Starting phenix.real_space_refine on Fri Jul 3 12:14:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7cq5_30436/07_2026/7cq5_30436.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cq5_30436/07_2026/7cq5_30436.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cq5_30436/07_2026/7cq5_30436.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cq5_30436/07_2026/7cq5_30436.map" model { file = "/net/cci-nas-00/data/ceres_data/7cq5_30436/07_2026/7cq5_30436.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cq5_30436/07_2026/7cq5_30436.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7cq5_30436/07_2026/7cq5_30436.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7cq5_30436/07_2026/7cq5_30436.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 S 92 5.16 5 Cl 4 4.86 5 C 9007 2.51 5 N 2328 2.21 5 O 2505 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13942 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1630 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1637 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 5289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 681, 5289 Classifications: {'peptide': 681} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 28, 'TRANS': 652} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 5264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 679, 5264 Classifications: {'peptide': 679} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 28, 'TRANS': 650} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CL': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CL': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.11, per 1000 atoms: 0.22 Number of scatterers: 13942 At special positions: 0 Unit cell: (134.23, 114.745, 136.395, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 4 17.00 S 92 16.00 P 6 15.00 O 2505 8.00 N 2328 7.00 C 9007 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 115 " distance=2.02 Simple disulfide: pdb=" SG CYS A 112 " - pdb=" SG CYS A 171 " distance=2.03 Simple disulfide: pdb=" SG CYS A 174 " - pdb=" SG CYS A 255 " distance=2.04 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=2.04 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=2.03 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=2.03 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=3, 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=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 638.4 milliseconds 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3328 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 11 sheets defined 66.2% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 81 through 105 removed outlier: 4.152A pdb=" N LEU A 87 " --> pdb=" O GLU A 83 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER A 94 " --> pdb=" O ASP A 90 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA A 96 " --> pdb=" O ALA A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 115 removed outlier: 3.915A pdb=" N CYS A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 128 removed outlier: 3.618A pdb=" N VAL A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 147 Processing helix chain 'A' and resid 153 through 170 Processing helix chain 'A' and resid 183 through 203 removed outlier: 3.578A pdb=" N ASN A 203 " --> pdb=" O CYS A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 222 removed outlier: 3.672A pdb=" N CYS A 221 " --> pdb=" O TYR A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 245 removed outlier: 3.641A pdb=" N TYR A 228 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU A 245 " --> pdb=" O MET A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 271 removed outlier: 3.890A pdb=" N ALA A 261 " --> pdb=" O ASP A 257 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG A 271 " --> pdb=" O LYS A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 294 removed outlier: 3.760A pdb=" N VAL A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 306 removed outlier: 3.580A pdb=" N HIS A 306 " --> pdb=" O SER A 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 90 removed outlier: 3.908A pdb=" N GLU B 86 " --> pdb=" O PRO B 82 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N LEU B 87 " --> pdb=" O GLU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 105 removed outlier: 3.585A pdb=" N ALA B 96 " --> pdb=" O ALA B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 115 Processing helix chain 'B' and resid 115 through 128 Processing helix chain 'B' and resid 153 through 170 Processing helix chain 'B' and resid 170 through 175 removed outlier: 4.169A pdb=" N CYS B 174 " --> pdb=" O ASN B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 203 removed outlier: 3.637A pdb=" N ASN B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 244 removed outlier: 3.589A pdb=" N THR B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 270 removed outlier: 3.634A pdb=" N ALA B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 306 removed outlier: 3.756A pdb=" N VAL B 285 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU B 295 " --> pdb=" O PHE B 291 " (cutoff:3.500A) Proline residue: B 296 - end of helix Processing helix chain 'C' and resid 104 through 115 Processing helix chain 'C' and resid 121 through 170 removed outlier: 3.579A pdb=" N ARG C 126 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TRP C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG C 157 " --> pdb=" O GLY C 153 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN C 162 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS C 165 " --> pdb=" O GLY C 161 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N GLU C 168 " --> pdb=" O ASP C 164 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LYS C 169 " --> pdb=" O LYS C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 196 removed outlier: 4.104A pdb=" N SER C 175 " --> pdb=" O GLY C 171 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE C 193 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL C 194 " --> pdb=" O GLY C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 202 removed outlier: 3.525A pdb=" N ALA C 201 " --> pdb=" O GLU C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 215 Processing helix chain 'C' and resid 223 through 240 removed outlier: 3.553A pdb=" N ILE C 235 " --> pdb=" O VAL C 231 " (cutoff:3.500A) 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: 3.690A pdb=" N SER C 262 " --> pdb=" O ALA C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 280 Processing helix chain 'C' and resid 282 through 302 removed outlier: 3.530A pdb=" N ARG C 286 " --> pdb=" O ASP C 282 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP C 287 " --> pdb=" O THR C 283 " (cutoff:3.500A) removed outlier: 3.672A 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 346 Processing helix chain 'C' and resid 374 through 406 removed outlier: 3.788A pdb=" N ARG C 405 " --> pdb=" O MET C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 434 removed outlier: 3.603A pdb=" N ALA C 425 " --> pdb=" O ALA C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 466 Processing helix chain 'C' and resid 469 through 480 Processing helix chain 'C' and resid 486 through 505 removed outlier: 3.781A pdb=" N PHE C 499 " --> pdb=" O LEU C 495 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR C 505 " --> pdb=" O ALA C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 536 Processing helix chain 'C' and resid 543 through 560 removed outlier: 3.682A pdb=" N TYR C 547 " --> pdb=" O ASP C 543 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C 549 " --> pdb=" O GLY C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 574 Processing helix chain 'C' and resid 579 through 596 removed outlier: 3.865A pdb=" N VAL C 596 " --> pdb=" O ILE C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 608 Processing helix chain 'C' and resid 626 through 630 Processing helix chain 'C' and resid 644 through 652 Processing helix chain 'C' and resid 681 through 690 Processing helix chain 'C' and resid 707 through 711 Processing helix chain 'C' and resid 720 through 724 Processing helix chain 'C' and resid 729 through 732 Processing helix chain 'C' and resid 753 through 765 removed outlier: 3.618A pdb=" N LEU C 760 " --> pdb=" O ARG C 756 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 115 Processing helix chain 'D' and resid 121 through 170 removed outlier: 3.517A pdb=" N LYS D 125 " --> pdb=" O THR D 121 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG D 126 " --> pdb=" O VAL D 122 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TRP D 127 " --> pdb=" O GLU D 123 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS D 165 " --> pdb=" O GLY D 161 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N GLU D 168 " --> pdb=" O ASP D 164 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LYS D 169 " --> pdb=" O LYS D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 196 removed outlier: 3.786A pdb=" N SER D 175 " --> pdb=" O GLY D 171 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TRP D 179 " --> pdb=" O SER D 175 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE D 193 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL D 194 " --> pdb=" O GLY D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 202 Processing helix chain 'D' and resid 205 through 215 Processing helix chain 'D' and resid 223 through 240 Processing helix chain 'D' and resid 248 through 262 removed outlier: 4.470A pdb=" N HIS D 252 " --> pdb=" O GLY D 248 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER D 262 " --> pdb=" O ALA D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 302 Processing helix chain 'D' and resid 303 through 314 Processing helix chain 'D' and resid 320 through 346 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 406 removed outlier: 3.773A pdb=" N ARG D 405 " --> pdb=" O MET D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 434 removed outlier: 3.503A pdb=" N ILE D 415 " --> pdb=" O CYS D 411 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU D 416 " --> pdb=" O LEU D 412 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA D 417 " --> pdb=" O GLN D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 466 Processing helix chain 'D' and resid 469 through 478 Processing helix chain 'D' and resid 486 through 504 removed outlier: 3.718A pdb=" N PHE D 499 " --> pdb=" O LEU D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 536 Processing helix chain 'D' and resid 539 through 542 Processing helix chain 'D' and resid 543 through 560 removed outlier: 3.706A pdb=" N TYR D 547 " --> pdb=" O ASP D 543 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU D 549 " --> pdb=" O GLY D 545 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET D 550 " --> pdb=" O LYS D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 574 removed outlier: 3.556A pdb=" N VAL D 568 " --> pdb=" O LEU D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 578 No H-bonds generated for 'chain 'D' and resid 576 through 578' Processing helix chain 'D' and resid 579 through 596 Processing helix chain 'D' and resid 600 through 609 removed outlier: 3.514A pdb=" N HIS D 605 " --> pdb=" O LEU D 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 623 removed outlier: 4.072A pdb=" N HIS D 623 " --> pdb=" O VAL D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 644 through 651 removed outlier: 3.728A pdb=" N ASP D 649 " --> pdb=" O GLY D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 681 through 690 removed outlier: 3.654A pdb=" N LEU D 688 " --> pdb=" O LEU D 684 " (cutoff:3.500A) Processing helix chain 'D' and resid 728 through 732 removed outlier: 3.817A pdb=" N GLU D 732 " --> pdb=" O ASP D 729 " (cutoff:3.500A) Processing helix chain 'D' and resid 753 through 764 removed outlier: 3.503A pdb=" N LYS D 759 " --> pdb=" O PRO D 755 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU D 760 " --> pdb=" O ARG D 756 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE D 761 " --> pdb=" O VAL D 757 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU D 764 " --> pdb=" O LEU D 760 " (cutoff:3.500A) Processing helix chain 'D' and resid 784 through 789 removed outlier: 3.696A pdb=" N ARG D 789 " --> pdb=" O LYS D 785 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 95 through 96 removed outlier: 4.167A pdb=" N GLU C 95 " --> pdb=" O LYS C 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 265 through 266 Processing sheet with id=AA3, first strand: chain 'C' and resid 438 through 439 Processing sheet with id=AA4, first strand: chain 'C' and resid 638 through 639 removed outlier: 6.304A pdb=" N LEU C 638 " --> pdb=" O VAL C 664 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 641 through 643 removed outlier: 4.078A pdb=" N GLU C 642 " --> pdb=" O MET C 735 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 747 through 749 removed outlier: 6.947A pdb=" N VAL C 748 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 95 through 96 removed outlier: 4.335A pdb=" N GLU D 95 " --> pdb=" O LYS D 217 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 438 through 439 Processing sheet with id=AA9, first strand: chain 'D' and resid 638 through 639 removed outlier: 6.361A pdb=" N LEU D 638 " --> pdb=" O VAL D 664 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 641 through 643 removed outlier: 3.551A pdb=" N GLU D 642 " --> pdb=" O MET D 735 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 747 through 749 removed outlier: 6.539A pdb=" N VAL D 748 " --> pdb=" O VAL D 772 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLY D 780 " --> pdb=" O VAL D 771 " (cutoff:3.500A) 817 hydrogen bonds defined for protein. 2388 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.27 Time building geometry restraints manager: 1.53 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: 3794 1.33 - 1.46: 3367 1.46 - 1.58: 6942 1.58 - 1.71: 10 1.71 - 1.83: 140 Bond restraints: 14253 Sorted by residual: bond pdb=" CG1 ILE C 206 " pdb=" CD1 ILE C 206 " ideal model delta sigma weight residual 1.513 1.432 0.081 3.90e-02 6.57e+02 4.33e+00 bond pdb=" CA ASP C 98 " pdb=" CB ASP C 98 " ideal model delta sigma weight residual 1.532 1.562 -0.030 1.48e-02 4.57e+03 4.06e+00 bond pdb=" O5' ATP D 901 " pdb=" PA ATP D 901 " ideal model delta sigma weight residual 1.579 1.601 -0.022 1.10e-02 8.26e+03 4.03e+00 bond pdb=" C LEU B 77 " pdb=" N PRO B 78 " ideal model delta sigma weight residual 1.334 1.381 -0.047 2.34e-02 1.83e+03 4.01e+00 bond pdb=" O2B ATP C 901 " pdb=" PB ATP C 901 " ideal model delta sigma weight residual 1.529 1.485 0.044 2.20e-02 2.07e+03 3.92e+00 ... (remaining 14248 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.51: 19101 3.51 - 7.02: 236 7.02 - 10.52: 35 10.52 - 14.03: 0 14.03 - 17.54: 2 Bond angle restraints: 19374 Sorted by residual: angle pdb=" PB ATP C 901 " pdb=" O3B ATP C 901 " pdb=" PG ATP C 901 " ideal model delta sigma weight residual 139.87 133.22 6.65 1.00e+00 1.00e+00 