Starting phenix.real_space_refine on Thu Sep 18 04:40:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cq5_30436/09_2025/7cq5_30436.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cq5_30436/09_2025/7cq5_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 { model { file = "/net/cci-nas-00/data/ceres_data/7cq5_30436/09_2025/7cq5_30436.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cq5_30436/09_2025/7cq5_30436.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7cq5_30436/09_2025/7cq5_30436.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cq5_30436/09_2025/7cq5_30436.map" } 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-2.0-5805/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 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: 3.32, per 1000 atoms: 0.24 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: 1.08 Conformation dependent library (CDL) restraints added in 613.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.45 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: 2.30 Time building geometry restraints manager: 1.40 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: 8029 16.18 - 32.36: 393 32.36 - 48.54: 88 48.54 - 64.71: 21 64.71 - 80.89: 9 Dihedral angle restraints: 8540 sinusoidal: 3399 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 8537 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: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.840 Find NCS groups from input model: 0.270 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:6.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 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 : 10.935 80.892 5176 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 aren 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 covalent geometry : bond 0.00704 (14253) covalent geometry : angle 1.05083 (19374) SS BOND : bond 0.00405 ( 12) SS BOND : angle 1.66676 ( 24) hydrogen bonds : bond 0.21018 ( 817) hydrogen bonds : angle 6.97234 ( 2388) Misc. bond : bond 0.00280 ( 3) link_BETA1-4 : bond 0.00092 ( 2) link_BETA1-4 : angle 4.00899 ( 6) link_NAG-ASN : bond 0.00406 ( 2) link_NAG-ASN : angle 3.06260 ( 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 : 0.450 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: 0.7282 time to fit residues: 220.3971 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 : 0.352 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3628 r_free = 0.3628 target = 0.136594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.109110 restraints weight = 17327.422| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.45 r_work: 0.3164 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1939 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= 0.151 Angle : 0.676 11.091 19410 Z= 0.349 Chirality : 0.042 0.199 2265 Planarity : 0.006 0.051 2420 Dihedral : 8.589 80.443 2061 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 2.91 % Allowed : 9.07 % Favored : 88.02 % 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 aren not related in a simple way. whole: -1.09 (0.19), residues: 1746 helix: 0.22 (0.15), residues: 1121 sheet: -3.05 (0.86), residues: 5 loop : -2.47 (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 0.019 0.002 PHE C 329 TRP 0.029 0.002 TRP D 179 HIS 0.006 0.001 HIS C 658 Details of bonding type rmsd covalent geometry : bond 0.00329 (14253) covalent geometry : angle 0.67278 (19374) SS BOND : bond 0.00175 ( 12) SS BOND : angle 0.89914 ( 24) hydrogen bonds : bond 0.05553 ( 817) hydrogen bonds : angle 4.20916 ( 2388) Misc. bond : bond 0.00199 ( 3) link_BETA1-4 : bond 0.00731 ( 2) link_BETA1-4 : angle 2.59304 ( 6) link_NAG-ASN : bond 0.00172 ( 2) link_NAG-ASN : angle 2.25977 ( 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 213 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 169 time to evaluate : 0.348 Fit side-chains REVERT: A 148 MET cc_start: 0.7252 (mmm) cc_final: 0.7049 (mmm) REVERT: A 164 THR cc_start: 0.8984 (m) cc_final: 0.8769 (t) REVERT: A 198 THR cc_start: 0.7602 (p) cc_final: 0.7359 (t) REVERT: B 110 ARG cc_start: 0.8229 (mtt180) cc_final: 0.7762 (mpt-90) REVERT: B 148 MET cc_start: 0.7536 (mpp) cc_final: 0.7138 (mpp) REVERT: B 167 GLN cc_start: 0.8139 (mt0) cc_final: 0.7810 (mp10) REVERT: B 170 ASN cc_start: 0.8229 (m-40) cc_final: 0.7728 (t0) REVERT: B 225 ARG cc_start: 0.7384 (ttm110) cc_final: 0.7123 (ttm110) REVERT: B 260 ASP cc_start: 0.8446 (t70) cc_final: 0.8164 (t70) REVERT: C 110 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8043 (tt0) REVERT: C 123 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7230 (tm-30) REVERT: C 168 GLU cc_start: 0.7262 (pm20) cc_final: 0.7049 (pm20) REVERT: C 271 ARG cc_start: 0.6068 (mmt90) cc_final: 0.5690 (mmm160) REVERT: C 514 PHE cc_start: 0.8799 (OUTLIER) cc_final: 0.8499 (m-80) REVERT: C 617 GLU cc_start: 0.7843 (pt0) cc_final: 0.7223 (pm20) REVERT: C 631 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.7411 (pp-130) REVERT: C 640 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.7856 (ttm-80) REVERT: C 641 ARG cc_start: 0.7555 (mtm-85) cc_final: 0.7174 (mtt90) REVERT: C 707 ARG cc_start: 0.7751 (mtm180) cc_final: 0.6915 (mtm-85) REVERT: C 717 ARG cc_start: 0.6882 (mpt180) cc_final: 0.5555 (mmt180) REVERT: C 778 VAL cc_start: 0.8961 (OUTLIER) cc_final: 0.8678 (t) REVERT: C 786 ASP cc_start: 0.8394 (OUTLIER) cc_final: 0.7939 (p0) REVERT: D 349 MET cc_start: 0.7651 (OUTLIER) cc_final: 0.6823 (tmt) REVERT: D 649 ASP cc_start: 0.8392 (m-30) cc_final: 0.8174 (m-30) REVERT: D 728 GLN cc_start: 0.7793 (tp40) cc_final: 0.7369 (tp40) outliers start: 44 outliers final: 15 residues processed: 197 average time/residue: 0.6934 time to fit residues: 146.9327 Evaluate side-chains 168 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 150 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 131 optimal weight: 0.8980 chunk 157 optimal weight: 0.7980 chunk 50 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 468 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.139849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.114581 restraints weight = 17866.112| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.43 r_work: 0.3223 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14272 Z= 0.118 Angle : 0.583 9.800 19410 Z= 0.299 Chirality : 0.040 0.160 2265 Planarity : 0.004 0.049 2420 Dihedral : 7.778 76.688 2058 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.38 % Allowed : 10.79 % Favored : 86.83 % 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 aren not related in a simple way. whole: 0.16 (0.21), residues: 1746 helix: 1.31 (0.16), residues: 1120 sheet: -2.89 (1.20), residues: 5 loop : -2.20 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 405 TYR 0.013 0.001 TYR A 116 PHE 0.016 0.001 PHE C 329 TRP 0.020 0.002 TRP D 524 HIS 0.005 0.001 HIS C 658 Details of bonding type rmsd covalent geometry : bond 0.00247 (14253) covalent geometry : angle 0.57998 (19374) SS BOND : bond 0.00296 ( 12) SS BOND : angle 0.76486 ( 24) hydrogen bonds : bond 0.04413 ( 817) hydrogen bonds : angle 3.78469 ( 2388) Misc. bond : bond 0.00140 ( 3) link_BETA1-4 : bond 0.00469 ( 2) link_BETA1-4 : angle 2.39513 ( 6) link_NAG-ASN : bond 0.00588 ( 2) link_NAG-ASN : angle 2.02177 ( 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 200 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 164 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: A 86 GLU cc_start: 0.6315 (OUTLIER) cc_final: 0.6106 (pm20) REVERT: A 168 GLU cc_start: 0.7623 (tm-30) cc_final: 0.7313 (tm-30) REVERT: B 110 ARG cc_start: 0.8055 (mtt180) cc_final: 0.7694 (mpt-90) REVERT: B 148 MET cc_start: 0.7446 (mpp) cc_final: 0.6995 (mpp) REVERT: B 152 MET cc_start: 0.7686 (ttm) cc_final: 0.7360 (ttt) REVERT: B 170 ASN cc_start: 0.8162 (m-40) cc_final: 0.7719 (t0) REVERT: B 260 ASP cc_start: 0.8378 (t70) cc_final: 0.8135 (t70) REVERT: C 123 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7293 (tm-30) REVERT: C 168 GLU cc_start: 0.7166 (pm20) cc_final: 0.6920 (pm20) REVERT: C 271 ARG cc_start: 0.6206 (mmt90) cc_final: 0.5743 (mmm160) REVERT: C 617 GLU cc_start: 0.7870 (pt0) cc_final: 0.7267 (pm20) REVERT: C 631 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.7615 (pp-130) REVERT: C 640 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7842 (ttm-80) REVERT: C 641 ARG cc_start: 0.7584 (mtm-85) cc_final: 0.7192 (mtt90) REVERT: C 707 ARG cc_start: 0.7737 (mtm180) cc_final: 0.6993 (mtm-85) REVERT: C 717 ARG cc_start: 0.6680 (mpt180) cc_final: 0.5359 (mmt180) REVERT: C 778 VAL cc_start: 0.8908 (OUTLIER) cc_final: 0.8633 (t) REVERT: C 786 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.7927 (p0) REVERT: D 540 ILE cc_start: 0.8143 (mm) cc_final: 0.7871 (pt) REVERT: D 725 HIS cc_start: 0.7051 (m-70) cc_final: 0.6536 (t-170) REVERT: D 777 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7225 (mp10) outliers start: 36 outliers final: 13 residues processed: 188 average time/residue: 0.7190 time to fit residues: 145.5283 Evaluate side-chains 163 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain C residue 123 GLU 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 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: 0.9990 chunk 108 optimal weight: 7.9990 chunk 151 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 776 ASN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.136866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.109528 restraints weight = 17342.323| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.39 r_work: 0.3168 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2610 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= 0.122 Angle : 0.580 9.227 19410 Z= 0.297 Chirality : 0.040 0.158 2265 Planarity : 0.004 0.048 2420 Dihedral : 7.640 75.548 2058 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.58 % Allowed : 11.32 % Favored : 86.10 % 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 aren not related in a simple way. whole: 0.69 (0.21), residues: 1746 helix: 1.78 (0.16), residues: 1119 sheet: -2.28 (1.57), residues: 5 loop : -2.12 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 767 TYR 0.015 0.001 TYR C 715 PHE 0.015 0.001 PHE C 392 TRP 0.021 0.002 TRP D 524 HIS 0.005 0.001 HIS C 658 Details of bonding type rmsd covalent geometry : bond 0.00266 (14253) covalent geometry : angle 0.57691 (19374) SS BOND : bond 0.00160 ( 12) SS BOND : angle 0.68403 ( 24) hydrogen bonds : bond 0.04321 ( 817) hydrogen bonds : angle 3.65859 ( 2388) Misc. bond : bond 0.00233 ( 3) link_BETA1-4 : bond 0.00702 ( 2) link_BETA1-4 : angle 2.43575 ( 6) link_NAG-ASN : bond 0.00703 ( 2) link_NAG-ASN : angle 2.36772 ( 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 190 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 151 time to evaluate : 0.559 Fit side-chains REVERT: A 86 GLU cc_start: 0.6413 (OUTLIER) cc_final: 0.5240 (tm-30) REVERT: A 167 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.6752 (mp10) REVERT: A 168 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7224 (tm-30) REVERT: B 110 ARG cc_start: 0.7886 (mtt180) cc_final: 0.7567 (mpt-90) REVERT: B 148 MET cc_start: 0.7426 (mpp) cc_final: 0.6967 (mpp) REVERT: B 152 MET cc_start: 0.7664 (ttm) cc_final: 0.7421 (ttt) REVERT: B 170 ASN cc_start: 0.8125 (m-40) cc_final: 0.7643 (t0) REVERT: C 123 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7286 (tm-30) REVERT: C 168 GLU cc_start: 0.7137 (pm20) cc_final: 0.6841 (pm20) REVERT: C 271 ARG cc_start: 0.6179 (mmt90) cc_final: 0.5689 (mmm160) REVERT: C 274 LYS cc_start: 0.6328 (OUTLIER) cc_final: 0.5254 (pmmt) REVERT: C 514 PHE cc_start: 0.8850 (OUTLIER) cc_final: 0.8519 (m-80) REVERT: C 617 GLU cc_start: 0.7838 (pt0) cc_final: 0.7218 (pm20) REVERT: C 631 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.7702 (pp-130) REVERT: C 640 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7828 (ttm-80) REVERT: C 717 ARG cc_start: 0.6986 (mpt180) cc_final: 0.5358 (mmt180) REVERT: C 778 VAL cc_start: 0.8926 (OUTLIER) cc_final: 0.8634 (t) REVERT: C 786 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.8009 (p0) REVERT: D 97 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7869 (pt) REVERT: D 269 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7701 (mt) REVERT: D 332 MET cc_start: 0.8939 (mmm) cc_final: 0.8535 (mmm) REVERT: D 540 ILE cc_start: 0.8143 (mm) cc_final: 0.7858 (pt) REVERT: D 725 HIS cc_start: 0.7062 (m-70) cc_final: 0.6525 (t-170) REVERT: D 777 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7235 (mp10) outliers start: 39 outliers final: 15 residues processed: 174 average time/residue: 0.7171 time to fit residues: 134.7394 Evaluate side-chains 171 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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 C residue 123 GLU Chi-restraints excluded: chain C residue 274 LYS 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 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 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 775 ARG Chi-restraints excluded: chain D residue 777 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 131 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 65 optimal weight: 0.1980 chunk 37 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 ASN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.133774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.106352 restraints weight = 17336.312| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.44 r_work: 0.3120 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14272 Z= 0.162 Angle : 0.637 9.905 19410 Z= 0.324 Chirality : 0.043 0.162 2265 Planarity : 0.004 0.051 2420 Dihedral : 7.780 78.256 2056 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % 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 aren not related in a simple way. whole: 0.77 (0.21), residues: 1746 helix: 1.84 (0.16), residues: 1120 sheet: -2.03 (1.77), residues: 5 loop : -2.09 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 561 TYR 0.020 0.002 TYR C 715 PHE 0.018 0.002 PHE D 613 TRP 0.021 0.002 TRP D 524 HIS 0.006 0.001 HIS C 658 Details of bonding type rmsd covalent geometry : bond 0.00379 (14253) covalent geometry : angle 0.63202 (19374) SS BOND : bond 0.00201 ( 12) SS BOND : angle 0.75152 ( 24) hydrogen bonds : bond 0.04871 ( 817) hydrogen bonds : angle 3.71006 ( 2388) Misc. bond : bond 0.00446 ( 3) link_BETA1-4 : bond 0.00975 ( 2) link_BETA1-4 : angle 3.28451 ( 6) link_NAG-ASN : bond 0.01530 ( 2) link_NAG-ASN : angle 2.98552 ( 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 201 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 154 time to evaluate : 0.447 Fit side-chains REVERT: A 86 GLU cc_start: 0.6439 (OUTLIER) cc_final: 0.5300 (tm-30) REVERT: A 152 MET