D 759 LYS cc_start: 0.7271 (ttpt) cc_final: 0.6667 (ttmt) REVERT: D 785 LYS cc_start: 0.7616 (mtpt) cc_final: 0.6769 (mptt) outliers start: 30 outliers final: 12 residues processed: 177 average time/residue: 1.4086 time to fit residues: 270.3364 Evaluate side-chains 178 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain B residue 110 ARG 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 325 TRP Chi-restraints excluded: chain C residue 438 CYS Chi-restraints excluded: chain C residue 439 GLN Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 480 ASP Chi-restraints excluded: chain C residue 599 GLU Chi-restraints excluded: chain C residue 639 ARG Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 325 TRP Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 617 GLU Chi-restraints excluded: chain D residue 731 ARG Chi-restraints excluded: chain D residue 754 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 93 optimal weight: 9.9990 chunk 80 optimal weight: 0.9990 chunk 116 optimal weight: 0.5980 chunk 125 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN ** D 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.139261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.107063 restraints weight = 17268.267| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.62 r_work: 0.3050 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 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 0.077 13695 Z= 0.123 Angle : 0.576 11.239 18603 Z= 0.296 Chirality : 0.040 0.151 2179 Planarity : 0.004 0.048 2324 Dihedral : 4.390 26.091 1915 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 1.92 % Allowed : 13.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.21), residues: 1672 helix: 1.85 (0.16), residues: 1065 sheet: None (None), residues: 0 loop : -2.49 (0.24), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 524 HIS 0.004 0.001 HIS C 605 PHE 0.013 0.001 PHE D 392 TYR 0.014 0.001 TYR A 116 ARG 0.004 0.000 ARG B 144 Details of bonding type rmsd link_NAG-ASN : bond 0.00485 ( 2) link_NAG-ASN : angle 2.23508 ( 6) link_BETA1-4 : bond 0.00429 ( 2) link_BETA1-4 : angle 1.44484 ( 6) hydrogen bonds : bond 0.04016 ( 739) hydrogen bonds : angle 3.76442 ( 2190) SS BOND : bond 0.00262 ( 11) SS BOND : angle 0.98589 ( 22) covalent geometry : bond 0.00281 (13679) covalent geometry : angle 0.57355 (18569) Misc. bond : bond 0.00241 ( 1) *********************** 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 198 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 170 time to evaluate : 1.699 Fit side-chains REVERT: A 144 ARG cc_start: 0.7557 (pmt-80) cc_final: 0.7091 (pmm150) REVERT: A 160 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8132 (mt-10) REVERT: A 195 HIS cc_start: 0.8279 (OUTLIER) cc_final: 0.7896 (t-90) REVERT: A 201 GLU cc_start: 0.7155 (tt0) cc_final: 0.6893 (mm-30) REVERT: A 237 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7946 (tm-30) REVERT: B 168 GLU cc_start: 0.8527 (tp30) cc_final: 0.7758 (tp30) REVERT: B 229 LYS cc_start: 0.8448 (mmpt) cc_final: 0.7912 (mtmt) REVERT: B 265 THR cc_start: 0.9216 (t) cc_final: 0.9008 (m) REVERT: C 99 TYR cc_start: 0.7572 (t80) cc_final: 0.7249 (t80) REVERT: C 111 GLU cc_start: 0.6263 (tt0) cc_final: 0.5479 (mt-10) REVERT: C 480 ASP cc_start: 0.8479 (OUTLIER) cc_final: 0.8243 (m-30) REVERT: C 599 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7541 (pm20) REVERT: C 737 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.6501 (pp) REVERT: C 741 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.6503 (pmm) REVERT: D 97 LEU cc_start: 0.6228 (OUTLIER) cc_final: 0.5908 (pp) REVERT: D 103 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.6945 (tm-30) REVERT: D 217 LYS cc_start: 0.8284 (mtpp) cc_final: 0.7947 (mtmt) REVERT: D 566 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8996 (tt) REVERT: D 617 GLU cc_start: 0.6505 (OUTLIER) cc_final: 0.5318 (mm-30) REVERT: D 731 ARG cc_start: 0.5716 (ptm-80) cc_final: 0.4925 (mmp-170) REVERT: D 759 LYS cc_start: 0.7045 (ttpt) cc_final: 0.6498 (ttmt) REVERT: D 785 LYS cc_start: 0.7475 (mtpt) cc_final: 0.6592 (mptt) outliers start: 28 outliers final: 13 residues processed: 186 average time/residue: 1.7395 time to fit residues: 353.4005 Evaluate side-chains 186 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 1.258 ------------------------------------------------------------------------------- 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 325 TRP Chi-restraints excluded: chain C residue 438 CYS Chi-restraints excluded: chain C residue 439 GLN Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 480 ASP Chi-restraints excluded: chain C residue 599 GLU Chi-restraints excluded: chain C residue 639 ARG Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 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 566 LEU Chi-restraints excluded: chain D residue 617 GLU Chi-restraints excluded: chain D residue 733 CYS Chi-restraints excluded: chain D residue 754 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 2 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 138 optimal weight: 0.3980 chunk 162 optimal weight: 0.0870 chunk 166 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 12 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN ** D 