4.42e+01 angle pdb=" PB ATP D 901 " pdb=" O3B ATP D 901 " pdb=" PG ATP D 901 " ideal model delta sigma weight residual 139.87 134.19 5.68 1.00e+00 1.00e+00 3.23e+01 angle pdb=" CA ASP C 98 " pdb=" CB ASP C 98 " pdb=" CG ASP C 98 " ideal model delta sigma weight residual 112.60 118.22 -5.62 1.00e+00 1.00e+00 3.16e+01 angle pdb=" PA ATP D 901 " pdb=" O3A ATP D 901 " pdb=" PB ATP D 901 " ideal model delta sigma weight residual 136.83 131.25 5.58 1.00e+00 1.00e+00 3.11e+01 angle pdb=" C LEU C 97 " pdb=" N ASP C 98 " pdb=" CA ASP C 98 " ideal model delta sigma weight residual 122.63 130.28 -7.65 1.44e+00 4.82e-01 2.82e+01 ... (remaining 19369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.18: 7940 16.18 - 32.36: 371 32.36 - 48.54: 64 48.54 - 64.71: 12 64.71 - 80.89: 7 Dihedral angle restraints: 8394 sinusoidal: 3253 harmonic: 5141 Sorted by residual: dihedral pdb=" CA ASP A 90 " pdb=" C ASP A 90 " pdb=" N PHE A 91 " pdb=" CA PHE A 91 " ideal model delta harmonic sigma weight residual 180.00 153.55 26.45 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA CYS A 115 " pdb=" C CYS A 115 " pdb=" N TYR A 116 " pdb=" CA TYR A 116 " ideal model delta harmonic sigma weight residual 180.00 154.18 25.82 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA SER D 447 " pdb=" C SER D 447 " pdb=" N TYR D 448 " pdb=" CA TYR D 448 " ideal model delta harmonic sigma weight residual 180.00 156.05 23.95 0 5.00e+00 4.00e-02 2.29e+01 ... (remaining 8391 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1796 0.067 - 0.133: 401 0.133 - 0.199: 52 0.199 - 0.266: 12 0.266 - 0.332: 4 Chirality restraints: 2265 Sorted by residual: chirality pdb=" CG LEU D 687 " pdb=" CB LEU D 687 " pdb=" CD1 LEU D 687 " pdb=" CD2 LEU D 687 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CG LEU A 89 " pdb=" CB LEU A 89 " pdb=" CD1 LEU A 89 " pdb=" CD2 LEU A 89 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CA ASP C 98 " pdb=" N ASP C 98 " pdb=" C ASP C 98 " pdb=" CB ASP C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.60e+00 ... (remaining 2262 not shown) Planarity restraints: 2422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 179 " 0.030 2.00e-02 2.50e+03 2.49e-02 1.56e+01 pdb=" CG TRP C 179 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 TRP C 179 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP C 179 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 179 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 179 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP C 179 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 179 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 179 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP C 179 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 179 " 0.031 2.00e-02 2.50e+03 2.41e-02 1.45e+01 pdb=" CG TRP D 179 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP D 179 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP D 179 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 179 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP D 179 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 179 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 179 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 179 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 179 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 503 " -0.022 2.00e-02 2.50e+03 1.76e-02 7.75e+00 pdb=" CG TRP C 503 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP C 503 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP C 503 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP C 503 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 503 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 503 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 503 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 503 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 503 " 0.002 2.00e-02 2.50e+03 ... (remaining 2419 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 745 2.73 - 3.27: 13715 3.27 - 3.81: 22842 3.81 - 4.36: 28158 4.36 - 4.90: 48020 Nonbonded interactions: 113480 Sorted by model distance: nonbonded pdb=" OG SER D 298 " pdb=" OG1 THR D 335 " model vdw 2.185 3.040 nonbonded pdb=" O MET C 368 " pdb=" OH TYR C 579 " model vdw 2.246 3.040 nonbonded pdb=" O MET D 368 " pdb=" OH TYR D 579 " model vdw 2.263 3.040 nonbonded pdb=" O LEU C 500 " pdb=" OG1 THR C 504 " model vdw 2.280 3.040 nonbonded pdb=" O ILE D 163 " pdb=" OG1 THR D 167 " model vdw 2.286 3.040 ... (remaining 113475 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 306) selection = (chain 'B' and (resid 73 through 130 or resid 142 through 245 or resid 253 throu \ gh 306)) } ncs_group { reference = (chain 'C' and (resid 94 through 652 or (resid 653 through 656 and (name N or na \ me CA or name C or name O or name CB )) or resid 657 through 664 or resid 673 th \ rough 694 or resid 706 through 789 or (resid 790 and (name N or name CA or name \ C or name O or name CB )) or resid 901 through 903)) 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 619 or (resid 620 and (name N o \ r name CA or name C or name O or name CB )) or resid 621 through 694 or resid 70 \ 6 through 903)) } 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: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.410 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 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 : 0.007 0.081 14272 Z= 0.299 Angle : 1.055 17.538 19410 Z= 0.575 Chirality : 0.059 0.332 2265 Planarity : 0.008 0.067 2420 Dihedral : 10.229 80.892 5030 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 0.46 % Allowed : 2.98 % Favored : 96.56 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.83 (0.16), residues: 1746 helix: -2.22 (0.11), residues: 1107 sheet: -3.08 (1.18), residues: 5 loop : -2.89 (0.21), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG C 280 TYR 0.026 0.003 TYR A 188 PHE 0.038 0.004 PHE D 288 TRP 0.067 0.005 TRP C 179 HIS 0.015 0.002 HIS D 479 Details of bonding type rmsd/Z covalent geometry : bond 0.00704 / 0.30 (14253) covalent geometry : angle 1.05083 / 0.57 (19374) SS BOND : bond 0.00405 / 0.26 ( 12) SS BOND : angle 1.66676 / 0.93 ( 24) hydrogen bonds : bond 0.21018 / 13.81 ( 817) hydrogen bonds : angle 6.97234 / 4.85 ( 2388) Misc. bond : bond 0.00280 / 0.14 ( 3) link_BETA1-4 : bond 0.00092 / 0.05 ( 2) link_BETA1-4 : angle 4.00899 / 2.04 ( 6) link_NAG-ASN : bond 0.00406 / 0.20 ( 2) link_NAG-ASN : angle 3.06260 / 1.70 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 275 time to evaluate : 0.536 Fit side-chains revert: symmetry clash REVERT: A 83 GLU cc_start: 0.7176 (mt-10) cc_final: 0.6965 (tm-30) REVERT: A 198 THR cc_start: 0.7701 (p) cc_final: 0.7496 (t) REVERT: B 222 LYS cc_start: 0.6868 (tmtp) cc_final: 0.6652 (mtpt) REVERT: B 260 ASP cc_start: 0.8093 (t70) cc_final: 0.7746 (t70) REVERT: C 271 ARG cc_start: 0.6363 (mmt90) cc_final: 0.6138 (ttp-170) REVERT: C 617 GLU cc_start: 0.7248 (pt0) cc_final: 0.6872 (pm20) REVERT: C 717 ARG cc_start: 0.6694 (mpt180) cc_final: 0.5634 (mmt180) REVERT: D 691 LYS cc_start: 0.8609 (mttm) cc_final: 0.8389 (mtmt) REVERT: D 728 GLN cc_start: 0.7985 (tp40) cc_final: 0.7630 (tp40) outliers start: 7 outliers final: 4 residues processed: 282 average time/residue: 0.7107 time to fit residues: 215.9579 Evaluate side-chains 166 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 162 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 611 