cc_start: 0.7356 (tpt) cc_final: 0.7059 (tpt) REVERT: A 167 GLN cc_start: 0.7699 (OUTLIER) cc_final: 0.6878 (mp10) REVERT: A 168 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7347 (tm-30) REVERT: B 110 ARG cc_start: 0.7989 (mtt180) cc_final: 0.7624 (mpt-90) REVERT: B 148 MET cc_start: 0.7479 (mpp) cc_final: 0.7010 (mpp) REVERT: B 170 ASN cc_start: 0.8170 (m-40) cc_final: 0.7686 (t0) REVERT: C 123 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7363 (tm-30) REVERT: C 168 GLU cc_start: 0.7188 (pm20) cc_final: 0.6846 (pm20) REVERT: C 271 ARG cc_start: 0.6198 (mmt90) cc_final: 0.5712 (mmm160) REVERT: C 368 MET cc_start: 0.8310 (mmt) cc_final: 0.8058 (mmt) REVERT: C 514 PHE cc_start: 0.8917 (OUTLIER) cc_final: 0.8561 (m-80) REVERT: C 617 GLU cc_start: 0.7931 (pt0) cc_final: 0.7273 (pm20) REVERT: C 631 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.7788 (pp-130) REVERT: C 640 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.7895 (ttm-80) REVERT: C 705 ARG cc_start: 0.5691 (ttp-170) cc_final: 0.5344 (ttm110) REVERT: C 717 ARG cc_start: 0.7171 (mpt180) cc_final: 0.5435 (mmt180) REVERT: C 778 VAL cc_start: 0.8957 (OUTLIER) cc_final: 0.8639 (t) REVERT: D 97 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7307 (mt) REVERT: D 269 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7626 (mt) REVERT: D 332 MET cc_start: 0.8943 (mmm) cc_final: 0.8654 (mmm) REVERT: D 349 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.6728 (tmt) REVERT: D 540 ILE cc_start: 0.8250 (mm) cc_final: 0.7939 (pt) REVERT: D 571 MET cc_start: 0.9161 (mtp) cc_final: 0.8933 (mtp) REVERT: D 781 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8687 (mt) outliers start: 47 outliers final: 22 residues processed: 185 average time/residue: 0.6625 time to fit residues: 132.6795 Evaluate side-chains 178 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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 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 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 D residue 97 LEU Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 214 ASN 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 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: 0.0370 chunk 103 optimal weight: 0.0020 chunk 136 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 142 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 chunk 119 optimal weight: 0.6980 chunk 104 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.5066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3625 r_free = 0.3625 target = 0.136699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.109425 restraints weight = 17195.238| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.46 r_work: 0.3165 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14272 Z= 0.111 Angle : 0.557 9.625 19410 Z= 0.284 Chirality : 0.039 0.153 2265 Planarity : 0.004 0.051 2420 Dihedral : 7.508 73.639 2056 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.91 % Allowed : 11.91 % Favored : 85.18 % 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 aren not related in a simple way. whole: 1.12 (0.21), residues: 1746 helix: 2.16 (0.16), residues: 1113 sheet: -2.25 (1.77), residues: 5 loop : -2.00 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 561 TYR 0.012 0.001 TYR C 505 PHE 0.014 0.001 PHE C 392 TRP 0.023 0.001 TRP D 524 HIS 0.004 0.001 HIS C 658 Details of bonding type rmsd covalent geometry : bond 0.00230 (14253) covalent geometry : angle 0.55332 (19374) SS BOND : bond 0.00144 ( 12) SS BOND : angle 0.60365 ( 24) hydrogen bonds : bond 0.04069 ( 817) hydrogen bonds : angle 3.57426 ( 2388) Misc. bond : bond 0.00202 ( 3) link_BETA1-4 : bond 0.00713 ( 2) link_BETA1-4 : angle 2.35265 ( 6) link_NAG-ASN : bond 0.00917 ( 2) link_NAG-ASN : angle 2.72273 ( 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 195 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 151 time to evaluate : 0.548 Fit side-chains REVERT: A 86 GLU cc_start: 0.6373 (pm20) cc_final: 0.5383 (tm-30) REVERT: A 152 MET cc_start: 0.7291 (tpt) cc_final: 0.6957 (tpt) REVERT: A 167 GLN cc_start: 0.7643 (OUTLIER) cc_final: 0.6822 (mp10) REVERT: A 198 THR cc_start: 0.7681 (p) cc_final: 0.7459 (t) REVERT: A 201 GLU cc_start: 0.7363 (tp30) cc_final: 0.6708 (tp30) REVERT: B 110 ARG cc_start: 0.8004 (mtt180) cc_final: 0.7655 (mpt-90) REVERT: B 148 MET cc_start: 0.7515 (mpp) cc_final: 0.7068 (mpp) REVERT: B 152 MET cc_start: 0.7512 (ttt) cc_final: 0.7288 (mmm) REVERT: B 170 ASN cc_start: 0.8151 (m-40) cc_final: 0.7670 (t0) REVERT: B 242 ASN cc_start: 0.6560 (t0) cc_final: 0.6298 (t160) REVERT: C 168 GLU cc_start: 0.7071 (pm20) cc_final: 0.6786 (pm20) REVERT: C 271 ARG cc_start: 0.6141 (mmt90) cc_final: 0.5646 (mmm160) REVERT: C 368 MET cc_start: 0.8300 (mmt) cc_final: 0.8056 (mmt) REVERT: C 514 PHE cc_start: 0.8848 (OUTLIER) cc_final: 0.8521 (m-80) REVERT: C 617 GLU cc_start: 0.7941 (pt0) cc_final: 0.7322 (pm20) REVERT: C 628 ARG cc_start: 0.8193 (ttm-80) cc_final: 0.7637 (ttm110) REVERT: C 631 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.7699 (pp-130) REVERT: C 640 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.7842 (ttm-80) REVERT: C 705 ARG cc_start: 0.5670 (ttp-170) cc_final: 0.5314 (ttm110) REVERT: C 717 ARG cc_start: 0.7083 (mpt180) cc_final: 0.5393 (mmt180) REVERT: C 778 VAL cc_start: 0.8918 (OUTLIER) cc_final: 0.8656 (t) REVERT: C 786 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.8007 (p0) REVERT: D 97 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7283 (mt) REVERT: D 269 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7580 (mt) REVERT: D 332 MET cc_start: 0.8934 (mmm) cc_final: 0.8663 (mmm) REVERT: D 349 MET cc_start: 0.7712 (OUTLIER) cc_final: 0.6685 (tmm) REVERT: D 540 ILE cc_start: 0.8318 (mm) cc_final: 0.8009 (pt) REVERT: D 571 MET cc_start: 0.9143 (mtp) cc_final: 0.8905 (mtp) REVERT: D 725 HIS cc_start: 0.7189 (m-70) cc_final: 0.6635 (t70) REVERT: D 781 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8599 (mt) outliers start: 44 outliers final: 19 residues processed: 184 average time/residue: 0.6651 time to fit residues: 132.7880 Evaluate side-chains 175 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 214 ASN Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 261 ILE 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 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 775 ARG 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: 0.0270 chunk 94 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 137 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 113 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.1842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 ASN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN D 774 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.135147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.107581 restraints weight = 17099.362| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.47 r_work: 0.3138 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2842 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= 0.135 Angle : 0.591 9.254 19410 Z= 0.303 Chirality : 0.041 0.157 2265 Planarity : 0.004 0.050 2420 Dihedral : 7.606 76.566 2056 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.71 % Allowed : 12.44 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.21), residues: 1746 helix: 2.18 (0.16), residues: 1113 sheet: -1.99 (1.86), residues: 5 loop : -2.01 (0.25), residues: 628 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 0.021 0.002 TRP D 524 HIS 0.005 0.001 HIS C 658 Details of bonding type rmsd covalent geometry : bond 0.00307 (14253) covalent geometry : angle 0.58697 (19374) SS BOND : bond 0.00151 ( 12) SS BOND : angle 0.69271 ( 24) hydrogen bonds : bond 0.04430 ( 817) hydrogen bonds : angle 3.59627 ( 2388) Misc. bond : bond 0.00219 ( 3) link_BETA1-4 : bond 0.00759 ( 2) link_BETA1-4 : angle 2.57553 ( 6) link_NAG-ASN : bond 0.01085 ( 2) link_NAG-ASN : angle 3.07990 ( 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 190 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 149 time to evaluate : 0.541 Fit side-chains REVERT: A 86 GLU cc_start: 0.6383 (OUTLIER) cc_final: 0.5391 (tm-30) REVERT: A 152 MET cc_start: 0.7338 (tpt) cc_final: 0.6962 (tpt) REVERT: A 167 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.6869 (mp10) REVERT: A 201 GLU cc_start: 0.7505 (tp30) cc_final: 0.6886 (tp30) REVERT: B 110 ARG cc_start: 0.8064 (mtt180) cc_final: 0.7688 (mpt-90) REVERT: B 148 MET cc_start: 0.7523 (mpp) cc_final: 0.7072 (mpp) REVERT: B 170 ASN cc_start: 0.8174 (m-40) cc_final: 0.7735 (t0) REVERT: B 254 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8505 (mp) REVERT: C 168 GLU cc_start: 0.7082 (pm20) cc_final: 0.6779 (pm20) REVERT: C 368 MET cc_start: 0.8296 (mmt) cc_final: 0.8080 (mmt) REVERT: C 514 PHE cc_start: 0.8903 (OUTLIER) cc_final: 0.8568 (m-80) REVERT: C 617 GLU cc_start: 0.7971 (pt0) cc_final: 0.7346 (pm20) REVERT: C 631 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.7752 (pp-130) REVERT: C 640 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.7850 (ttm-80) REVERT: C 705 ARG cc_start: 0.5736 (ttp-170) cc_final: 0.5358 (ttm110) REVERT: C 717 ARG cc_start: 0.7206 (mpt180) cc_final: 0.5464 (mmt180) REVERT: C 778 VAL cc_start: 0.8938 (OUTLIER) cc_final: 0.8668 (t) REVERT: D 97 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7256 (mt) REVERT: D 269 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7609 (mt) REVERT: D 332 MET cc_start: 0.8923 (mmm) cc_final: 0.8572 (mmm) REVERT: D 349 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.6707 (tmm) REVERT: D 540 ILE cc_start: 0.8352 (mm) cc_final: 0.8042 (pt) REVERT: D 571 MET cc_start: 0.9198 (mtp) cc_final: 0.8966 (mtp) REVERT: D 725 HIS cc_start: 0.7231 (m-70) cc_final: 0.6663 (t70) REVERT: D 