Starting phenix.real_space_refine on Wed Aug 27 00:16:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lr0_23493/08_2025/7lr0_23493_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lr0_23493/08_2025/7lr0_23493.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lr0_23493/08_2025/7lr0_23493_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lr0_23493/08_2025/7lr0_23493_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lr0_23493/08_2025/7lr0_23493.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lr0_23493/08_2025/7lr0_23493.map" } resolution = 3.81 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= 0.015 sd= 0.095 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: 7 Type Number sf(0) Gaussians P 20 5.49 5 S 124 5.16 5 Na 1 4.78 5 C 14364 2.51 5 N 3440 2.21 5 O 3964 1.98 5 H 20936 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 42849 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 10445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 10445 Classifications: {'peptide': 646} Link IDs: {'PTRANS': 17, 'TRANS': 628} Chain breaks: 1 Chain: "B" Number of atoms: 10445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 10445 Classifications: {'peptide': 646} Link IDs: {'PTRANS': 17, 'TRANS': 628} Chain breaks: 1 Chain: "C" Number of atoms: 10445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 10445 Classifications: {'peptide': 646} Link IDs: {'PTRANS': 17, 'TRANS': 628} Chain breaks: 1 Chain: "D" Number of atoms: 10445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 10445 Classifications: {'peptide': 646} Link IDs: {'PTRANS': 17, 'TRANS': 628} Chain breaks: 1 Chain: "A" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 312 Unusual residues: {' NA': 1, '4DY': 1, 'POV': 8} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-2': 2, 'POV:plan-3': 2, 'POV:plan-1': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 267 Unusual residues: {'4DY': 1, 'POV': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-2': 2, 'POV:plan-3': 2, 'POV:plan-1': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 267 Unusual residues: {'4DY': 1, 'POV': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-2': 2, 'POV:plan-3': 2, 'POV:plan-1': 1} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 223 Unusual residues: {'4DY': 1, 'POV': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-2': 2, 'POV:plan-3': 2, 'POV:plan-1': 1} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 8.33, per 1000 atoms: 0.19 Number of scatterers: 42849 At special positions: 0 Unit cell: (131.97, 131.97, 118.69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 124 16.00 P 20 15.00 Na 1 11.00 O 3964 8.00 N 3440 7.00 C 14364 6.00 H 20936 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=0, symmetry=0 Time building additional restraints: 4.30 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 238.4 nanoseconds 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4888 Finding SS restraints... Secondary structure from input PDB file: 121 helices and 8 sheets defined 61.9% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 115 through 126 removed outlier: 3.561A pdb=" N ALA A 124 " --> pdb=" O PHE A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 141 Processing helix chain 'A' and resid 147 through 151 removed outlier: 3.846A pdb=" N LYS A 151 " --> pdb=" O SER A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 166 Processing helix chain 'A' and resid 167 through 171 Processing helix chain 'A' and resid 173 through 185 removed outlier: 3.526A pdb=" N ALA A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 193 Processing helix chain 'A' and resid 205 through 213 Processing helix chain 'A' and resid 215 through 226 Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 262 through 272 Processing helix chain 'A' and resid 288 through 297 removed outlier: 3.513A pdb=" N GLU A 295 " --> pdb=" O HIS A 291 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 322 removed outlier: 3.503A pdb=" N THR A 308 " --> pdb=" O THR A 304 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU A 315 " --> pdb=" O TYR A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 330 Processing helix chain 'A' and resid 337 through 346 Processing helix chain 'A' and resid 347 through 356 removed outlier: 3.533A pdb=" N LEU A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 404 removed outlier: 3.669A pdb=" N ALA A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR A 403 " --> pdb=" O GLU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 415 removed outlier: 3.918A pdb=" N LEU A 415 " --> pdb=" O ARG A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 430 removed outlier: 3.500A pdb=" N GLN A 425 " --> pdb=" O ASN A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 456 Processing helix chain 'A' and resid 470 through 499 removed outlier: 3.765A pdb=" N TYR A 489 " --> pdb=" O SER A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 512 removed outlier: 3.655A pdb=" N VAL A 510 " --> pdb=" O LYS A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 534 removed outlier: 3.904A pdb=" N MET A 516 " --> pdb=" O SER A 512 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 517 " --> pdb=" O TYR A 513 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER A 522 " --> pdb=" O PHE A 518 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL A 530 " --> pdb=" O LEU A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 555 removed outlier: 3.510A pdb=" N SER A 542 " --> pdb=" O GLU A 538 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 555 " --> pdb=" O TRP A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 558 No H-bonds generated for 'chain 'A' and resid 556 through 558' Processing helix chain 'A' and resid 561 through 573 removed outlier: 4.072A pdb=" N TYR A 567 " --> pdb=" O GLN A 563 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE A 571 " --> pdb=" O TYR A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 601 removed outlier: 3.642A pdb=" N VAL A 588 " --> pdb=" O PHE A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 645 removed outlier: 4.314A pdb=" N THR A 643 " --> pdb=" O LEU A 639 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 644 " --> pdb=" O PHE A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 688 removed outlier: 3.853A pdb=" N LEU A 665 " --> pdb=" O PHE A 661 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 680 " --> pdb=" O LEU A 676 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU A 683 " --> pdb=" O MET A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 714 removed outlier: 3.526A pdb=" N LYS A 696 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR A 706 " --> pdb=" O GLN A 702 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE A 714 " --> pdb=" O THR A 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 126 removed outlier: 3.561A pdb=" N ALA B 124 " --> pdb=" O PHE B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 141 Processing helix chain 'B' and resid 147 through 151 removed outlier: 3.845A pdb=" N LYS B 151 " --> pdb=" O SER B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 166 Processing helix chain 'B' and resid 167 through 171 Processing helix chain 'B' and resid 173 through 185 removed outlier: 3.525A pdb=" N ALA B 182 " --> pdb=" O LEU B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 193 Processing helix chain 'B' and resid 205 through 213 Processing helix chain 'B' and resid 215 through 226 Processing helix chain 'B' and resid 252 through 259 Processing helix chain 'B' and resid 262 through 272 Processing helix chain 'B' and resid 288 through 297 removed outlier: 3.513A pdb=" N GLU B 295 " --> pdb=" O HIS B 291 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 322 removed outlier: 3.503A pdb=" N THR B 308 " --> pdb=" O THR B 304 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER B 309 " --> pdb=" O LYS B 305 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU B 315 " --> pdb=" O TYR B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 330 Processing helix chain 'B' and resid 337 through 346 Processing helix chain 'B' and resid 347 through 356 removed outlier: 3.533A pdb=" N LEU B 355 " --> pdb=" O LEU B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 404 removed outlier: 3.670A pdb=" N ALA B 402 " --> pdb=" O LEU B 398 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR B 403 " --> pdb=" O GLU B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 415 removed outlier: 3.918A pdb=" N LEU B 415 " --> pdb=" O ARG B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 430 Processing helix chain 'B' and resid 432 through 456 Processing helix chain 'B' and resid 470 through 499 removed outlier: 3.766A pdb=" N TYR B 489 " --> pdb=" O SER B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 512 removed outlier: 3.655A pdb=" N VAL B 510 " --> pdb=" O LYS B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 534 removed outlier: 3.903A pdb=" N MET B 516 " --> pdb=" O SER B 512 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU B 517 " --> pdb=" O TYR B 513 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B 522 " --> pdb=" O PHE B 518 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL B 530 " --> pdb=" O LEU B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 555 removed outlier: 3.511A pdb=" N SER B 542 " --> pdb=" O GLU B 538 