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 GLN B 170 ASN C 115 ASN ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 HIS C 348 ASN C 555 GLN ** C 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 GLN D 396 ASN D 439 GLN D 555 GLN ** D 623 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 658 HIS D 659 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.136491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.109042 restraints weight = 17340.718| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.44 r_work: 0.3167 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14272 Z= 0.149 Angle : 0.671 11.334 19410 Z= 0.347 Chirality : 0.042 0.202 2265 Planarity : 0.006 0.051 2420 Dihedral : 6.125 77.519 1915 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 2.85 % Allowed : 9.07 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.19), residues: 1746 helix: 0.25 (0.15), residues: 1121 sheet: -2.99 (0.90), residues: 5 loop : -2.46 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 104 TYR 0.017 0.002 TYR C 715 PHE 0.020 0.002 PHE C 329 TRP 0.030 0.002 TRP D 179 HIS 0.006 0.001 HIS C 658 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (14253) covalent geometry : angle 0.66814 / 0.35 (19374) SS BOND : bond 0.00224 / 0.14 ( 12) SS BOND : angle 0.89385 / 0.52 ( 24) hydrogen bonds : bond 0.05410 / 3.61 ( 817) hydrogen bonds : angle 4.16737 / 2.91 ( 2388) Misc. bond : bond 0.00218 / 0.11 ( 3) link_BETA1-4 : bond 0.00382 / 0.20 ( 2) link_BETA1-4 : angle 2.55583 / 1.31 ( 6) link_NAG-ASN : bond 0.00258 / 0.12 ( 2) link_NAG-ASN : angle 2.23141 / 1.21 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 172 time to evaluate : 0.613 Fit side-chains REVERT: A 148 MET cc_start: 0.7205 (mmm) cc_final: 0.7001 (mmm) REVERT: A 164 THR cc_start: 0.8989 (m) cc_final: 0.8769 (t) REVERT: A 198 THR cc_start: 0.7589 (p) cc_final: 0.7345 (t) REVERT: B 110 ARG cc_start: 0.8224 (mtt180) cc_final: 0.7757 (mpt-90) REVERT: B 148 MET cc_start: 0.7547 (mpp) cc_final: 0.7141 (mpp) REVERT: B 167 GLN cc_start: 0.8172 (mt0) cc_final: 0.7838 (mp10) REVERT: B 170 ASN cc_start: 0.8236 (m-40) cc_final: 0.7711 (t0) REVERT: B 260 ASP cc_start: 0.8449 (t70) cc_final: 0.8166 (t70) REVERT: C 110 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8042 (tt0) REVERT: C 123 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7241 (tm-30) REVERT: C 168 GLU cc_start: 0.7265 (pm20) cc_final: 0.7038 (pm20) REVERT: C 271 ARG cc_start: 0.5999 (mmt90) cc_final: 0.5624 (mmm160) REVERT: C 514 PHE cc_start: 0.8805 (OUTLIER) cc_final: 0.8495 (m-80) REVERT: C 617 GLU cc_start: 0.7849 (pt0) cc_final: 0.7225 (pm20) REVERT: C 631 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.7528 (pp-130) REVERT: C 640 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.7828 (ttm-80) REVERT: C 641 ARG cc_start: 0.7570 (mtm-85) cc_final: 0.7191 (mtt90) REVERT: C 707 ARG cc_start: 0.7764 (mtm180) cc_final: 0.6908 (mtm-85) REVERT: C 717 ARG cc_start: 0.6883 (mpt180) cc_final: 0.5550 (mmt180) REVERT: C 778 VAL cc_start: 0.8964 (OUTLIER) cc_final: 0.8672 (t) REVERT: D 349 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.6830 (tmt) REVERT: D 728 GLN cc_start: 0.7794 (tp40) cc_final: 0.7282 (tp40) outliers start: 43 outliers final: 14 residues processed: 199 average time/residue: 0.6669 time to fit residues: 143.5586 Evaluate side-chains 163 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 631 MET Chi-restraints excluded: chain C residue 640 ARG Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 265 ARG Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 349 MET Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 734 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 110 optimal weight: 0.0980 chunk 152 optimal weight: 3.9990 chunk 150 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 131 optimal weight: 0.7980 chunk 157 optimal weight: 0.6980 chunk 50 optimal weight: 0.1980 chunk 5 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 GLN B 113 GLN B 242 ASN ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 HIS D 373 HIS D 439 GLN D 468 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.139861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.114573 restraints weight = 17871.078| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.44 r_work: 0.3236 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14272 Z= 0.117 Angle : 0.589 9.768 19410 Z= 0.300 Chirality : 0.040 0.159 2265 Planarity : 0.004 0.049 2420 Dihedral : 5.441 54.131 1912 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.51 % Allowed : 10.72 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.21), residues: 1746 helix: 1.29 (0.16), residues: 1118 sheet: -3.00 (1.17), residues: 5 loop : -2.22 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 405 TYR 0.012 0.001 TYR A 116 PHE 0.016 0.001 PHE C 329 TRP 0.020 0.002 TRP D 524 HIS 0.004 0.001 HIS C 658 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 (14253) covalent geometry : angle 0.58614 / 0.30 (19374) SS BOND : bond 0.00239 / 0.13 ( 12) SS BOND : angle 0.74843 / 0.39 ( 24) hydrogen bonds : bond 0.04416 / 2.95 ( 817) hydrogen bonds : angle 3.81098 / 2.67 ( 2388) Misc. bond : bond 0.00351 / 0.18 ( 3) link_BETA1-4 : bond 0.00498 / 0.25 ( 2) link_BETA1-4 : angle 2.25330 / 1.13 ( 6) link_NAG-ASN : bond 0.00281 / 0.13 ( 2) link_NAG-ASN : angle 2.45161 / 1.40 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 157 time to evaluate : 0.381 Fit side-chains REVERT: A 86 GLU cc_start: 0.6359 (OUTLIER) cc_final: 0.6152 (pm20) REVERT: A 168 GLU cc_start: 0.7602 (tm-30) cc_final: 0.7233 (tm-30) REVERT: B 110 ARG cc_start: 0.8068 (mtt180) cc_final: 0.7694 (mpt-90) REVERT: B 148 MET cc_start: 0.7418 (mpp) cc_final: 0.6983 (mpp) REVERT: B 152 MET cc_start: 0.7670 (ttm) cc_final: 0.7386 (ttt) REVERT: B 170 ASN cc_start: 0.8161 (m-40) cc_final: 0.7717 (t0) REVERT: B 260 ASP cc_start: 0.8417 (t70) cc_final: 0.8161 (t70) REVERT: C 123 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7274 (tm-30) REVERT: C 168 GLU cc_start: 0.7235 (pm20) cc_final: 0.7017 (pm20) REVERT: C 271 ARG cc_start: 0.6245 (mmt90) cc_final: 0.5863 (mmm160) REVERT: C 617 GLU cc_start: 0.7875 (pt0) cc_final: 0.7269 (pm20) REVERT: C 631 MET cc_start: 0.8317 (OUTLIER) cc_final: 0.7603 (pp-130) REVERT: C 640 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.7845 (ttm-80) REVERT: C 641 ARG cc_start: 0.7562 (mtm-85) cc_final: 0.7175 (mtt90) REVERT: C 707 ARG cc_start: 0.7779 (mtm180) cc_final: 0.6993 (mtm-85) REVERT: C 717 ARG cc_start: 0.6625 (mpt180) cc_final: 0.5336 (mmt180) REVERT: C 778 VAL cc_start: 0.8903 (OUTLIER) cc_final: 0.8637 (t) REVERT: C 786 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7809 (p0) REVERT: D 540 ILE cc_start: 0.8134 (mm) cc_final: 0.7860 (pt) REVERT: D 725 HIS cc_start: 0.7043 (m-70) cc_final: 0.6525 (t-170) REVERT: D 728 GLN cc_start: 0.7744 (tp40) cc_final: 0.7324 (tp40) REVERT: D 777 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7210 (mp10) outliers start: 38 outliers final: 15 residues processed: 185 average time/residue: 0.6592 time to fit residues: 131.7936 Evaluate side-chains 167 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 631 MET Chi-restraints excluded: chain C residue 640 ARG Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 786 ASP Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 265 ARG Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 775 ARG Chi-restraints excluded: chain D residue 777 