781 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8666 (mt) outliers start: 41 outliers final: 20 residues processed: 179 average time/residue: 0.7470 time to fit residues: 144.8810 Evaluate side-chains 172 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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 242 ASN Chi-restraints excluded: chain B residue 254 LEU 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 D residue 97 LEU Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 214 ASN Chi-restraints excluded: chain D residue 216 VAL 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 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 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: 1.9990 chunk 22 optimal weight: 3.9990 chunk 159 optimal weight: 0.9990 chunk 42 optimal weight: 0.3980 chunk 99 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 chunk 64 optimal weight: 0.8980 chunk 149 optimal weight: 0.3980 chunk 26 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN B 93 ASN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.135306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.108177 restraints weight = 17047.519| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.42 r_work: 0.3149 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2907 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= 0.127 Angle : 0.611 11.759 19410 Z= 0.306 Chirality : 0.040 0.172 2265 Planarity : 0.004 0.050 2420 Dihedral : 7.547 75.599 2056 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.45 % Allowed : 13.17 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.21), residues: 1746 helix: 2.25 (0.16), residues: 1112 sheet: -2.16 (1.82), residues: 5 loop : -1.99 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 271 TYR 0.014 0.001 TYR C 505 PHE 0.015 0.001 PHE C 392 TRP 0.022 0.002 TRP D 524 HIS 0.004 0.001 HIS C 658 Details of bonding type rmsd covalent geometry : bond 0.00280 (14253) covalent geometry : angle 0.60602 (19374) SS BOND : bond 0.00141 ( 12) SS BOND : angle 0.69011 ( 24) hydrogen bonds : bond 0.04276 ( 817) hydrogen bonds : angle 3.58025 ( 2388) Misc. bond : bond 0.00410 ( 3) link_BETA1-4 : bond 0.01063 ( 2) link_BETA1-4 : angle 2.83571 ( 6) link_NAG-ASN : bond 0.01307 ( 2) link_NAG-ASN : angle 3.60443 ( 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 183 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 146 time to evaluate : 0.573 Fit side-chains REVERT: A 86 GLU cc_start: 0.6296 (OUTLIER) cc_final: 0.5292 (tm-30) REVERT: A 152 MET cc_start: 0.7371 (tpt) cc_final: 0.6985 (tpt) REVERT: A 160 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6370 (mp0) REVERT: A 167 GLN cc_start: 0.7624 (OUTLIER) cc_final: 0.6854 (mp10) REVERT: A 201 GLU cc_start: 0.7495 (tp30) cc_final: 0.6848 (tp30) REVERT: B 104 ARG cc_start: 0.8525 (mtt90) cc_final: 0.8311 (mtt90) REVERT: B 110 ARG cc_start: 0.8001 (mtt180) cc_final: 0.7640 (mpt-90) REVERT: B 148 MET cc_start: 0.7493 (mpp) cc_final: 0.7027 (mpp) REVERT: B 170 ASN cc_start: 0.8177 (m-40) cc_final: 0.7710 (t0) REVERT: B 241 MET cc_start: 0.7298 (ttp) cc_final: 0.7031 (ttm) REVERT: B 254 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8502 (mp) REVERT: C 168 GLU cc_start: 0.6917 (pm20) cc_final: 0.6627 (pm20) REVERT: C 368 MET cc_start: 0.8363 (mmt) cc_final: 0.8151 (mmt) REVERT: C 514 PHE cc_start: 0.8871 (OUTLIER) cc_final: 0.8541 (m-80) REVERT: C 617 GLU cc_start: 0.7948 (pt0) cc_final: 0.7337 (pm20) REVERT: C 628 ARG cc_start: 0.8183 (ttm-80) cc_final: 0.7632 (ttm110) REVERT: C 640 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7852 (ttm-80) REVERT: C 705 ARG cc_start: 0.5785 (ttp-170) cc_final: 0.5409 (ttm110) REVERT: C 717 ARG cc_start: 0.7227 (mpt180) cc_final: 0.5472 (mmt180) REVERT: C 778 VAL cc_start: 0.8926 (OUTLIER) cc_final: 0.8684 (t) REVERT: D 97 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7234 (mt) REVERT: D 269 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7596 (mt) REVERT: D 332 MET cc_start: 0.8932 (mmm) cc_final: 0.8682 (mmm) REVERT: D 349 MET cc_start: 0.7736 (OUTLIER) cc_final: 0.6691 (tmm) REVERT: D 540 ILE cc_start: 0.8250 (mm) cc_final: 0.8030 (pt) REVERT: D 571 MET cc_start: 0.9201 (mtp) cc_final: 0.8972 (mtp) REVERT: D 725 HIS cc_start: 0.7253 (m-70) cc_final: 0.6644 (t70) REVERT: D 781 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8646 (mt) outliers start: 37 outliers final: 19 residues processed: 172 average time/residue: 0.7424 time to fit residues: 138.2033 Evaluate side-chains 173 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 167 GLN Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 254 LEU 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 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 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 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 775 ARG Chi-restraints excluded: chain D residue 781 