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.138984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.107010 restraints weight = 17161.154| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.58 r_work: 0.3067 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2917 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= 0.128 Angle : 0.592 11.215 18603 Z= 0.303 Chirality : 0.040 0.143 2179 Planarity : 0.004 0.049 2324 Dihedral : 4.413 26.231 1915 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 1.92 % Allowed : 14.01 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.21), residues: 1672 helix: 1.97 (0.16), residues: 1060 sheet: None (None), residues: 0 loop : -2.48 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 524 HIS 0.004 0.001 HIS C 605 PHE 0.013 0.001 PHE D 392 TYR 0.014 0.001 TYR A 116 ARG 0.007 0.000 ARG A 110 Details of bonding type rmsd link_NAG-ASN : bond 0.00566 ( 2) link_NAG-ASN : angle 2.32027 ( 6) link_BETA1-4 : bond 0.00389 ( 2) link_BETA1-4 : angle 1.31457 ( 6) hydrogen bonds : bond 0.04016 ( 739) hydrogen bonds : angle 3.73392 ( 2190) SS BOND : bond 0.00267 ( 11) SS BOND : angle 0.99037 ( 22) covalent geometry : bond 0.00297 (13679) covalent geometry : angle 0.58950 (18569) Misc. bond : bond 0.00116 ( 1) ********************** 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 193 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 2.038 Fit side-chains REVERT: A 110 ARG cc_start: 0.8747 (mtt-85) cc_final: 0.8483 (mmt90) REVERT: A 144 ARG cc_start: 0.7439 (pmt-80) cc_final: 0.6986 (pmm150) REVERT: A 160 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8146 (mt-10) REVERT: A 195 HIS cc_start: 0.8254 (OUTLIER) cc_final: 0.7920 (t-90) REVERT: A 201 GLU cc_start: 0.7162 (tt0) cc_final: 0.6924 (mm-30) REVERT: B 168 GLU cc_start: 0.8532 (tp30) cc_final: 0.7780 (tp30) REVERT: B 229 LYS cc_start: 0.8470 (mmpt) cc_final: 0.7955 (mtmt) REVERT: C 99 TYR cc_start: 0.7523 (t80) cc_final: 0.7117 (t80) REVERT: C 103 GLU cc_start: 0.5617 (tt0) cc_final: 0.5345 (tm-30) REVERT: C 111 GLU cc_start: 0.6203 (tt0) cc_final: 0.5411 (mt-10) REVERT: C 480 ASP cc_start: 0.8474 (OUTLIER) cc_final: 0.8233 (m-30) REVERT: C 599 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7559 (pm20) REVERT: C 737 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.6249 (pp) REVERT: C 741 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.6509 (pmm) REVERT: D 97 LEU cc_start: 0.6308 (OUTLIER) cc_final: 0.5986 (pp) REVERT: D 103 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.6977 (tm-30) REVERT: D 217 LYS cc_start: 0.8294 (mtpp) cc_final: 0.7973 (mtmt) REVERT: D 566 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.9015 (tt) REVERT: D 617 GLU cc_start: 0.6534 (OUTLIER) cc_final: 0.5355 (mm-30) REVERT: D 731 ARG cc_start: 0.5689 (ptm-80) cc_final: 0.4841 (mmp-170) REVERT: D 759 LYS cc_start: 0.7056 (ttpt) cc_final: 0.6486 (ttpt) REVERT: D 785 LYS cc_start: 0.7508 (mtpt) cc_final: 0.6639 (mptt) outliers start: 28 outliers final: 11 residues processed: 180 average time/residue: 2.0617 time to fit residues: 403.6968 Evaluate side-chains 177 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 2.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 HIS 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 325 TRP Chi-restraints excluded: chain C residue 438 CYS Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 480 ASP Chi-restraints excluded: chain C residue 599 GLU Chi-restraints excluded: chain C residue 639 ARG Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 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 566 LEU Chi-restraints excluded: chain D residue 617 GLU Chi-restraints excluded: chain D residue 733 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 92 optimal weight: 0.0000 chunk 144 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 65 optimal weight: 0.0070 chunk 39 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 overall best weight: 0.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 ASN C 263 GLN ** D 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.141857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.110040 restraints weight = 17208.703| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.60 r_work: 0.3121 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 13695 Z= 0.114 Angle : 0.570 9.916 18603 Z= 0.293 Chirality : 0.039 0.174 2179 Planarity : 0.004 0.049 2324 Dihedral : 4.238 25.346 1915 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 1.37 % Allowed : 14.56 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.22), residues: 1672 helix: 2.17 (0.16), residues: 1064 sheet: None (None), residues: 0 loop : -2.44 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 524 HIS 0.004 0.001 HIS D 373 PHE 0.011 0.001 PHE D 392 TYR 0.015 0.001 TYR D 370 ARG 0.007 0.000 ARG A 110 Details of bonding type rmsd link_NAG-ASN : bond 0.00603 ( 2) link_NAG-ASN : angle 2.30691 ( 6) link_BETA1-4 : bond 0.00372 ( 2) link_BETA1-4 : angle 1.50095 ( 6) hydrogen bonds : bond 0.03610 ( 739) hydrogen bonds : angle 3.65118 ( 2190) SS BOND : bond 0.00309 ( 11) SS BOND : angle 1.01135 ( 22) covalent geometry : bond 0.00252 (13679) covalent geometry : angle 0.56765 (18569) Misc. bond : bond 0.00222 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11992.91 seconds wall clock time: 217 minutes 49.54 seconds (13069.54 seconds total)