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 18 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 151 optimal weight: 0.9980 chunk 126 optimal weight: 0.7980 chunk 47 optimal weight: 0.0980 chunk 14 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 GLN B 128 ASN ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 GLN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 ASN D 607 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.135262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.108088 restraints weight = 17338.264| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.44 r_work: 0.3150 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14272 Z= 0.137 Angle : 0.602 9.459 19410 Z= 0.308 Chirality : 0.041 0.157 2265 Planarity : 0.004 0.050 2420 Dihedral : 5.412 57.250 1912 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.91 % Allowed : 11.18 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.21), residues: 1746 helix: 1.73 (0.16), residues: 1118 sheet: -2.44 (1.49), residues: 5 loop : -2.13 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 561 TYR 0.018 0.002 TYR C 715 PHE 0.016 0.002 PHE C 392 TRP 0.021 0.002 TRP D 524 HIS 0.005 0.001 HIS C 658 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (14253) covalent geometry : angle 0.59869 / 0.31 (19374) SS BOND : bond 0.00170 / 0.11 ( 12) SS BOND : angle 0.70354 / 0.42 ( 24) hydrogen bonds : bond 0.04602 / 3.07 ( 817) hydrogen bonds : angle 3.71640 / 2.60 ( 2388) Misc. bond : bond 0.00180 / 0.09 ( 3) link_BETA1-4 : bond 0.00929 / 0.48 ( 2) link_BETA1-4 : angle 2.66128 / 1.28 ( 6) link_NAG-ASN : bond 0.00881 / 0.45 ( 2) link_NAG-ASN : angle 2.42147 / 1.41 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 150 time to evaluate : 0.497 Fit side-chains REVERT: A 86 GLU cc_start: 0.6379 (OUTLIER) cc_final: 0.5218 (tm-30) REVERT: A 167 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.6780 (mp10) REVERT: A 168 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7250 (tm-30) REVERT: B 110 ARG cc_start: 0.7966 (mtt180) cc_final: 0.7603 (mpt-90) REVERT: B 148 MET cc_start: 0.7445 (mpp) cc_final: 0.6968 (mpp) REVERT: B 152 MET cc_start: 0.7715 (ttm) cc_final: 0.7461 (ttt) REVERT: B 170 ASN cc_start: 0.8117 (m-40) cc_final: 0.7668 (t0) REVERT: C 123 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7309 (tm-30) REVERT: C 168 GLU cc_start: 0.7175 (pm20) cc_final: 0.6938 (pm20) REVERT: C 271 ARG cc_start: 0.6188 (mmt90) cc_final: 0.5682 (mmm160) REVERT: C 274 LYS cc_start: 0.6419 (OUTLIER) cc_final: 0.5376 (pmmt) REVERT: C 514 PHE cc_start: 0.8872 (OUTLIER) cc_final: 0.8515 (m-80) REVERT: C 617 GLU cc_start: 0.7845 (pt0) cc_final: 0.7206 (pm20) REVERT: C 631 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.7758 (pp-130) REVERT: C 640 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.7856 (ttm-80) REVERT: C 717 ARG cc_start: 0.7037 (mpt180) cc_final: 0.5307 (mmt180) REVERT: C 778 VAL cc_start: 0.8945 (OUTLIER) cc_final: 0.8639 (t) REVERT: C 786 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.8014 (p0) REVERT: D 269 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7620 (mt) REVERT: D 332 MET cc_start: 0.8958 (mmm) cc_final: 0.8560 (mmm) REVERT: D 349 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.6626 (tmt) REVERT: D 540 ILE cc_start: 0.8160 (mm) cc_final: 0.7862 (pt) REVERT: D 777 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7258 (mp10) REVERT: D 781 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8632 (mt) outliers start: 44 outliers final: 18 residues processed: 177 average time/residue: 0.7140 time to fit residues: 136.4545 Evaluate side-chains 174 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 167 GLN Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 631 MET Chi-restraints excluded: chain C residue 640 ARG Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 786 ASP Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 265 ARG Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 349 MET Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 646 VAL Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 775 ARG Chi-restraints excluded: chain D residue 777 GLN Chi-restraints excluded: chain D residue 781 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 131 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 65 optimal weight: 0.0770 chunk 37 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 242 ASN C 776 ASN ** D 183 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 = 0.3591 r_free = 0.3591 target = 0.134129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.106831 restraints weight = 17334.274| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.44 r_work: 0.3125 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14272 Z= 0.148 Angle : 0.615 10.075 19410 Z= 0.314 Chirality : 0.042 0.158 2265 Planarity : 0.004 0.051 2420 Dihedral : 5.252 57.329 1910 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 3.11 % Allowed : 11.58 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.21), residues: 1746 helix: 1.88 (0.16), residues: 1112 sheet: -2.14 (1.69), residues: 5 loop : -2.07 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 561 TYR 0.019 0.002 TYR C 715 PHE 0.016 0.002 PHE C 392 TRP 0.021 0.002 TRP D 524 HIS 0.005 0.001 HIS C 658 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (14253) covalent geometry : angle 0.61105 / 0.31 (19374) SS BOND : bond 0.00197 / 0.12 ( 12) SS BOND : angle 0.71730 / 0.41 ( 24) hydrogen bonds : bond 0.04729 / 3.15 ( 817) hydrogen bonds : angle 3.69872 / 2.60 ( 2388) Misc. bond : bond 0.00355 / 0.18 ( 3) link_BETA1-4 : bond 0.00662 / 0.33 ( 2) link_BETA1-4 : angle 3.03838 / 1.54 ( 6) link_NAG-ASN : bond 0.00902 / 0.45 ( 2) link_NAG-ASN : angle 2.47060 / 1.45 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 149 time to evaluate : 0.559 Fit side-chains REVERT: A 86 GLU cc_start: 0.6474 (OUTLIER) cc_final: 0.5306 (tm-30) REVERT: A 167 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.6895 (mp10) REVERT: A 168 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7240 (tm-30) REVERT: B 110 ARG cc_start: 0.7978 (mtt180) cc_final: 0.7619 (mpt-90) REVERT: B 148 MET cc_start: 0.7417 (mpp) cc_final: 0.6947 (mpp) REVERT: B 170 ASN cc_start: 0.8150 (m-40) cc_final: 0.7690 (t0) REVERT: C 123 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7392 (tm-30) REVERT: C 168 GLU cc_start: 0.7191 (pm20) cc_final: 0.6917 (pm20) REVERT: C 271 ARG cc_start: 0.6174 (mmt90) cc_final: 0.5714 (mmm160) REVERT: C 368 MET cc_start: 0.8310 (mmt) cc_final: 0.8081 (mmt) REVERT: C 514 PHE cc_start: 0.8906 (OUTLIER) cc_final: 0.8553 (m-80) REVERT: C 617 GLU cc_start: 0.7998 (pt0) cc_final: 0.7382 (pm20) REVERT: C 631 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.7743 (pp-130) REVERT: C 640 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.7875 (ttm-80) REVERT: C 705 ARG cc_start: 0.5676 (ttp-170) cc_final: 0.5339 (ttm110) REVERT: C 717 ARG cc_start: 0.7171 (mpt180) cc_final: 0.5446 (mmt180) REVERT: C 778 VAL cc_start: 0.8961 (OUTLIER) cc_final: 0.8650 (t) REVERT: C 786 ASP cc_start: 0.8396 (OUTLIER) cc_final: 0.8082 (p0) REVERT: D 97 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7266 (mt) REVERT: D 269 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7641 (mt) REVERT: D 332 MET cc_start: 0.8928 (mmm) cc_final: 0.8627 (mmm) REVERT: D 540 ILE cc_start: 0.8238 (mm) cc_final: 0.7936 (pt) REVERT: D 781 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8668 (mt) outliers start: 47 outliers final: 22 residues processed: 180 average time/residue: 0.7171 time to fit residues: 139.9771 Evaluate side-chains 175 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 141 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 167 GLN Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 631 MET Chi-restraints excluded: chain C residue 640 ARG Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 786 ASP Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 265 ARG Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 646 VAL Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 775 ARG Chi-restraints excluded: chain D residue 781 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 107 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 142 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 119 optimal weight: 0.7980 chunk 104 optimal weight: 0.9990 chunk 158 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 ASN ** D 183 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 = 0.3592 r_free = 0.3592 target = 0.134167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.106829 restraints weight = 17146.028| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.43 r_work: 0.3130 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14272 Z= 0.143 Angle : 0.616 9.939 19410 Z= 0.313 Chirality : 0.041 0.158 2265 Planarity : 0.004 0.051 2420 Dihedral : 5.236 57.070 1910 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.04 % Allowed : 12.05 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.21), residues: 1746 helix: 2.02 (0.16), residues: 1111 sheet: -2.15 (1.73), residues: 5 loop : -2.05 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 561 TYR 0.017 0.002 TYR C 715 PHE 0.016 0.002 PHE C 392 TRP 0.022 0.002 TRP D 524 HIS 0.005 0.001 HIS C 658 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (14253) covalent geometry : angle 0.61148 / 0.31 (19374) SS BOND : bond 0.00160 / 0.11 ( 12) SS BOND : angle 0.70349 / 0.40 ( 24) hydrogen bonds : bond 0.04638 / 3.09 ( 817) hydrogen bonds : angle 3.67464 / 2.58 ( 2388) Misc. bond : bond 0.00314 / 0.16 ( 3) link_BETA1-4 : bond 0.00898 / 0.45 ( 2) link_BETA1-4 : angle 3.06170 / 1.49 ( 6) link_NAG-ASN : bond 0.01335 / 0.68 ( 2) link_NAG-ASN : angle 3.19558 / 1.89 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 142 time to evaluate : 0.576 Fit side-chains REVERT: A 86 GLU cc_start: 0.6458 (OUTLIER) cc_final: 0.5281 (tm-30) REVERT: A 167 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.6864 (mp10) REVERT: A 198 THR cc_start: 0.7693 (p) cc_final: 0.7475 (t) REVERT: A 201 GLU cc_start: 0.7382 (tp30) cc_final: 0.6688 (tp30) REVERT: B 110 ARG cc_start: 0.7986 (mtt180) cc_final: 0.7615 (mpt-90) REVERT: B 148 MET cc_start: 0.7440 (mpp) cc_final: 0.6968 (mpp) REVERT: B 152 MET cc_start: 0.7574 (ttt) cc_final: 0.7272 (mmm) REVERT: B 170 ASN cc_start: 0.8168 (m-40) cc_final: 0.7692 (t0) REVERT: C 123 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7369 (tm-30) REVERT: C 168 GLU cc_start: 0.7118 (pm20) cc_final: 0.6818 (pm20) REVERT: C 271 ARG cc_start: 0.6165 (mmt90) cc_final: 0.5635 (mmm160) REVERT: C 514 PHE cc_start: 0.8902 (OUTLIER) cc_final: 0.8539 (m-80) REVERT: C 617 GLU cc_start: 0.7956 (pt0) cc_final: 0.7329 (pm20) REVERT: C 631 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.7773 (pp-130) REVERT: C 640 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.7899 (ttm-80) REVERT: C 705 ARG cc_start: 0.5722 (ttp-170) cc_final: 0.5343 (ttm110) REVERT: C 717 ARG cc_start: 0.7216 (mpt180) cc_final: 0.5482 (mmt180) REVERT: C 778 VAL cc_start: 0.8937 (OUTLIER) cc_final: 0.8647 (t) REVERT: C 786 ASP cc_start: 0.8393 (OUTLIER) cc_final: 0.8076 (p0) REVERT: D 97 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7286 (mt) REVERT: D 269 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7614 (mt) REVERT: D 332 MET cc_start: 0.8943 (mmm) cc_final: 0.8707 (mmm) REVERT: D 349 MET cc_start: 0.7755 (OUTLIER) cc_final: 0.6778 (tmt) REVERT: D 540 ILE cc_start: 0.8246 (mm) cc_final: 0.7934 (pt) REVERT: D 777 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7326 (mp10) REVERT: D 781 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8680 (mt) outliers start: 46 outliers final: 20 residues processed: 175 average time/residue: 0.7233 time to fit residues: 137.1772 Evaluate side-chains 173 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 140 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 167 GLN Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 609 GLN Chi-restraints excluded: chain C residue 631 MET Chi-restraints excluded: chain C residue 640 ARG Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 786 ASP Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 265 ARG Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 349 MET Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 646 VAL Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 775 ARG Chi-restraints excluded: chain D residue 777 GLN Chi-restraints excluded: chain D residue 781 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 66 optimal weight: 0.3980 chunk 94 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 137 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 ASN ** D 183 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 = 0.3601 r_free = 0.3601 target = 0.134774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.107534 restraints weight = 17138.159| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.43 r_work: 0.3138 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14272 Z= 0.129 Angle : 0.594 9.457 19410 Z= 0.303 Chirality : 0.041 0.162 2265 Planarity : 0.004 0.051 2420 Dihedral : 5.149 56.590 1910 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.18 % Allowed : 12.05 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.21), residues: 1746 helix: 2.16 (0.16), residues: 1110 sheet: -2.15 (1.77), residues: 5 loop : -2.02 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 561 TYR 0.016 0.001 TYR C 715 PHE 0.016 0.001 PHE C 329 TRP 0.022 0.002 TRP D 524 HIS 0.004 0.001 HIS C 658 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (14253) covalent geometry : angle 0.58868 / 0.30 (19374) SS BOND : bond 0.00143 / 0.10 ( 12) SS BOND : angle 0.65863 / 0.37 ( 24) hydrogen bonds : bond 0.04400 / 2.94 ( 817) hydrogen bonds : angle 3.61599 / 2.54 ( 2388) Misc. bond : bond 0.00257 / 0.13 ( 3) link_BETA1-4 : bond 0.00513 / 0.25 ( 2) link_BETA1-4 : angle 2.71467 / 1.43 ( 6) link_NAG-ASN : bond 0.01030 / 0.50 ( 2) link_NAG-ASN : angle 3.62157 / 2.