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 155 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 115 optimal weight: 5.9990 chunk 143 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 160 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.134121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.106927 restraints weight = 17115.337| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.42 r_work: 0.3131 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2919 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 : 0.620 12.912 19410 Z= 0.314 Chirality : 0.042 0.228 2265 Planarity : 0.004 0.050 2420 Dihedral : 7.708 78.060 2056 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.51 % Allowed : 13.17 % Favored : 84.32 % 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 aren not related in a simple way. whole: 1.15 (0.21), residues: 1746 helix: 2.20 (0.16), residues: 1113 sheet: -2.04 (1.84), residues: 5 loop : -2.01 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 405 TYR 0.016 0.002 TYR D 505 PHE 0.016 0.002 PHE C 392 TRP 0.020 0.002 TRP D 524 HIS 0.005 0.001 HIS C 658 Details of bonding type rmsd covalent geometry : bond 0.00329 (14253) covalent geometry : angle 0.61489 (19374) SS BOND : bond 0.00147 ( 12) SS BOND : angle 0.68938 ( 24) hydrogen bonds : bond 0.04556 ( 817) hydrogen bonds : angle 3.62294 ( 2388) Misc. bond : bond 0.00370 ( 3) link_BETA1-4 : bond 0.01013 ( 2) link_BETA1-4 : angle 2.77106 ( 6) link_NAG-ASN : bond 0.01532 ( 2) link_NAG-ASN : angle 3.80358 ( 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 184 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 0.495 Fit side-chains REVERT: A 86 GLU cc_start: 0.6305 (OUTLIER) cc_final: 0.5330 (tm-30) REVERT: A 152 MET cc_start: 0.7428 (tpt) cc_final: 0.7049 (tpt) REVERT: A 160 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6397 (mp0) REVERT: A 167 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.6836 (mp10) REVERT: A 201 GLU cc_start: 0.7530 (tp30) cc_final: 0.6914 (tp30) REVERT: B 104 ARG cc_start: 0.8559 (mtt90) cc_final: 0.8346 (mtt90) REVERT: B 110 ARG cc_start: 0.8051 (mtt180) cc_final: 0.7674 (mpt-90) REVERT: B 148 MET cc_start: 0.7514 (mpp) cc_final: 0.7036 (mpp) REVERT: B 170 ASN cc_start: 0.8183 (m-40) cc_final: 0.7723 (t0) REVERT: B 254 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8470 (mp) REVERT: C 168 GLU cc_start: 0.6938 (pm20) cc_final: 0.6638 (pm20) REVERT: C 368 MET cc_start: 0.8525 (mmt) cc_final: 0.8301 (mmt) REVERT: C 514 PHE cc_start: 0.8885 (OUTLIER) cc_final: 0.8539 (m-80) REVERT: C 617 GLU cc_start: 0.7958 (pt0) cc_final: 0.7354 (pm20) REVERT: C 640 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.7916 (ttm-80) REVERT: C 705 ARG cc_start: 0.5835 (ttp-170) cc_final: 0.5448 (ttm110) REVERT: C 717 ARG cc_start: 0.7248 (mpt180) cc_final: 0.5453 (mmt180) REVERT: C 732 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7936 (mm-30) REVERT: C 778 VAL cc_start: 0.8949 (OUTLIER) cc_final: 0.8686 (t) REVERT: D 97 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7287 (mt) REVERT: D 269 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7633 (mt) REVERT: D 332 MET cc_start: 0.8907 (mmm) cc_final: 0.8663 (mmm) REVERT: D 349 MET cc_start: 0.7746 (OUTLIER) cc_final: 0.6691 (tmm) REVERT: D 540 ILE cc_start: 0.8281 (mm) cc_final: 0.8049 (pt) REVERT: D 725 HIS cc_start: 0.7283 (m-70) cc_final: 0.6645 (t70) REVERT: D 781 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8700 (mt) outliers start: 38 outliers final: 19 residues processed: 172 average time/residue: 0.7749 time to fit residues: 143.9751 Evaluate side-chains 174 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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 167 GLN Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 254 LEU 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 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 261 ILE 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 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 781 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 0.0770 chunk 10 optimal weight: 1.9990 chunk 108 optimal weight: 0.0770 chunk 54 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 134 optimal weight: 0.4980 chunk 29 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 ASN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 607 GLN D 623 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.137556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.110516 restraints weight = 17161.794| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.38 r_work: 0.3188 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14272 Z= 0.110 Angle : 0.574 11.217 19410 Z= 0.288 Chirality : 0.039 0.212 2265 Planarity : 0.004 0.051 2420 Dihedral : 7.327 72.351 2056 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.85 % Allowed : 14.03 % Favored : 84.12 % 