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU B 555 " --> pdb=" O TRP B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 558 No H-bonds generated for 'chain 'B' and resid 556 through 558' Processing helix chain 'B' and resid 561 through 573 removed outlier: 4.073A pdb=" N TYR B 567 " --> pdb=" O GLN B 563 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE B 571 " --> pdb=" O TYR B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 601 removed outlier: 3.641A pdb=" N VAL B 588 " --> pdb=" O PHE B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 645 removed outlier: 4.315A pdb=" N THR B 643 " --> pdb=" O LEU B 639 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE B 644 " --> pdb=" O PHE B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 688 removed outlier: 3.853A pdb=" N LEU B 665 " --> pdb=" O PHE B 661 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU B 680 " --> pdb=" O LEU B 676 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU B 683 " --> pdb=" O MET B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 714 removed outlier: 3.526A pdb=" N LYS B 696 " --> pdb=" O ALA B 692 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR B 706 " --> pdb=" O GLN B 702 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE B 714 " --> pdb=" O THR B 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 126 removed outlier: 3.561A pdb=" N ALA C 124 " --> pdb=" O PHE C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 132 removed outlier: 3.634A pdb=" N GLU C 132 " --> pdb=" O GLN C 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 129 through 132' Processing helix chain 'C' and resid 133 through 141 Processing helix chain 'C' and resid 147 through 151 removed outlier: 3.845A pdb=" N LYS C 151 " --> pdb=" O SER C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 166 Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 173 through 185 removed outlier: 3.526A pdb=" N ALA C 182 " --> pdb=" O LEU C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 193 Processing helix chain 'C' and resid 205 through 213 Processing helix chain 'C' and resid 215 through 226 Processing helix chain 'C' and resid 252 through 259 Processing helix chain 'C' and resid 262 through 272 Processing helix chain 'C' and resid 288 through 297 removed outlier: 3.513A pdb=" N GLU C 295 " --> pdb=" O HIS C 291 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 322 removed outlier: 3.503A pdb=" N THR C 308 " --> pdb=" O THR C 304 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER C 309 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU C 315 " --> pdb=" O TYR C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 330 Processing helix chain 'C' and resid 337 through 346 Processing helix chain 'C' and resid 347 through 356 removed outlier: 3.532A pdb=" N LEU C 355 " --> pdb=" O LEU C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 404 removed outlier: 3.669A pdb=" N ALA C 402 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR C 403 " --> pdb=" O GLU C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 415 removed outlier: 3.500A pdb=" N MET C 414 " --> pdb=" O ASN C 410 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU C 415 " --> pdb=" O ARG C 411 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 410 through 415' Processing helix chain 'C' and resid 417 through 430 Processing helix chain 'C' and resid 432 through 456 Processing helix chain 'C' and resid 470 through 499 removed outlier: 3.766A pdb=" N TYR C 489 " --> pdb=" O SER C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 512 removed outlier: 3.654A pdb=" N VAL C 510 " --> pdb=" O LYS C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 534 removed outlier: 3.903A pdb=" N MET C 516 " --> pdb=" O SER C 512 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU C 517 " --> pdb=" O TYR C 513 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER C 522 " --> pdb=" O PHE C 518 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL C 530 " --> pdb=" O LEU C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 555 removed outlier: 3.510A pdb=" N SER C 542 " --> pdb=" O GLU C 538 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU C 555 " --> pdb=" O TRP C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 558 No H-bonds generated for 'chain 'C' and resid 556 through 558' Processing helix chain 'C' and resid 561 through 573 removed outlier: 4.073A pdb=" N TYR C 567 " --> pdb=" O GLN C 563 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE C 571 " --> pdb=" O TYR C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 601 removed outlier: 3.642A pdb=" N VAL C 588 " --> pdb=" O PHE C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 645 removed outlier: 4.314A pdb=" N THR C 643 " --> pdb=" O LEU C 639 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE C 644 " --> pdb=" O PHE C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 688 removed outlier: 3.853A pdb=" N LEU C 665 " --> pdb=" O PHE C 661 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU C 680 " --> pdb=" O LEU C 676 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU C 683 " --> pdb=" O MET C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 714 removed outlier: 3.525A pdb=" N LYS C 696 " --> pdb=" O ALA C 692 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR C 706 " --> pdb=" O GLN C 702 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE C 714 " --> pdb=" O THR C 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 126 removed outlier: 3.561A pdb=" N ALA D 124 " --> pdb=" O PHE D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 141 Processing helix chain 'D' and resid 147 through 151 removed outlier: 3.846A pdb=" N LYS D 151 " --> pdb=" O SER D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 166 Processing helix chain 'D' and resid 167 through 171 Processing helix chain 'D' and resid 173 through 185 removed outlier: 3.525A pdb=" N ALA D 182 " --> pdb=" O LEU D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 193 Processing helix chain 'D' and resid 205 through 213 Processing helix chain 'D' and resid 215 through 226 Processing helix chain 'D' and resid 252 through 259 Processing helix chain 'D' and resid 262 through 272 Processing helix chain 'D' and resid 288 through 297 removed outlier: 3.513A pdb=" N GLU D 295 " --> pdb=" O HIS D 291 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 322 removed outlier: 3.503A pdb=" N THR D 308 " --> pdb=" O THR D 304 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER D 309 " --> pdb=" O LYS D 305 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU D 315 " --> pdb=" O TYR D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 330 Processing helix chain 'D' and resid 337 through 346 Processing helix chain 'D' and resid 347 through 356 removed outlier: 3.533A pdb=" N LEU D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 404 removed outlier: 3.669A pdb=" N ALA D 402 " --> pdb=" O LEU D 398 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR D 403 " --> pdb=" O GLU D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 415 removed outlier: 3.917A pdb=" N LEU D 415 " --> pdb=" O ARG D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 430 Processing helix chain 'D' and resid 432 through 456 Processing helix chain 'D' and resid 470 through 499 removed outlier: 3.766A pdb=" N TYR D 489 " --> pdb=" O SER D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 512 removed outlier: 3.654A pdb=" N VAL D 510 " --> pdb=" O LYS D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 534 removed outlier: 3.904A pdb=" N MET D 516 " --> pdb=" O SER D 512 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU D 517 " --> pdb=" O TYR D 513 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER D 522 " --> pdb=" O PHE D 518 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL D 530 " --> pdb=" O LEU D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 555 removed outlier: 3.510A pdb=" N SER D 542 " --> pdb=" O GLU D 538 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU D 555 " --> pdb=" O TRP D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 558 No H-bonds generated for 'chain 'D' and resid 556 through 558' Processing helix chain 'D' and resid 561 through 573 removed outlier: 4.072A pdb=" N TYR D 567 " --> pdb=" O GLN D 563 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE D 571 " --> pdb=" O TYR D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 601 removed outlier: 3.642A pdb=" N VAL D 588 " --> pdb=" O PHE D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 645 removed outlier: 4.315A pdb=" N THR D 643 " --> pdb=" O LEU D 639 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE D 644 " --> pdb=" O PHE D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 688 removed outlier: 3.852A pdb=" N LEU D 665 " --> pdb=" O PHE D 661 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU D 680 " --> pdb=" O LEU D 676 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU D 683 " --> pdb=" O MET D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 714 removed outlier: 3.525A pdb=" N LYS D 696 " --> pdb=" O ALA D 692 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR D 706 " --> pdb=" O GLN D 702 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE D 714 " --> pdb=" O THR D 710 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 371 through 372 removed