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 149 time to evaluate : 0.409 Fit side-chains REVERT: A 86 GLU cc_start: 0.6347 (OUTLIER) cc_final: 0.5147 (tm-30) REVERT: A 167 GLN cc_start: 0.7636 (OUTLIER) cc_final: 0.6824 (mp10) REVERT: A 201 GLU cc_start: 0.7490 (tp30) cc_final: 0.6832 (tp30) REVERT: B 110 ARG cc_start: 0.7944 (mtt180) cc_final: 0.7615 (mpt-90) REVERT: B 148 MET cc_start: 0.7465 (mpp) cc_final: 0.7053 (mpp) REVERT: B 152 MET cc_start: 0.7527 (ttt) cc_final: 0.7280 (mmm) REVERT: B 170 ASN cc_start: 0.8207 (m-40) cc_final: 0.7684 (t0) REVERT: C 168 GLU cc_start: 0.7035 (pm20) cc_final: 0.6740 (pm20) REVERT: C 368 MET cc_start: 0.8297 (mmt) cc_final: 0.8088 (mmt) REVERT: C 514 PHE cc_start: 0.8885 (OUTLIER) cc_final: 0.8551 (m-80) REVERT: C 617 GLU cc_start: 0.7956 (pt0) cc_final: 0.7332 (pm20) REVERT: C 640 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.7897 (ttm-80) REVERT: C 705 ARG cc_start: 0.5797 (ttp-170) cc_final: 0.5410 (ttm110) REVERT: C 717 ARG cc_start: 0.7186 (mpt180) cc_final: 0.5416 (mmt180) REVERT: C 778 VAL cc_start: 0.8930 (OUTLIER) cc_final: 0.8677 (t) REVERT: C 786 ASP cc_start: 0.8356 (OUTLIER) cc_final: 0.8058 (p0) REVERT: D 97 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7286 (mt) REVERT: D 269 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7609 (mt) REVERT: D 332 MET cc_start: 0.8968 (mmm) cc_final: 0.8721 (mmm) REVERT: D 349 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.6732 (tmm) REVERT: D 540 ILE cc_start: 0.8273 (mm) cc_final: 0.7952 (pt) REVERT: D 725 HIS cc_start: 0.7256 (m-70) cc_final: 0.6640 (t70) REVERT: D 781 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8664 (mt) outliers start: 48 outliers final: 20 residues processed: 185 average time/residue: 0.6800 time to fit residues: 136.4291 Evaluate side-chains 175 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 167 GLN Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 609 GLN Chi-restraints excluded: chain C residue 640 ARG Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 786 ASP Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 265 ARG Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 349 MET Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 562 MET Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 646 VAL Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 775 ARG Chi-restraints excluded: chain D residue 781 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 172 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 159 optimal weight: 0.9990 chunk 42 optimal weight: 0.0570 chunk 99 optimal weight: 0.0030 chunk 112 optimal weight: 6.9990 chunk 64 optimal weight: 0.8980 chunk 149 optimal weight: 0.4980 chunk 26 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.4910 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 ASN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 607 GLN D 774 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.137774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.110676 restraints weight = 17039.813| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.45 r_work: 0.3184 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14272 Z= 0.111 Angle : 0.587 13.298 19410 Z= 0.290 Chirality : 0.039 0.207 2265 Planarity : 0.004 0.051 2420 Dihedral : 4.929 57.157 1910 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.58 % Allowed : 13.37 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.21), residues: 1746 helix: 2.36 (0.16), residues: 1110 sheet: -2.07 (1.88), residues: 5 loop : -1.97 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 271 TYR 0.011 0.001 TYR C 505 PHE 0.015 0.001 PHE C 329 TRP 0.024 0.001 TRP C 524 HIS 0.003 0.001 HIS C 658 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (14253) covalent geometry : angle 0.58047 / 0.29 (19374) SS BOND : bond 0.00109 / 0.07 ( 12) SS BOND : angle 0.59628 / 0.33 ( 24) hydrogen bonds : bond 0.03852 / 2.57 ( 817) hydrogen bonds : angle 3.51844 / 2.47 ( 2388) Misc. bond : bond 0.00267 / 0.14 ( 3) link_BETA1-4 : bond 0.01318 / 0.67 ( 2) link_BETA1-4 : angle 2.51368 / 1.23 ( 6) link_NAG-ASN : bond 0.01386 / 0.69 ( 2) link_NAG-ASN : angle 4.22528 / 2.48 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 157 time to evaluate : 0.554 Fit side-chains REVERT: A 86 GLU cc_start: 0.6231 (OUTLIER) cc_final: 0.5125 (tm-30) REVERT: A 160 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6351 (mp0) REVERT: A 201 GLU cc_start: 0.7489 (tp30) cc_final: 0.6893 (tp30) REVERT: B 110 ARG cc_start: 0.8009 (mtt180) cc_final: 0.7679 (mpt-90) REVERT: B 148 MET cc_start: 0.7498 (mpp) cc_final: 0.7021 (mpp) REVERT: B 152 MET cc_start: 0.7522 (ttt) cc_final: 0.7282 (mmm) REVERT: B 170 ASN cc_start: 0.8208 (m-40) cc_final: 0.7713 (t0) REVERT: B 281 ASP cc_start: 0.7699 (t0) cc_final: 0.7197 (t0) REVERT: C 105 GLN cc_start: 0.8188 (tp40) cc_final: 0.7858 (tp40) REVERT: C 168 GLU cc_start: 0.6909 (pm20) cc_final: 0.6613 (pm20) REVERT: C 368 MET cc_start: 0.8285 (mmt) cc_final: 0.8071 (mmt) REVERT: C 514 PHE cc_start: 0.8833 (OUTLIER) cc_final: 0.8549 (m-80) REVERT: C 599 GLU cc_start: 0.7836 (mp0) cc_final: 0.7602 (pm20) REVERT: C 617 GLU cc_start: 0.7917 (pt0) cc_final: 0.7287 (pm20) REVERT: C 628 ARG cc_start: 0.8151 (ttm-80) cc_final: 0.7609 (ttm110) REVERT: C 640 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.7811 (ttm-80) REVERT: C 705 ARG cc_start: 0.5722 (ttp-170) cc_final: 0.5286 (ttm110) REVERT: C 717 ARG cc_start: 0.7171 (mpt180) cc_final: 0.5411 (mmt180) REVERT: C 778 VAL cc_start: 0.8908 (OUTLIER) cc_final: 0.8708 (t) REVERT: D 97 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7246 (mt) REVERT: D 269 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7556 (mt) REVERT: D 540 ILE cc_start: 0.8171 (mm) cc_final: 0.7960 (pt) REVERT: D 725 HIS cc_start: 0.7279 (m-70) cc_final: 0.6685 (t70) outliers start: 39 outliers final: 15 residues processed: 182 average time/residue: 0.6961 time to fit residues: 137.4924 Evaluate side-chains 168 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 640 ARG Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 265 ARG Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 562 MET Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 663 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 155 optimal weight: 3.9990 chunk 162 optimal weight: 0.4980 chunk 37 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 115 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 160 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 93 optimal weight: 10.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 ASN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 607 GLN ** D 623 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 774 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.136464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.109416 restraints weight = 17176.626| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.43 r_work: 0.3168 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14272 Z= 0.117 Angle : 0.582 11.496 19410 Z= 0.294 Chirality : 0.040 0.212 2265 Planarity : 0.004 0.049 2420 Dihedral : 4.930 57.288 1910 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 1.92 % Allowed : 14.16 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.21), residues: 1746 helix: 2.40 (0.16), residues: 1110 sheet: -1.86 (1.91), residues: 5 loop : -1.95 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 405 TYR 0.013 0.001 TYR C 505 PHE 0.014 0.001 PHE C 392 TRP 0.022 0.002 TRP C 524 HIS 0.004 0.001 HIS C 658 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (14253) covalent geometry : angle 0.57760 / 0.29 (19374) SS BOND : bond 0.00116 / 0.09 ( 12) SS BOND : angle 0.60844 / 0.33 ( 24) hydrogen bonds : bond 0.04057 / 2.71 ( 817) hydrogen bonds : angle 3.50966 / 2.47 ( 2388) Misc. bond : bond 0.00257 / 0.13 ( 3) link_BETA1-4 : bond 0.00701 / 0.34 ( 2) link_BETA1-4 : angle 2.57537 / 1.34 ( 6) link_NAG-ASN : bond 0.01160 / 0.57 ( 2) link_NAG-ASN : angle 3.26571 / 1.85 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 147 time to evaluate : 0.583 Fit side-chains REVERT: A 86 GLU cc_start: 0.6288 (OUTLIER) cc_final: 0.5269 (tm-30) REVERT: A 160 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6410 (mp0) REVERT: A 201 GLU cc_start: 0.7538 (tp30) cc_final: 0.6951 (tp30) REVERT: B 110 ARG cc_start: 0.7992 (mtt180) cc_final: 0.7665 (mpt-90) REVERT: B 148 MET cc_start: 0.7497 (mpp) cc_final: 0.7011 (mpp) REVERT: B 170 ASN cc_start: 0.8159 (m-40) cc_final: 0.7685 (t0) REVERT: B 241 MET cc_start: 0.7264 (ttp) cc_final: 0.6984 (ttm) REVERT: B 281 ASP cc_start: 0.7680 (t0) cc_final: 0.7164 (t0) REVERT: C 105 GLN cc_start: 0.8223 (tp40) cc_final: 0.7893 (tp40) REVERT: C 168 GLU cc_start: 0.6886 (pm20) cc_final: 0.6579 (pm20) REVERT: C 368 MET cc_start: 0.8437 (mmt) cc_final: 0.8232 (mmt) REVERT: C 514 PHE cc_start: 0.8824 (OUTLIER) cc_final: 0.8526 (m-80) REVERT: C 599 GLU cc_start: 0.7819 (mp0) cc_final: 0.7586 (pm20) REVERT: C 617 GLU cc_start: 0.7934 (pt0) cc_final: 0.7320 (pm20) REVERT: C 628 ARG cc_start: 0.8164 (ttm-80) cc_final: 0.7632 (ttm110) REVERT: C 640 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.7794 (ttm-80) REVERT: C 705 ARG cc_start: 0.5824 (ttp-170) cc_final: 0.5416 (ttm110) REVERT: C 717 ARG cc_start: 0.7156 (mpt180) cc_final: 0.5372 (mmt180) REVERT: C 732 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7894 (mm-30) REVERT: C 778 VAL cc_start: 0.8933 (OUTLIER) cc_final: 0.8708 (t) REVERT: C 786 ASP cc_start: 0.8269 (OUTLIER) cc_final: 0.8035 (p0) REVERT: D 97 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7271 (mt) REVERT: D 269 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7639 (mt) REVERT: D 540 ILE cc_start: 0.8172 (mm) cc_final: 0.7958 (pt) REVERT: D 725 HIS cc_start: 0.7333 (m-70) cc_final: 0.6679 (t70) REVERT: D 781 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8671 (mt) outliers start: 29 outliers final: 13 residues processed: 168 average time/residue: 0.6870 time to fit residues: 125.4240 Evaluate side-chains 165 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 640 ARG Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 786 ASP Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 562 MET Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 684 LEU Chi-restraints excluded: chain D residue 781 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 108 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 79 optimal weight: 0.4980 chunk 26 optimal weight: 7.9990 chunk 134 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 ASN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 607 GLN ** D 623 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 774 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.134753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.107365 restraints weight = 17181.669| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.48 r_work: 0.3134 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14272 Z= 0.139 Angle : 0.620 12.048 19410 Z= 0.313 Chirality : 0.041 0.219 2265 Planarity : 0.004 0.049 2420 Dihedral : 5.080 57.013 1910 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 1.72 % Allowed : 14.43 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.21), residues: 1746 helix: 2.35 (0.16), residues: 1110 sheet: -1.95 (1.86), residues: 5 loop : -1.97 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 405 TYR 0.016 0.002 TYR C 505 PHE 0.016 0.001 PHE C 329 TRP 0.021 0.002 TRP D 524 HIS 0.004 0.001 HIS C 658 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (14253) covalent geometry : angle 0.61659 / 0.31 (19374) SS BOND : bond 0.00139 / 0.10 ( 12) SS BOND : angle 0.67425 / 0.37 ( 24) hydrogen bonds : bond 0.04463 / 2.98 ( 817) hydrogen bonds : angle 3.58383 / 2.52 ( 2388) Misc. bond : bond 0.00378 / 0.19 ( 3) link_BETA1-4 : bond 0.00991 / 0.49 ( 2) link_BETA1-4 : angle 2.56067 / 1.26 ( 6) link_NAG-ASN : bond 0.01482 / 0.75 ( 2) link_NAG-ASN : angle 3.07813 / 1.78 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 146 time to evaluate : 0.631 Fit side-chains REVERT: A 86 GLU cc_start: 0.6217 (OUTLIER) cc_final: 0.5013 (tm-30) REVERT: A 167 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.6824 (mp10) REVERT: A 201 GLU cc_start: 0.7541 (tp30) cc_final: 0.6974 (tp30) REVERT: B 110 ARG cc_start: 0.8056 (mtt180) cc_final: 0.7685 (mpt-90) REVERT: B 148 MET cc_start: 0.7488 (mpp) cc_final: 0.7023 (mpp) REVERT: B 170 ASN cc_start: 0.8243 (m-40) cc_final: 0.7710 (t0) REVERT: B 241 MET cc_start: 0.7272 (ttp) cc_final: 0.7005 (ttm) REVERT: B 281 ASP cc_start: 0.7683 (t0) cc_final: 0.7177 (t0) REVERT: C 168 GLU cc_start: 0.6875 (pm20) cc_final: 0.6584 (pm20) REVERT: C 514 PHE cc_start: 0.8864 (OUTLIER) cc_final: 0.8533 (m-80) REVERT: C 599 GLU cc_start: 0.7841 (mp0) cc_final: 0.7580 (pm20) REVERT: C 617 GLU cc_start: 0.8060 (pt0) cc_final: 0.7377 (pm20) REVERT: C 640 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.7890 (ttm-80) REVERT: C 705 ARG cc_start: 0.5889 (ttp-170) cc_final: 0.5468 (ttm110) REVERT: C 732 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7938 (mm-30) REVERT: C 778 VAL cc_start: 0.8927 (OUTLIER) cc_final: 0.8702 (t) REVERT: D 97 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7328 (mt) REVERT: D 269 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7613 (mt) REVERT: D 540 ILE cc_start: 0.8207 (mm) cc_final: 0.7987 (pt) REVERT: D 725 HIS cc_start: 0.7385 (m-70) cc_final: 0.6686 (t70) REVERT: D 781 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8704 (mt) outliers start: 26 outliers final: 14 residues processed: 163 average time/residue: 0.7246 time to fit residues: 128.2894 Evaluate side-chains 163 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 167 GLN Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 640 ARG Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 786 ASP Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 562 MET Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 684 LEU Chi-restraints excluded: chain D residue 781 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 162 optimal weight: 1.9990 chunk 164 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 97 optimal weight: 0.5980 chunk 135 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 161 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 306 HIS B 93 ASN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 607 GLN ** D 623 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.134419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.106853 restraints weight = 17013.541| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.49 r_work: 0.3132 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14272 Z= 0.142 Angle : 0.635 13.513 19410 Z= 0.319 Chirality : 0.042 0.232 2265 Planarity : 0.004 0.049 2420 Dihedral : 5.162 56.469 1910 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 1.79 % Allowed : 14.36 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.21), residues: 1746 helix: 2.31 (0.16), residues: 1110 sheet: -2.07 (1.81), residues: 5 loop : -2.00 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 561 TYR 0.016 0.002 TYR C 715 PHE 0.016 0.001 PHE C 392 TRP 0.021 0.002 TRP D 524 HIS 0.007 0.001 HIS A 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (14253) covalent geometry : angle 0.63161 / 0.32 (19374) SS BOND : bond 0.00144 / 0.11 ( 12) SS BOND : angle 0.68547 / 0.37 ( 24) hydrogen bonds : bond 0.04534 / 3.03 ( 817) hydrogen bonds : angle 3.61349 / 2.54 ( 2388) Misc. bond : bond 0.00382 / 0.20 ( 3) link_BETA1-4 : bond 0.00966 / 0.47 ( 2) link_BETA1-4 : angle 2.64630 / 1.34 ( 6) link_NAG-ASN : bond 0.01108 / 0.56 ( 2) link_NAG-ASN : angle 2.67552 / 1.53 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5166.02 seconds wall clock time: 88 minutes 37.14 seconds (5317.14 seconds total)