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 aren not related in a simple way. whole: 1.41 (0.21), residues: 1746 helix: 2.43 (0.16), residues: 1109 sheet: -2.09 (1.89), residues: 5 loop : -1.96 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 271 TYR 0.010 0.001 TYR C 715 PHE 0.014 0.001 PHE C 392 TRP 0.025 0.001 TRP C 524 HIS 0.004 0.001 HIS C 658 Details of bonding type rmsd covalent geometry : bond 0.00231 (14253) covalent geometry : angle 0.57018 (19374) SS BOND : bond 0.00114 ( 12) SS BOND : angle 0.61564 ( 24) hydrogen bonds : bond 0.03772 ( 817) hydrogen bonds : angle 3.50000 ( 2388) Misc. bond : bond 0.00346 ( 3) link_BETA1-4 : bond 0.00652 ( 2) link_BETA1-4 : angle 2.66105 ( 6) link_NAG-ASN : bond 0.01162 ( 2) link_NAG-ASN : angle 3.03343 ( 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 180 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.520 Fit side-chains REVERT: A 86 GLU cc_start: 0.6251 (OUTLIER) cc_final: 0.5113 (tm-30) REVERT: A 152 MET cc_start: 0.7416 (tpt) cc_final: 0.7056 (tpt) REVERT: A 160 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6394 (mp0) REVERT: A 201 GLU cc_start: 0.7514 (tp30) cc_final: 0.7071 (tp30) REVERT: B 110 ARG cc_start: 0.7929 (mtt180) cc_final: 0.7665 (mpt-90) REVERT: B 148 MET cc_start: 0.7463 (mpp) cc_final: 0.6985 (mpp) REVERT: B 170 ASN cc_start: 0.8173 (m-40) cc_final: 0.7706 (t0) REVERT: C 105 GLN cc_start: 0.8207 (tp40) cc_final: 0.7872 (tp40) REVERT: C 168 GLU cc_start: 0.6823 (pm20) cc_final: 0.6547 (pm20) REVERT: C 514 PHE cc_start: 0.8794 (OUTLIER) cc_final: 0.8509 (m-80) REVERT: C 599 GLU cc_start: 0.7820 (mp0) cc_final: 0.7583 (pm20) REVERT: C 617 GLU cc_start: 0.7910 (pt0) cc_final: 0.7341 (pm20) REVERT: C 628 ARG cc_start: 0.8148 (ttm-80) cc_final: 0.7627 (ttm110) REVERT: C 640 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.7804 (ttm-80) REVERT: C 705 ARG cc_start: 0.5775 (ttp-170) cc_final: 0.5359 (ttm110) REVERT: C 717 ARG cc_start: 0.7122 (mpt180) cc_final: 0.5372 (mmt180) REVERT: C 732 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7956 (mm-30) REVERT: C 786 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.8023 (p0) REVERT: D 97 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7236 (mt) REVERT: D 269 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7603 (mt) REVERT: D 540 ILE cc_start: 0.8163 (mm) cc_final: 0.7956 (pt) REVERT: D 725 HIS cc_start: 0.7307 (m-70) cc_final: 0.6669 (t70) REVERT: D 781 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8605 (mt) outliers start: 28 outliers final: 13 residues processed: 170 average time/residue: 0.7468 time to fit residues: 136.9652 Evaluate side-chains 167 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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 220 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 254 LEU 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 786 ASP Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 216 VAL 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 663 VAL 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: 0.8980 chunk 164 optimal weight: 0.1980 chunk 94 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 135 optimal weight: 0.7980 chunk 74 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 161 optimal weight: 8.9990 chunk 86 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 82 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 ASN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 607 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.137071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.109892 restraints weight = 17001.049| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.44 r_work: 0.3176 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3096 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 : 0.600 16.973 19410 Z= 0.298 Chirality : 0.040 0.220 2265 Planarity : 0.004 0.050 2420 Dihedral : 7.328 73.450 2056 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 1.65 % Allowed : 14.36 % Favored : 83.98 % 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 aren not related in a simple way. whole: 1.44 (0.21), residues: 1746 helix: 2.46 (0.16), residues: 1110 sheet: -1.87 (1.92), residues: 5 loop : -1.96 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 405 TYR 0.012 0.001 TYR C 505 PHE 0.014 0.001 PHE C 392 TRP 0.023 0.002 TRP C 524 HIS 0.004 0.001 HIS C 658 Details of bonding type rmsd covalent geometry : bond 0.00255 (14253) covalent geometry : angle 0.59603 (19374) SS BOND : bond 0.00116 ( 12) SS BOND : angle 0.61003 ( 24) hydrogen bonds : bond 0.03955 ( 817) hydrogen bonds : angle 3.48619 ( 2388) Misc. bond : bond 0.00450 ( 3) link_BETA1-4 : bond 0.00992 ( 2) link_BETA1-4 : angle 2.51927 ( 6) link_NAG-ASN : bond 0.01271 ( 2) link_NAG-ASN : angle 3.33232 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5436.11 seconds wall clock time: 93 minutes 14.63 seconds (5594.63 seconds total)