outlier: 4.086A pdb=" N PHE A 371 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N HIS A 380 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 728 through 732 removed outlier: 3.571A pdb=" N LEU A 728 " --> pdb=" O ARG A 741 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL A 730 " --> pdb=" O ASP A 739 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASP A 739 " --> pdb=" O VAL A 730 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 371 through 372 removed outlier: 4.086A pdb=" N PHE B 371 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N HIS B 380 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 728 through 732 removed outlier: 3.572A pdb=" N LEU B 728 " --> pdb=" O ARG B 741 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL B 730 " --> pdb=" O ASP B 739 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASP B 739 " --> pdb=" O VAL B 730 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 371 through 372 removed outlier: 4.086A pdb=" N PHE C 371 " --> pdb=" O LEU C 383 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS C 380 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 728 through 732 removed outlier: 3.572A pdb=" N LEU C 728 " --> pdb=" O ARG C 741 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL C 730 " --> pdb=" O ASP C 739 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASP C 739 " --> pdb=" O VAL C 730 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 371 through 372 removed outlier: 4.085A pdb=" N PHE D 371 " --> pdb=" O LEU D 383 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS D 380 " --> pdb=" O GLU D 748 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 728 through 732 removed outlier: 3.571A pdb=" N LEU D 728 " --> pdb=" O ARG D 741 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL D 730 " --> pdb=" O ASP D 739 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ASP D 739 " --> pdb=" O VAL D 730 " (cutoff:3.500A) 1034 hydrogen bonds defined for protein. 3042 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: 8.70 Time building geometry restraints manager: 5.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 20888 1.02 - 1.22: 95 1.22 - 1.42: 9231 1.42 - 1.62: 12822 1.62 - 1.82: 240 Bond restraints: 43276 Sorted by residual: bond pdb=" C31 POV A 909 " pdb=" O31 POV A 909 " ideal model delta sigma weight residual 1.327 1.407 -0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" C31 POV A 901 " pdb=" O31 POV A 901 " ideal model delta sigma weight residual 1.327 1.406 -0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" C31 POV B 901 " pdb=" O31 POV B 901 " ideal model delta sigma weight residual 1.327 1.405 -0.078 2.00e-02 2.50e+03 1.54e+01 bond pdb=" C31 POV C 901 " pdb=" O31 POV C 901 " ideal model delta sigma weight residual 1.327 1.404 -0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" C31 POV B 907 " pdb=" O31 POV B 907 " ideal model delta sigma weight residual 1.327 1.402 -0.075 2.00e-02 2.50e+03 1.41e+01 ... (remaining 43271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 75432 2.74 - 5.47: 1729 5.47 - 8.21: 179 8.21 - 10.94: 52 10.94 - 13.68: 36 Bond angle restraints: 77428 Sorted by residual: angle pdb=" N PRO B 463 " pdb=" CA PRO B 463 " pdb=" C PRO B 463 " ideal model delta sigma weight residual 110.70 117.36 -6.66 1.22e+00 6.72e-01 2.98e+01 angle pdb=" N PRO D 463 " pdb=" CA PRO D 463 " pdb=" C PRO D 463 " ideal model delta sigma weight residual 110.70 117.34 -6.64 1.22e+00 6.72e-01 2.96e+01 angle pdb=" N PRO A 463 " pdb=" CA PRO A 463 " pdb=" C PRO A 463 " ideal model delta sigma weight residual 110.70 117.33 -6.63 1.22e+00 6.72e-01 2.96e+01 angle pdb=" N PRO C 463 " pdb=" CA PRO C 463 " pdb=" C PRO C 463 " ideal model delta sigma weight residual 110.70 117.33 -6.63 1.22e+00 6.72e-01 2.95e+01 angle pdb=" CA TYR B 513 " pdb=" C TYR B 513 " pdb=" O TYR B 513 " ideal model delta sigma weight residual 120.82 115.91 4.91 1.05e+00 9.07e-01 2.19e+01 ... (remaining 77423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.55: 19897 30.55 - 61.09: 654 61.09 - 91.64: 81 91.64 - 122.19: 12 122.19 - 152.73: 12 Dihedral angle restraints: 20656 sinusoidal: 11404 harmonic: 9252 Sorted by residual: dihedral pdb=" CA GLY B 725 " pdb=" C GLY B 725 " pdb=" N LYS B 726 " pdb=" CA LYS B 726 " ideal model delta harmonic sigma weight residual 180.00 147.90 32.10 0 5.00e+00 4.00e-02 4.12e+01 dihedral pdb=" CA GLY D 725 " pdb=" C GLY D 725 " pdb=" N LYS D 726 " pdb=" CA LYS D 726 " ideal model delta harmonic sigma weight residual 180.00 147.92 32.08 0 5.00e+00 4.00e-02 4.12e+01 dihedral pdb=" CA GLY C 725 " pdb=" C GLY C 725 " pdb=" N LYS C 726 " pdb=" CA LYS C 726 " ideal model delta harmonic sigma weight residual 180.00 147.93 32.07 0 5.00e+00 4.00e-02 4.11e+01 ... (remaining 20653 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2248 0.052 - 0.104: 821 0.104 - 0.156: 151 0.156 - 0.208: 45 0.208 - 0.261: 7 Chirality restraints: 3272 Sorted by residual: chirality pdb=" CA PHE C 431 " pdb=" N PHE C 431 " pdb=" C PHE C 431 " pdb=" CB PHE C 431 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA PHE A 431 " pdb=" N PHE A 431 " pdb=" C PHE A 431 " pdb=" CB PHE A 431 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA PHE D 431 " pdb=" N PHE D 431 " pdb=" C PHE D 431 " pdb=" CB PHE D 431 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 3269 not shown) Planarity restraints: 6196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 4DY A 903 " -0.312 2.00e-02 2.50e+03 2.63e-01 8.65e+02 pdb=" C22 4DY A 903 " 0.084 2.00e-02 2.50e+03 pdb=" C24 4DY A 903 " -0.185 2.00e-02 2.50e+03 pdb=" N21 4DY A 903 " 0.454 2.00e-02 2.50e+03 pdb=" O23 4DY A 903 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 678 " 0.223 2.00e-02 2.50e+03 2.40e-01 8.64e+02 pdb=" CG ASN B 678 " -0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN B 678 " -0.186 2.00e-02 2.50e+03 pdb=" ND2 ASN B 678 " -0.003 2.00e-02 2.50e+03 pdb="HD21 ASN B 678 " -0.361 2.00e-02 2.50e+03 pdb="HD22 ASN B 678 " 0.361 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 4DY D 904 " 0.312 2.00e-02 2.50e+03 2.63e-01 8.64e+02 pdb=" C22 4DY D 904 " -0.083 2.00e-02 2.50e+03 pdb=" C24 4DY D 904 " 0.185 2.00e-02 2.50e+03 pdb=" N21 4DY D 904 " -0.454 2.00e-02 2.50e+03 pdb=" O23 4DY D 904 " 0.040 2.00e-02 2.50e+03 ... (remaining 6193 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 5143 2.26 - 2.84: 98129 2.84 - 3.43: 108918 3.43 - 4.01: 148714 4.01 - 4.60: 234136 Nonbonded interactions: 595040 Sorted by model distance: nonbonded pdb=" OE2 GLU D 418 " pdb="HH12 ARG D 422 " model vdw 1.672 2.450 nonbonded pdb=" OE2 GLU B 418 " pdb="HH12 ARG B 422 " model vdw 1.672 2.450 nonbonded pdb=" OE2 GLU C 418 " pdb="HH12 ARG C 422 " model vdw 1.672 2.450 nonbonded pdb=" OE2 GLU A 418 " pdb="HH12 ARG A 422 " model vdw 1.673 2.450 nonbonded pdb=" OD1 ASP C 298 " pdb="HD21 ASN C 303 " model vdw 1.684 2.450 ... (remaining 595035 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 111 through 778 or (resid 901 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name O11 or name O12 or name O13 or name O14 or \ name O21 or name O22 or name O31 or name O32 or name P or name C210 or name C211 \ or name C212 or name C213 or name C214 or name C215 or name C216 or name C217 o \ r name C218)) or resid 902 or (resid 905 and (name C23 or name C24 or name C25 o \ r name C26 or name C27 or name C28 or name C29)) or (resid 906 through 907 and ( \ name C29 or name C210 or name C211 or name C212 or name C213 or name C214 or nam \ e C215 or name C216 or name C217 or name C218)))) selection = (chain 'B' and (resid 111 through 778 or (resid 901 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name O11 or name O12 or name O13 or name O14 or \ name O21 or name O22 or name O31 or name O32 or name P or name C210 or name C211 \ or name C212 or name C213 or name C214 or name C215 or name C216 or name C217 o \ r name C218)) or resid 902 or (resid 905 and (name C23 or name C24 or name C25 o \ r name C26 or name C27 or name C28 or name C29)) or (resid 906 through 907 and ( \ name C29 or name C210 or name C211 or name C212 or name C213 or name C214 or nam \ e C215 or name C216 or name C217 or name C218)))) selection = (chain 'C' and (resid 111 through 778 or (resid 901 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name O11 or name O12 or name O13 or name O14 or \ name O21 or name O22 or name O31 or name O32 or name P or name C210 or name C211 \ or name C212 or name C213 or name C214 or name C215 or name C216 or name C217 o \ r name C218)) or resid 902 or (resid 905 and (name C23 or name C24 or name C25 o \ r name C26 or name C27 or name C28 or name C29)) or (resid 906 through 907 and ( \ name C29 or name C210 or name C211 or name C212 or name C213 or name C214 or nam \ e C215 or name C216 or name C217 or name C218)))) selection = (chain 'D' and (resid 111 through 901 or (resid 902 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name C38 or name C39 or name O11 or name O12 or \ name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P o \ r name C210 or name C211 or name C212 or name C213 or name C214 or name C215 or \ name C216 or name C217 or name C218 or name C310 or name C311)) or (resid 905 an \ d (name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name \ C29)) or (resid 906 through 907 and (name C29 or name C210 or name C211 or name \ C212 or name C213 or name C214 or name C215 or name C216 or name C217 or name C2 \ 18)))) } 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=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.310 Extract box with map and model: 0.670 Check model and map are aligned: 0.140 Set scattering table: 0.120 Process input model: 38.840 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 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 : 0.013 0.090 22340 Z= 0.582 Angle : 1.332 13.675 30028 Z= 0.664 Chirality : 0.056 0.261 3272 Planarity : 0.012 0.263 3688 Dihedral : 16.166 152.731 8588 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.37 % Favored : 88.32 % Rotamer: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -4.75 (0.13), residues: 2568 helix: -2.85 (0.10), residues: 1428 sheet: -4.41 (0.46), residues: 48 loop : -3.42 (0.17), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 719 TYR 0.019 0.003 TYR D 248 PHE 0.023 0.003 PHE B 651 TRP 0.020 0.003 TRP B 374 HIS 0.007 0.002 HIS D 291 Details of bonding type rmsd covalent geometry : bond 0.01336 (22340) covalent geometry : angle 1.33192 (30028) hydrogen bonds : bond 0.27460 ( 1034) hydrogen bonds : angle 8.95364 ( 3042) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Evaluate side-chains 770 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 770 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ARG cc_start: 0.8771 (pmt170) cc_final: 0.8362 (ttp-170) REVERT: A 218 LEU cc_start: 0.9393 (mm) cc_final: 0.9135 (mm) REVERT: A 225 ASN cc_start: 0.8123 (m110) cc_final: 0.7731 (m110) REVERT: A 259 CYS cc_start: 0.8800 (m) cc_final: 0.8480 (t) REVERT: A 304 THR cc_start: 0.9185 (m) cc_final: 0.8814 (p) REVERT: A 407 GLU cc_start: 0.8298 (mt-10) cc_final: 0.7970 (tm-30) REVERT: A 495 ILE cc_start: 0.9133 (mm) cc_final: 0.8494 (mm) REVERT: A 543 MET cc_start: 0.8998 (ttp) cc_final: 0.8718 (ttt) REVERT: A 583 MET cc_start: 0.7677 (mmm) cc_final: 0.7403 (mmt) REVERT: A 591 PHE cc_start: 0.8029 (t80) cc_final: 0.7793 (t80) REVERT: A 723 ARG cc_start: 0.7036 (tpm170) cc_final: 0.6671 (tpm170) REVERT: A 750 ASN cc_start: 0.8528 (t160) cc_final: 0.8073 (t0) REVERT: B 116 ARG cc_start: 0.8836 (pmt170) cc_final: 0.8481 (ttp-170) REVERT: B 240 LYS cc_start: 0.7273 (mtpp) cc_final: 0.6987 (mmmm) REVERT: B 304 THR cc_start: 0.9343 (m) cc_final: 0.8958 (p) REVERT: B 407 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8106 (tm-30) REVERT: B 495 ILE cc_start: 0.9114 (mm) cc_final: 0.8537 (mm) REVERT: B 583 MET cc_start: 0.8068 (mmm) cc_final: 0.7802 (mmp) REVERT: B 723 ARG cc_start: 0.7127 (tpm170) cc_final: 0.6505 (tpm170) REVERT: B 750 ASN cc_start: 0.8544 (t160) cc_final: 0.8095 (t0) REVERT: C 218 LEU cc_start: 0.9275 (mm) cc_final: 0.9041 (mm) REVERT: C 240 LYS cc_start: 0.7269 (mtpp) cc_final: 0.7025 (mmmm) REVERT: C 304 THR cc_start: 0.9406 (m) cc_final: 0.9053 (p) REVERT: C 495 ILE cc_start: 0.9107 (mm) cc_final: 0.8496 (mm) REVERT: C 583 MET cc_start: 0.8008 (mmm) cc_final: 0.7725 (mmp) REVERT: C 723 ARG cc_start: 0.7097 (tpm170) cc_final: 0.6571 (tpm170) REVERT: D 218 LEU cc_start: 0.9291 (mm) cc_final: 0.9053 (mm) REVERT: D 240 LYS cc_start: 0.7280 (mtpp) cc_final: 0.7063 (mmmm) REVERT: D 252 LEU cc_start: 0.9211 (tm) cc_final: 0.8878 (tm) REVERT: D 304 THR cc_start: 0.9401 (m) cc_final: 0.9027 (p) REVERT: D 390 ASP cc_start: 0.8049 (t70) cc_final: 0.7817 (p0) REVERT: D 495 ILE cc_start: 0.9119 (mm) cc_final: 0.8511 (mm) REVERT: D 583 MET cc_start: 0.8127 (mmm) cc_final: 0.7828 (mmp) REVERT: D 723 ARG cc_start: 0.7016 (tpm170) cc_final: 0.6504 (tpm170) REVERT: D 753 THR cc_start: 0.8651 (m) cc_final: 0.8360 (p) outliers start: 0 outliers final: 0 residues processed: 770 average time/residue: 0.4184 time to fit residues: 470.6364 Evaluate side-chains 497 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 497 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 5.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 0.4980 chunk 71 optimal weight: 20.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN A 215 ASN ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 GLN A 291 HIS A 303 ASN ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 654 ASN A 750 ASN B 172 ASN B 215 ASN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 GLN B 291 HIS B 303 ASN ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 654 ASN B 750 ASN C 172 ASN C 215 ASN ** C 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 GLN C 291 HIS C 303 ASN ** C 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 750 ASN D 172 ASN D 215 ASN ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 GLN D 291 HIS D 303 ASN ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 654 ASN D 750 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.167873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.128463 restraints weight = 86560.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.134375 restraints weight = 36564.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.138109 restraints weight = 21776.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.140159 restraints weight = 15857.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.141624 restraints weight = 13204.134| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3508 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3499 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22340 Z= 0.161 Angle : 0.711 8.238 30028 Z= 0.376 Chirality : 0.039 0.135 3272 Planarity : 0.005 0.064 3688 Dihedral : 18.241 145.619 3644 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.92 % Favored : 90.93 % Rotamer: Outliers : 1.22 % Allowed : 10.31 % Favored : 88.46 % 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: -2.82 (0.15), residues: 2568 helix: -0.78 (0.12), residues: 1488 sheet: -4.51 (0.42), residues: 64 loop : -3.37 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 476 TYR 0.018 0.002 TYR B 248 PHE 0.016 0.002 PHE D 519 TRP 0.012 0.002 TRP D 699 HIS 0.013 0.001 HIS A 366 Details of bonding type rmsd covalent geometry : bond 0.00353 (22340) covalent geometry : angle 0.71107 (30028) hydrogen bonds : bond 0.05651 ( 1034) hydrogen bonds : angle 5.05431 ( 3042) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Evaluate side-chains 572 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 544 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 LEU cc_start: 0.9259 (mm) cc_final: 0.9015 (mm) REVERT: A 304 THR cc_start: 0.9135 (m) cc_final: 0.8819 (p) REVERT: A 380 HIS cc_start: 0.8118 (p-80) cc_final: 0.7662 (p-80) REVERT: A 583 MET cc_start: 0.8250 (mmm) cc_final: 0.7745 (mmt) REVERT: A 591 PHE cc_start: 0.8314 (t80) cc_final: 0.8104 (t80) REVERT: A 653 GLU cc_start: 0.7072 (mt-10) cc_final: 0.6834 (tm-30) REVERT: A 723 ARG cc_start: 0.7099 (tpm170) cc_final: 0.6700 (tpm170) REVERT: A 750 ASN cc_start: 0.8561 (t0) cc_final: 0.8002 (t0) REVERT: A 773 ARG cc_start: 0.6222 (ptt90) cc_final: 0.5948 (ptm-80) REVERT: B 304 THR cc_start: 0.9313 (m) cc_final: 0.8981 (p) REVERT: B 311 TYR cc_start: 0.9175 (t80) cc_final: 0.8969 (t80) REVERT: B 500 GLN cc_start: 0.6942 (mp10) cc_final: 0.6625 (mp10) REVERT: B 583 MET cc_start: 0.8395 (mmm) cc_final: 0.7922 (mmp) REVERT: B 591 PHE cc_start: 0.8228 (t80) cc_final: 0.7905 (t80) REVERT: B 723 ARG cc_start: 0.7022 (tpm170) cc_final: 0.6562 (tpm170) REVERT: B 750 ASN cc_start: 0.8551 (t0) cc_final: 0.7989 (t0) REVERT: B 773 ARG cc_start: 0.5846 (ppt170) cc_final: 0.5490 (ptm-80) REVERT: C 304 THR cc_start: 0.9414 (m) cc_final: 0.9100 (p) REVERT: C 591 PHE cc_start: 0.8212 (t80) cc_final: 0.7898 (t80) REVERT: C 723 ARG cc_start: 0.6996 (tpm170) cc_final: 0.6625 (tpm170) REVERT: C 750 ASN cc_start: 0.8515 (t0) cc_final: 0.7968 (t0) REVERT: C 763 GLU cc_start: 0.7970 (tt0) cc_final: 0.7515 (tt0) REVERT: C 773 ARG cc_start: 0.5813 (ppt170) cc_final: 0.5461 (ptm-80) REVERT: D 304 THR cc_start: 0.9428 (m) cc_final: 0.9095 (p) REVERT: D 390 ASP cc_start: 0.7981 (t70) cc_final: 0.7704 (p0) REVERT: D 591 PHE cc_start: 0.8281 (t80) cc_final: 0.8025 (t80) REVERT: D 723 ARG cc_start: 0.7053 (tpm170) cc_final: 0.6628 (tpm170) REVERT: D 750 ASN cc_start: 0.8494 (t0) cc_final: 0.7966 (t0) REVERT: D 773 ARG cc_start: 0.5794 (ppt170) cc_final: 0.5447 (ptm-80) outliers start: 28 outliers final: 17 residues processed: 567 average time/residue: 0.3980 time to fit residues: 341.7187 Evaluate side-chains 469 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 452 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 473 ASP Chi-restraints excluded: chain D residue 631 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 79 optimal weight: 7.9990 chunk 232 optimal weight: 4.9990 chunk 144 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 193 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 252 optimal weight: 9.9990 chunk 180 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 GLN A 303 ASN ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 GLN B 303 ASN ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 ASN ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.168703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.123890 restraints weight = 93892.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.132101 restraints weight = 40028.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.134467 restraints weight = 22263.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.135105 restraints weight = 18259.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.135080 restraints weight = 16629.621| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3240 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 22340 Z= 0.258 Angle : 0.703 8.004 30028 Z= 0.376 Chirality : 0.040 0.187 3272 Planarity : 0.005 0.054 3688 Dihedral : 16.796 145.976 3644 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.50 % Favored : 90.34 % Rotamer: Outliers : 2.19 % Allowed : 13.07 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.31 (0.16), residues: 2568 helix: -0.24 (0.13), residues: 1496 sheet: -3.73 (0.57), residues: 48 loop : -3.47 (0.17), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 116 TYR 0.017 0.002 TYR A 673 PHE 0.017 0.002 PHE A 249 TRP 0.024 0.002 TRP A 374 HIS 0.004 0.001 HIS D 380 Details of bonding type rmsd covalent geometry : bond 0.00586 (22340) covalent geometry : angle 0.70305 (30028) hydrogen bonds : bond 0.05172 ( 1034) hydrogen bonds : angle 4.92904 ( 3042) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Evaluate side-chains 511 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 461 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 ARG cc_start: 0.7803 (mmt180) cc_final: 0.7560 (mmt180) REVERT: A 304 THR cc_start: 0.9228 (m) cc_final: 0.8889 (p) REVERT: A 583 MET cc_start: 0.8543 (mmm) cc_final: 0.8327 (mmp) REVERT: A 591 PHE cc_start: 0.8640 (t80) cc_final: 0.8401 (t80) REVERT: A 653 GLU cc_start: 0.7348 (mt-10) cc_final: 0.6938 (tm-30) REVERT: A 723 ARG cc_start: 0.7349 (tpm170) cc_final: 0.7095 (tpm170) REVERT: A 750 ASN cc_start: 0.8712 (t0) cc_final: 0.7945 (t0) REVERT: A 773 ARG cc_start: 0.6284 (ptt90) cc_final: 0.5938 (ptm-80) REVERT: B 304 THR cc_start: 0.9340 (m) cc_final: 0.9045 (p) REVERT: B 374 TRP cc_start: 0.8667 (p-90) cc_final: 0.8453 (p-90) REVERT: B 523 LEU cc_start: 0.9641 (mp) cc_final: 0.9402 (mm) REVERT: B 591 PHE cc_start: 0.8570 (t80) cc_final: 0.8308 (t80) REVERT: B 723 ARG cc_start: 0.7397 (tpm170) cc_final: 0.6998 (tpm170) REVERT: B 750 ASN cc_start: 0.8579 (t0) cc_final: 0.7926 (t0) REVERT: B 773 ARG cc_start: 0.5887 (ppt170) cc_final: 0.5573 (ptm-80) REVERT: C 236 ASP cc_start: 0.8191 (m-30) cc_final: 0.7949 (m-30) REVERT: C 304 THR cc_start: 0.9315 (m) cc_final: 0.9057 (p) REVERT: C 407 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8191 (tm-30) REVERT: C 523 LEU cc_start: 0.9661 (mp) cc_final: 0.9417 (mm) REVERT: C 591 PHE cc_start: 0.8594 (t80) cc_final: 0.8348 (t80) REVERT: C 723 ARG cc_start: 0.7401 (tpm170) cc_final: 0.7131 (tpm170) REVERT: C 750 ASN cc_start: 0.8595 (t0) cc_final: 0.7921 (t0) REVERT: C 763 GLU cc_start: 0.7984 (tt0) cc_final: 0.7594 (tt0) REVERT: C 773 ARG cc_start: 0.5850 (ppt170) cc_final: 0.5365 (ptm-80) REVERT: D 236 ASP cc_start: 0.8213 (m-30) cc_final: 0.7961 (m-30) REVERT: D 304 THR cc_start: 0.9328 (m) cc_final: 0.9067 (p) REVERT: D 591 PHE cc_start: 0.8581 (t80) cc_final: 0.8326 (t80) REVERT: D 723 ARG cc_start: 0.7516 (tpm170) cc_final: 0.7273 (tpm170) REVERT: D 750 ASN cc_start: 0.8617 (t0) cc_final: 0.7962 (t0) REVERT: D 773 ARG cc_start: 0.5753 (ppt170) cc_final: 0.5297 (ptm-80) outliers start: 50 outliers final: 44 residues processed: 489 average time/residue: 0.3850 time to fit residues: 288.8930 Evaluate side-chains 464 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 420 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 311 TYR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 495 ILE Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 311 TYR Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 478 THR Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 495 ILE Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 722 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 71 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 131 optimal weight: 9.9990 chunk 144 optimal weight: 6.9990 chunk 68 optimal weight: 20.0000 chunk 128 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 138 optimal weight: 7.9990 chunk 108 optimal weight: 0.9980 chunk 210 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 ASN ** D 500 GLN ** 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 = 0.4013 r_free = 0.4013 target = 0.172375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.129329 restraints weight = 93896.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.135974 restraints weight = 41888.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.138290 restraints weight = 23880.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.139002 restraints weight = 18879.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.139219 restraints weight = 18228.368| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3261 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3261 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.5192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22340 Z= 0.144 Angle : 0.597 7.977 30028 Z= 0.316 Chirality : 0.036 0.133 3272 Planarity : 0.004 0.050 3688 Dihedral : 15.774 137.699 3644 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.38 % Favored : 90.46 % Rotamer: Outliers : 2.23 % Allowed : 13.46 % Favored : 84.31 % 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: -1.89 (0.16), residues: 2568 helix: 0.16 (0.13), residues: 1516 sheet: -3.36 (0.61), residues: 48 loop : -3.48 (0.17), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 476 TYR 0.012 0.001 TYR A 353 PHE 0.016 0.001 PHE A 657 TRP 0.015 0.002 TRP A 374 HIS 0.008 0.001 HIS A 380 Details of bonding type rmsd covalent geometry : bond 0.00323 (22340) covalent geometry : angle 0.59704 (30028) hydrogen bonds : bond 0.04328 ( 1034) hydrogen bonds : angle 4.49667 ( 3042) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Evaluate side-chains 487 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 436 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.8675 (tpp) cc_final: 0.8266 (tpp) REVERT: A 218 LEU cc_start: 0.9161 (mm) cc_final: 0.8844 (tp) REVERT: A 237 PHE cc_start: 0.8631 (t80) cc_final: 0.8387 (t80) REVERT: A 256 LEU cc_start: 0.9629 (tt) cc_final: 0.9389 (mt) REVERT: A 262 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.7523 (mt0) REVERT: A 268 PHE cc_start: 0.8402 (t80) cc_final: 0.7949 (t80) REVERT: A 304 THR cc_start: 0.9089 (m) cc_final: 0.8806 (p) REVERT: A 549 MET cc_start: 0.8788 (mtm) cc_final: 0.8573 (mtm) REVERT: A 653 GLU cc_start: 0.7286 (mt-10) cc_final: 0.7051 (tm-30) REVERT: A 657 PHE cc_start: 0.8601 (m-80) cc_final: 0.8312 (m-80) REVERT: A 723 ARG cc_start: 0.7297 (tpm170) cc_final: 0.7069 (tpm170) REVERT: A 750 ASN cc_start: 0.8587 (t0) cc_final: 0.7981 (t0) REVERT: A 773 ARG cc_start: 0.6343 (ptt90) cc_final: 0.5959 (ptm-80) REVERT: B 116 ARG cc_start: 0.8846 (pmt170) cc_final: 0.8300 (tmm-80) REVERT: B 164 MET cc_start: 0.8735 (mmm) cc_final: 0.8468 (mmm) REVERT: B 236 ASP cc_start: 0.8181 (m-30) cc_final: 0.7960 (m-30) REVERT: B 304 THR cc_start: 0.9234 (m) cc_final: 0.9005 (p) REVERT: B 523 LEU cc_start: 0.9624 (mp) cc_final: 0.9386 (mm) REVERT: B 591 PHE cc_start: 0.8469 (t80) cc_final: 0.8196 (t80) REVERT: B 723 ARG cc_start: 0.7304 (tpm170) cc_final: 0.6987 (tpm170) REVERT: B 750 ASN cc_start: 0.8575 (t0) cc_final: 0.7935 (t0) REVERT: B 773 ARG cc_start: 0.6014 (ppt170) cc_final: 0.5662 (ptm-80) REVERT: C 236 ASP cc_start: 0.8104 (m-30) cc_final: 0.7847 (m-30) REVERT: C 304 THR cc_start: 0.9307 (m) cc_final: 0.9050 (p) REVERT: C 500 GLN cc_start: 0.7300 (mp10) cc_final: 0.6638 (mp10) REVERT: C 523 LEU cc_start: 0.9623 (mp) cc_final: 0.9367 (mm) REVERT: C 723 ARG cc_start: 0.7276 (tpm170) cc_final: 0.6996 (tpm170) REVERT: C 750 ASN cc_start: 0.8567 (t0) cc_final: 0.7910 (t0) REVERT: C 773 ARG cc_start: 0.5955 (ppt170) cc_final: 0.5600 (ptm-80) REVERT: D 236 ASP cc_start: 0.8135 (m-30) cc_final: 0.7880 (m-30) REVERT: D 304 THR cc_start: 0.9308 (m) cc_final: 0.9053 (p) REVERT: D 501 ARG cc_start: 0.7719 (mmp-170) cc_final: 0.7000 (ptt180) REVERT: D 723 ARG cc_start: 0.7474 (tpm170) cc_final: 0.7226 (tpm170) REVERT: D 773 ARG cc_start: 0.5811 (ppt170) cc_final: 0.5498 (ptm-80) outliers start: 51 outliers final: 41 residues processed: 461 average time/residue: 0.3762 time to fit residues: 267.3330 Evaluate side-chains 445 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 403 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 311 TYR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 495 ILE Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 311 TYR Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 478 THR Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 495 ILE Chi-restraints excluded: chain D residue 691 ILE Chi-restraints excluded: chain D residue 722 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 16 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 117 optimal weight: 0.9980 chunk 3 optimal weight: 20.0000 chunk 46 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 143 optimal weight: 0.0770 chunk 233 optimal weight: 0.8980 chunk 189 optimal weight: 7.9990 chunk 243 optimal weight: 2.9990 overall best weight: 1.5942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.170632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.128557 restraints weight = 93481.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.135081 restraints weight = 37868.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.136833 restraints weight = 22460.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.137479 restraints weight = 17914.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.138097 restraints weight = 17341.782| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3260 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3260 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.5501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 22340 Z= 0.139 Angle : 0.586 8.812 30028 Z= 0.310 Chirality : 0.036 0.142 3272 Planarity : 0.004 0.051 3688 Dihedral : 15.077 129.065 3644 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.07 % Favored : 90.77 % Rotamer: Outliers : 2.32 % Allowed : 14.16 % Favored : 83.52 % 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: -1.57 (0.16), residues: 2568 helix: 0.45 (0.14), residues: 1516 sheet: None (None), residues: 0 loop : -3.46 (0.16), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 502 TYR 0.013 0.001 TYR A 114 PHE 0.019 0.001 PHE D 657 TRP 0.029 0.002 TRP A 374 HIS 0.008 0.001 HIS C 380 Details of bonding type rmsd covalent geometry : bond 0.00311 (22340) covalent geometry : angle 0.58557 (30028) hydrogen bonds : bond 0.04089 ( 1034) hydrogen bonds : angle 4.38828 ( 3042) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Evaluate side-chains 487 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 434 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 PHE cc_start: 0.8534 (t80) cc_final: 0.8252 (t80) REVERT: A 268 PHE cc_start: 0.8417 (t80) cc_final: 0.7829 (t80) REVERT: A 304 THR cc_start: 0.9046 (m) cc_final: 0.8791 (p) REVERT: A 653 GLU cc_start: 0.7069 (mt-10) cc_final: 0.6779 (tm-30) REVERT: A 657 PHE cc_start: 0.8705 (m-80) cc_final: 0.8391 (m-80) REVERT: A 750 ASN cc_start: 0.8586 (t0) cc_final: 0.7976 (t0) REVERT: A 773 ARG cc_start: 0.6318 (ptt90) cc_final: 0.5976 (ptm-80) REVERT: B 116 ARG cc_start: 0.8831 (pmt170) cc_final: 0.8307 (tmm-80) REVERT: B 164 MET cc_start: 0.8749 (mmm) cc_final: 0.8465 (mmm) REVERT: B 236 ASP cc_start: 0.8192 (m-30) cc_final: 0.7934 (m-30) REVERT: B 304 THR cc_start: 0.9238 (m) cc_final: 0.8996 (p) REVERT: B 523 LEU cc_start: 0.9622 (mp) cc_final: 0.9359 (mm) REVERT: B 631 SER cc_start: 0.8689 (t) cc_final: 0.8124 (p) REVERT: B 657 PHE cc_start: 0.8625 (m-80) cc_final: 0.8315 (m-80) REVERT: B 750 ASN cc_start: 0.8585 (t0) cc_final: 0.7961 (t0) REVERT: B 773 ARG cc_start: 0.6144 (ppt170) cc_final: 0.5772 (ptm-80) REVERT: C 236 ASP cc_start: 0.8166 (m-30) cc_final: 0.7872 (m-30) REVERT: C 304 THR cc_start: 0.9283 (m) cc_final: 0.9023 (p) REVERT: C 407 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8195 (tm-30) REVERT: C 500 GLN cc_start: 0.7401 (mp10) cc_final: 0.6803 (mp10) REVERT: C 501 ARG cc_start: 0.7508 (mmp-170) cc_final: 0.6894 (ptt180) REVERT: C 523 LEU cc_start: 0.9626 (mp) cc_final: 0.9367 (mm) REVERT: C 631 SER cc_start: 0.8661 (t) cc_final: 0.8108 (p) REVERT: C 750 ASN cc_start: 0.8587 (t0) cc_final: 0.7891 (t0) REVERT: C 753 THR cc_start: 0.8719 (m) cc_final: 0.8200 (m) REVERT: C 763 GLU cc_start: 0.7992 (tt0) cc_final: 0.7609 (tt0) REVERT: C 773 ARG cc_start: 0.6070 (ppt170) cc_final: 0.5703 (ptm-80) REVERT: D 236 ASP cc_start: 0.8202 (m-30) cc_final: 0.7920 (m-30) REVERT: D 304 THR cc_start: 0.9256 (m) cc_final: 0.8986 (p) REVERT: D 500 GLN cc_start: 0.7438 (mp10) cc_final: 0.6811 (mp10) REVERT: D 501 ARG cc_start: 0.7671 (mmp-170) cc_final: 0.6923 (ptt180) REVERT: D 750 ASN cc_start: 0.8489 (t0) cc_final: 0.7847 (t0) REVERT: D 773 ARG cc_start: 0.5874 (ppt170) cc_final: 0.5557 (ptm-80) outliers start: 53 outliers final: 47 residues processed: 461 average time/residue: 0.3905 time to fit residues: 279.0606 Evaluate side-chains 446 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 399 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 709 ASP Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 311 TYR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 495 ILE Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 311 TYR Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 473 ASP Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 495 ILE Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 691 ILE Chi-restraints excluded: chain D residue 722 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 139 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 164 optimal weight: 0.9990 chunk 159 optimal weight: 3.9990 chunk 208 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 172 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN B 262 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.169595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.124976 restraints weight = 94015.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.133215 restraints weight = 39601.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.135408 restraints weight = 21903.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.136196 restraints weight = 18028.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.136342 restraints weight = 16599.932| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3248 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3248 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.5762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22340 Z= 0.150 Angle : 0.575 8.033 30028 Z= 0.306 Chirality : 0.036 0.181 3272 Planarity : 0.004 0.047 3688 Dihedral : 14.669 120.072 3644 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.38 % Favored : 90.46 % Rotamer: Outliers : 2.19 % Allowed : 15.17 % Favored : 82.65 % 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: -1.31 (0.17), residues: 2568 helix: 0.66 (0.14), residues: 1508 sheet: None (None), residues: 0 loop : -3.32 (0.17), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 723 TYR 0.012 0.001 TYR A 673 PHE 0.019 0.001 PHE A 582 TRP 0.012 0.001 TRP A 374 HIS 0.008 0.001 HIS D 380 Details of bonding type rmsd covalent geometry : bond 0.00334 (22340) covalent geometry : angle 0.57490 (30028) hydrogen bonds : bond 0.03937 ( 1034) hydrogen bonds : angle 4.36270 ( 3042) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Evaluate side-chains 467 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 417 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 THR cc_start: 0.9067 (m) cc_final: 0.8812 (p) REVERT: A 653 GLU cc_start: 0.7106 (mt-10) cc_final: 0.6870 (tm-30) REVERT: A 657 PHE cc_start: 0.8805 (m-80) cc_final: 0.8518 (m-80) REVERT: A 750 ASN cc_start: 0.8644 (t0) cc_final: 0.8084 (t0) REVERT: A 773 ARG cc_start: 0.6357 (ptt90) cc_final: 0.6027 (ptm-80) REVERT: B 116 ARG cc_start: 0.8840 (pmt170) cc_final: 0.8298 (tmm160) REVERT: B 164 MET cc_start: 0.8778 (mmm) cc_final: 0.8574 (mmm) REVERT: B 236 ASP cc_start: 0.8153 (m-30) cc_final: 0.7847 (m-30) REVERT: B 237 PHE cc_start: 0.8686 (t80) cc_final: 0.8405 (t80) REVERT: B 304 THR cc_start: 0.9248 (m) cc_final: 0.9012 (p) REVERT: B 495 ILE cc_start: 0.9149 (tp) cc_final: 0.8173 (tt) REVERT: B 500 GLN cc_start: 0.7728 (mp-120) cc_final: 0.7310 (mp10) REVERT: B 501 ARG cc_start: 0.7585 (mmp-170) cc_final: 0.7326 (mmp80) REVERT: B 523 LEU cc_start: 0.9618 (mp) cc_final: 0.9384 (mm) REVERT: B 631 SER cc_start: 0.8656 (t) cc_final: 0.8129 (p) REVERT: B 657 PHE cc_start: 0.8691 (m-80) cc_final: 0.8361 (m-80) REVERT: B 750 ASN cc_start: 0.8667 (t0) cc_final: 0.8057 (t0) REVERT: B 773 ARG cc_start: 0.6169 (ppt170) cc_final: 0.5804 (ptm-80) REVERT: C 236 ASP cc_start: 0.8164 (m-30) cc_final: 0.7866 (m-30) REVERT: C 304 THR cc_start: 0.9273 (m) cc_final: 0.9013 (p) REVERT: C 348 ILE cc_start: 0.9065 (pt) cc_final: 0.8808 (mt) REVERT: C 407 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8148 (tm-30) REVERT: C 495 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8638 (tp) REVERT: C 500 GLN cc_start: 0.7446 (mp10) cc_final: 0.7127 (mp10) REVERT: C 501 ARG cc_start: 0.7606 (mmp-170) cc_final: 0.6978 (ptt180) REVERT: C 523 LEU cc_start: 0.9626 (mp) cc_final: 0.9368 (mm) REVERT: C 631 SER cc_start: 0.8654 (t) cc_final: 0.8130 (p) REVERT: C 657 PHE cc_start: 0.8668 (m-80) cc_final: 0.8368 (m-80) REVERT: C 750 ASN cc_start: 0.8693 (t0) cc_final: 0.7986 (t0) REVERT: C 753 THR cc_start: 0.8723 (m) cc_final: 0.8228 (m) REVERT: C 763 GLU cc_start: 0.7965 (tt0) cc_final: 0.7632 (tt0) REVERT: C 773 ARG cc_start: 0.6135 (ppt170) cc_final: 0.5779 (ptm-80) REVERT: D 236 ASP cc_start: 0.8194 (m-30) cc_final: 0.7894 (m-30) REVERT: D 304 THR cc_start: 0.9270 (m) cc_final: 0.9011 (p) REVERT: D 407 GLU cc_start: 0.8349 (mt-10) cc_final: 0.8087 (tm-30) REVERT: D 500 GLN cc_start: 0.7412 (mp10) cc_final: 0.6844 (mp10) REVERT: D 501 ARG cc_start: 0.7746 (mmp-170) cc_final: 0.7505 (mmp80) REVERT: D 657 PHE cc_start: 0.8680 (m-80) cc_final: 0.8393 (m-80) REVERT: D 750 ASN cc_start: 0.8527 (t0) cc_final: 0.7877 (t0) REVERT: D 773 ARG cc_start: 0.5860 (ppt170) cc_final: 0.5561 (ptm-80) outliers start: 50 outliers final: 38 residues processed: 444 average time/residue: 0.3850 time to fit residues: 263.7192 Evaluate side-chains 437 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 398 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 709 ASP Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 311 TYR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 473 ASP Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 495 ILE Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 473 ASP Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 691 ILE Chi-restraints excluded: chain D residue 722 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 229 optimal weight: 7.9990 chunk 80 optimal weight: 7.9990 chunk 243 optimal weight: 3.9990 chunk 92 optimal weight: 0.0370 chunk 50 optimal weight: 0.7980 chunk 165 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 115 optimal weight: 2.9990 chunk 247 optimal weight: 1.9990 chunk 131 optimal weight: 20.0000 chunk 36 optimal weight: 9.9990 overall best weight: 1.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.169287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.124684 restraints weight = 93758.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.132804 restraints weight = 39373.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.134865 restraints weight = 22179.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.135564 restraints weight = 18150.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.135764 restraints weight = 17168.669| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3242 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3242 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.5923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22340 Z= 0.146 Angle : 0.570 8.243 30028 Z= 0.302 Chirality : 0.036 0.134 3272 Planarity : 0.004 0.046 3688 Dihedral : 14.448 110.896 3644 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.62 % Favored : 90.23 % Rotamer: Outliers : 2.14 % Allowed : 15.25 % Favored : 82.60 % 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 (0.17), residues: 2568 helix: 0.79 (0.14), residues: 1508 sheet: None (None), residues: 0 loop : -3.22 (0.17), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 502 TYR 0.012 0.001 TYR A 114 PHE 0.014 0.001 PHE D 431 TRP 0.009 0.001 TRP B 699 HIS 0.006 0.001 HIS D 380 Details of bonding type rmsd covalent geometry : bond 0.00326 (22340) covalent geometry : angle 0.57009 (30028) hydrogen bonds : bond 0.03841 ( 1034) hydrogen bonds : angle 4.28000 ( 3042) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Evaluate side-chains 476 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 427 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 THR cc_start: 0.9080 (m) cc_final: 0.8822 (p) REVERT: A 495 ILE cc_start: 0.8961 (OUTLIER) cc_final: 0.8706 (tp) REVERT: A 500 GLN cc_start: 0.7463 (mp10) cc_final: 0.7031 (mp10) REVERT: A 501 ARG cc_start: 0.7690 (mmp-170) cc_final: 0.7434 (mmp80) REVERT: A 653 GLU cc_start: 0.7055 (mt-10) cc_final: 0.6828 (tm-30) REVERT: A 657 PHE cc_start: 0.8805 (m-80) cc_final: 0.8542 (m-80) REVERT: A 750 ASN cc_start: 0.8685 (t0) cc_final: 0.8125 (t0) REVERT: A 773 ARG cc_start: 0.6406 (ptt90) cc_final: 0.6071 (ptm-80) REVERT: B 116 ARG cc_start: 0.8828 (pmt170) cc_final: 0.8273 (tmm160) REVERT: B 236 ASP cc_start: 0.8174 (m-30) cc_final: 0.7856 (m-30) REVERT: B 237 PHE cc_start: 0.8690 (t80) cc_final: 0.8341 (t80) REVERT: B 304 THR cc_start: 0.9233 (m) cc_final: 0.8979 (p) REVERT: B 495 ILE cc_start: 0.9103 (tp) cc_final: 0.8165 (tt) REVERT: B 500 GLN cc_start: 0.7787 (mp-120) cc_final: 0.7352 (mp10) REVERT: B 501 ARG cc_start: 0.7563 (mmp-170) cc_final: 0.6907 (ptt180) REVERT: B 523 LEU cc_start: 0.9622 (mp) cc_final: 0.9361 (mm) REVERT: B 631 SER cc_start: 0.8648 (t) cc_final: 0.8108 (p) REVERT: B 657 PHE cc_start: 0.8736 (m-80) cc_final: 0.8380 (m-80) REVERT: B 750 ASN cc_start: 0.8707 (t0) cc_final: 0.8057 (t0) REVERT: B 753 THR cc_start: 0.8679 (m) cc_final: 0.8194 (m) REVERT: B 773 ARG cc_start: 0.6184 (ppt170) cc_final: 0.5803 (ptm-80) REVERT: C 236 ASP cc_start: 0.8155 (m-30) cc_final: 0.7828 (m-30) REVERT: C 304 THR cc_start: 0.9264 (m) cc_final: 0.9003 (p) REVERT: C 348 ILE cc_start: 0.9071 (pt) cc_final: 0.8827 (mt) REVERT: C 407 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8157 (tm-30) REVERT: C 415 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8910 (mp) REVERT: C 495 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8607 (tp) REVERT: C 500 GLN cc_start: 0.7421 (mp10) cc_final: 0.7073 (mp10) REVERT: C 501 ARG cc_start: 0.7592 (mmp-170) cc_final: 0.6931 (ptt180) REVERT: C 523 LEU cc_start: 0.9616 (mp) cc_final: 0.9364 (mm) REVERT: C 631 SER cc_start: 0.8629 (t) cc_final: 0.8096 (p) REVERT: C 657 PHE cc_start: 0.8751 (m-80) cc_final: 0.8452 (m-80) REVERT: C 750 ASN cc_start: 0.8712 (t0) cc_final: 0.8026 (t0) REVERT: C 753 THR cc_start: 0.8718 (m) cc_final: 0.8236 (m) REVERT: C 763 GLU cc_start: 0.7936 (tt0) cc_final: 0.7720 (tt0) REVERT: C 773 ARG cc_start: 0.6151 (ppt170) cc_final: 0.5777 (ptm-80) REVERT: D 236 ASP cc_start: 0.8197 (m-30) cc_final: 0.7883 (m-30) REVERT: D 304 THR cc_start: 0.9255 (m) cc_final: 0.9000 (p) REVERT: D 500 GLN cc_start: 0.7491 (mp10) cc_final: 0.7138 (mp10) REVERT: D 501 ARG cc_start: 0.7818 (mmp-170) cc_final: 0.7574 (mmp80) REVERT: D 657 PHE cc_start: 0.8768 (m-80) cc_final: 0.8518 (m-80) REVERT: D 750 ASN cc_start: 0.8563 (t0) cc_final: 0.7944 (t0) REVERT: D 773 ARG cc_start: 0.5880 (ppt170) cc_final: 0.5569 (ptm-80) outliers start: 49 outliers final: 37 residues processed: 451 average time/residue: 0.3773 time to fit residues: 265.5552 Evaluate side-chains 440 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 400 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 709 ASP Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 473 ASP Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 495 ILE Chi-restraints excluded: chain C residue 516 MET Chi-restraints excluded: chain C residue 549 MET Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 473 ASP Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 516 MET Chi-restraints excluded: chain D residue 722 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 252 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 133 optimal weight: 10.0000 chunk 126 optimal weight: 9.9990 chunk 232 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 50 optimal weight: 0.5980 chunk 39 optimal weight: 6.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.168097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.123499 restraints weight = 94726.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.131531 restraints weight = 39421.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.133653 restraints weight = 22427.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.134350 restraints weight = 18287.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.134519 restraints weight = 17322.141| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3221 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3220 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.6081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22340 Z= 0.163 Angle : 0.590 10.642 30028 Z= 0.311 Chirality : 0.036 0.171 3272 Planarity : 0.004 0.042 3688 Dihedral : 14.358 102.501 3644 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.74 % Favored : 90.11 % Rotamer: Outliers : 2.19 % Allowed : 16.13 % Favored : 81.69 % 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: -1.11 (0.17), residues: 2568 helix: 0.80 (0.14), residues: 1508 sheet: None (None), residues: 0 loop : -3.17 (0.17), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 723 TYR 0.012 0.001 TYR A 114 PHE 0.015 0.001 PHE A 582 TRP 0.009 0.001 TRP D 274 HIS 0.012 0.001 HIS B 380 Details of bonding type rmsd covalent geometry : bond 0.00366 (22340) covalent geometry : angle 0.59044 (30028) hydrogen bonds : bond 0.03913 ( 1034) hydrogen bonds : angle 4.33794 ( 3042) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Evaluate side-chains 456 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 406 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 PHE cc_start: 0.8577 (t80) cc_final: 0.8229 (t80) REVERT: A 304 THR cc_start: 0.9077 (m) cc_final: 0.8809 (p) REVERT: A 495 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8669 (tp) REVERT: A 500 GLN cc_start: 0.7542 (mp10) cc_final: 0.7112 (mp10) REVERT: A 501 ARG cc_start: 0.7659 (mmp-170) cc_final: 0.7340 (mmp80) REVERT: A 653 GLU cc_start: 0.7109 (mt-10) cc_final: 0.6828 (tm-30) REVERT: A 657 PHE cc_start: 0.8865 (m-80) cc_final: 0.8599 (m-80) REVERT: A 750 ASN cc_start: 0.8705 (t0) cc_final: 0.8151 (t0) REVERT: A 773 ARG cc_start: 0.6422 (ptt90) cc_final: 0.6076 (ptm-80) REVERT: B 116 ARG cc_start: 0.8829 (pmt170) cc_final: 0.8267 (tmm-80) REVERT: B 236 ASP cc_start: 0.8165 (m-30) cc_final: 0.7844 (m-30) REVERT: B 304 THR cc_start: 0.9230 (m) cc_final: 0.8970 (p) REVERT: B 495 ILE cc_start: 0.9061 (tp) cc_final: 0.8330 (tt) REVERT: B 500 GLN cc_start: 0.7847 (mp-120) cc_final: 0.7463 (mp10) REVERT: B 501 ARG cc_start: 0.7541 (mmp-170) cc_final: 0.6853 (ptt180) REVERT: B 523 LEU cc_start: 0.9627 (mp) cc_final: 0.9369 (mm) REVERT: B 631 SER cc_start: 0.8659 (t) cc_final: 0.8098 (p) REVERT: B 657 PHE cc_start: 0.8819 (m-80) cc_final: 0.8486 (m-80) REVERT: B 750 ASN cc_start: 0.8745 (t0) cc_final: 0.8077 (t0) REVERT: B 753 THR cc_start: 0.8688 (m) cc_final: 0.8203 (m) REVERT: B 773 ARG cc_start: 0.6224 (ppt170) cc_final: 0.5833 (ptm-80) REVERT: C 116 ARG cc_start: 0.8855 (pmt170) cc_final: 0.8275 (tmm160) REVERT: C 236 ASP cc_start: 0.8201 (m-30) cc_final: 0.7864 (m-30) REVERT: C 304 THR cc_start: 0.9253 (m) cc_final: 0.8993 (p) REVERT: C 348 ILE cc_start: 0.9054 (pt) cc_final: 0.8813 (mt) REVERT: C 407 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8175 (tm-30) REVERT: C 500 GLN cc_start: 0.7486 (mp10) cc_final: 0.7055 (mp10) REVERT: C 501 ARG cc_start: 0.7594 (mmp-170) cc_final: 0.6896 (ptt180) REVERT: C 523 LEU cc_start: 0.9626 (mp) cc_final: 0.9379 (mm) REVERT: C 631 SER cc_start: 0.8631 (t) cc_final: 0.8072 (p) REVERT: C 657 PHE cc_start: 0.8797 (m-80) cc_final: 0.8513 (m-80) REVERT: C 750 ASN cc_start: 0.8752 (t0) cc_final: 0.8102 (t0) REVERT: C 753 THR cc_start: 0.8729 (m) cc_final: 0.8261 (m) REVERT: C 773 ARG cc_start: 0.6193 (ppt170) cc_final: 0.5798 (ptm-80) REVERT: D 164 MET cc_start: 0.8734 (mmm) cc_final: 0.8431 (mmm) REVERT: D 236 ASP cc_start: 0.8236 (m-30) cc_final: 0.7893 (m-30) REVERT: D 304 THR cc_start: 0.9258 (m) cc_final: 0.8995 (p) REVERT: D 500 GLN cc_start: 0.7580 (mp10) cc_final: 0.7177 (mp10) REVERT: D 501 ARG cc_start: 0.7785 (mmp-170) cc_final: 0.7546 (mmp80) REVERT: D 657 PHE cc_start: 0.8811 (m-80) cc_final: 0.8496 (m-80) REVERT: D 750 ASN cc_start: 0.8596 (t0) cc_final: 0.7963 (t0) REVERT: D 773 ARG cc_start: 0.5876 (ppt170) cc_final: 0.5565 (ptm-80) outliers start: 50 outliers final: 41 residues processed: 428 average time/residue: 0.3794 time to fit residues: 252.2204 Evaluate side-chains 434 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 392 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 709 ASP Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 473 ASP Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 546 SER Chi-restraints excluded: chain C residue 549 MET Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 473 ASP Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 722 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 77 optimal weight: 8.9990 chunk 253 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 141 optimal weight: 7.9990 chunk 105 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 182 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 218 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 299 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.157724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.113815 restraints weight = 88933.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.119392 restraints weight = 38877.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.122973 restraints weight = 24014.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.125161 restraints weight = 17975.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.126351 restraints weight = 15145.025| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3233 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3233 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.6214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22340 Z= 0.175 Angle : 0.591 8.394 30028 Z= 0.313 Chirality : 0.037 0.173 3272 Planarity : 0.004 0.046 3688 Dihedral : 14.309 91.906 3644 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.12 % Favored : 89.72 % Rotamer: Outliers : 2.19 % Allowed : 16.43 % Favored : 81.38 % 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: -1.05 (0.17), residues: 2568 helix: 0.83 (0.14), residues: 1508 sheet: None (None), residues: 0 loop : -3.12 (0.17), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 723 TYR 0.012 0.001 TYR B 673 PHE 0.024 0.001 PHE C 582 TRP 0.010 0.001 TRP D 274 HIS 0.009 0.001 HIS B 380 Details of bonding type rmsd covalent geometry : bond 0.00393 (22340) covalent geometry : angle 0.59065 (30028) hydrogen bonds : bond 0.03876 ( 1034) hydrogen bonds : angle 4.34335 ( 3042) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Evaluate side-chains 456 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 406 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 PHE cc_start: 0.8524 (t80) cc_final: 0.8130 (t80) REVERT: A 304 THR cc_start: 0.9095 (m) cc_final: 0.8828 (p) REVERT: A 500 GLN cc_start: 0.7504 (mp10) cc_final: 0.7038 (mp10) REVERT: A 501 ARG cc_start: 0.7741 (mmp-170) cc_final: 0.7423 (mmp80) REVERT: A 653 GLU cc_start: 0.7075 (mt-10) cc_final: 0.6820 (tm-30) REVERT: A 657 PHE cc_start: 0.8824 (m-80) cc_final: 0.8569 (m-80) REVERT: A 684 MET cc_start: 0.6404 (mtm) cc_final: 0.4036 (mtm) REVERT: A 750 ASN cc_start: 0.8751 (t0) cc_final: 0.8255 (t0) REVERT: A 773 ARG cc_start: 0.6478 (ptt90) cc_final: 0.6170 (ptm-80) REVERT: B 116 ARG cc_start: 0.8763 (pmt170) cc_final: 0.8337 (tmm-80) REVERT: B 164 MET cc_start: 0.8708 (mmm) cc_final: 0.8503 (mmm) REVERT: B 236 ASP cc_start: 0.8103 (m-30) cc_final: 0.7827 (m-30) REVERT: B 304 THR cc_start: 0.9234 (m) cc_final: 0.8982 (p) REVERT: B 313 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8350 (mm-30) REVERT: B 495 ILE cc_start: 0.9152 (tp) cc_final: 0.8423 (tt) REVERT: B 500 GLN cc_start: 0.7737 (mp-120) cc_final: 0.7406 (mp10) REVERT: B 501 ARG cc_start: 0.7628 (mmp-170) cc_final: 0.6974 (ptt180) REVERT: B 523 LEU cc_start: 0.9637 (mp) cc_final: 0.9377 (mm) REVERT: B 631 SER cc_start: 0.8637 (t) cc_final: 0.8064 (p) REVERT: B 657 PHE cc_start: 0.8792 (m-80) cc_final: 0.8507 (m-80) REVERT: B 750 ASN cc_start: 0.8807 (t0) cc_final: 0.8205 (t0) REVERT: B 753 THR cc_start: 0.8692 (m) cc_final: 0.8243 (m) REVERT: B 773 ARG cc_start: 0.6294 (ppt170) cc_final: 0.5927 (ptm-80) REVERT: C 116 ARG cc_start: 0.8793 (pmt170) cc_final: 0.8340 (tmm160) REVERT: C 236 ASP cc_start: 0.8102 (m-30) cc_final: 0.7811 (m-30) REVERT: C 237 PHE cc_start: 0.8591 (t80) cc_final: 0.8248 (t80) REVERT: C 304 THR cc_start: 0.9255 (m) cc_final: 0.9001 (p) REVERT: C 348 ILE cc_start: 0.9065 (pt) cc_final: 0.8854 (mt) REVERT: C 407 GLU cc_start: 0.8343 (mt-10) cc_final: 0.8133 (tm-30) REVERT: C 415 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8916 (mp) REVERT: C 500 GLN cc_start: 0.7398 (mp10) cc_final: 0.7001 (mp10) REVERT: C 501 ARG cc_start: 0.7656 (mmp-170) cc_final: 0.6993 (ptt180) REVERT: C 523 LEU cc_start: 0.9649 (mp) cc_final: 0.9394 (mm) REVERT: C 631 SER cc_start: 0.8597 (t) cc_final: 0.8038 (p) REVERT: C 657 PHE cc_start: 0.8765 (m-80) cc_final: 0.8464 (m-80) REVERT: C 750 ASN cc_start: 0.8802 (t0) cc_final: 0.8196 (t0) REVERT: C 753 THR cc_start: 0.8732 (m) cc_final: 0.8307 (m) REVERT: C 773 ARG cc_start: 0.6249 (ppt170) cc_final: 0.5897 (ptm-80) REVERT: D 116 ARG cc_start: 0.8793 (pmt170) cc_final: 0.8364 (tmm160) REVERT: D 236 ASP cc_start: 0.8120 (m-30) cc_final: 0.7827 (m-30) REVERT: D 304 THR cc_start: 0.9259 (m) cc_final: 0.8996 (p) REVERT: D 500 GLN cc_start: 0.7482 (mp10) cc_final: 0.7079 (mp10) REVERT: D 501 ARG cc_start: 0.7826 (mmp-170) cc_final: 0.7094 (ptt180) REVERT: D 657 PHE cc_start: 0.8824 (m-80) cc_final: 0.8521 (m-80) REVERT: D 750 ASN cc_start: 0.8650 (t0) cc_final: 0.8088 (t0) REVERT: D 773 ARG cc_start: 0.5946 (ppt170) cc_final: 0.5652 (ptm-80) outliers start: 50 outliers final: 43 residues processed: 424 average time/residue: 0.3891 time to fit residues: 254.3132 Evaluate side-chains 430 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 386 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 709 ASP Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain B residue 561 PHE Chi-restraints excluded: chain B residue 709 ASP Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 473 ASP Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 546 SER Chi-restraints excluded: chain C residue 549 MET Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 473 ASP Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 709 ASP Chi-restraints excluded: chain D residue 722 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 136 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 174 optimal weight: 0.0470 chunk 190 optimal weight: 5.9990 chunk 139 optimal weight: 4.9990 chunk 185 optimal weight: 0.9990 overall best weight: 2.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.158571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.117239 restraints weight = 88401.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.122681 restraints weight = 36862.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.123719 restraints weight = 22304.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.124843 restraints weight = 19666.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.124727 restraints weight = 17735.532| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.6335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22340 Z= 0.150 Angle : 0.590 13.019 30028 Z= 0.307 Chirality : 0.036 0.136 3272 Planarity : 0.003 0.039 3688 Dihedral : 13.957 88.054 3644 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.85 % Favored : 90.11 % Rotamer: Outliers : 1.92 % Allowed : 16.83 % Favored : 81.25 % 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: -0.92 (0.17), residues: 2568 helix: 0.96 (0.14), residues: 1492 sheet: -2.61 (0.70), residues: 48 loop : -3.05 (0.17), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 723 TYR 0.011 0.001 TYR A 114 PHE 0.021 0.001 PHE D 582 TRP 0.011 0.001 TRP B 274 HIS 0.010 0.001 HIS B 380 Details of bonding type rmsd covalent geometry : bond 0.00337 (22340) covalent geometry : angle 0.59047 (30028) hydrogen bonds : bond 0.03789 ( 1034) hydrogen bonds : angle 4.28708 ( 3042) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Evaluate side-chains 448 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 404 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 PHE cc_start: 0.8518 (t80) cc_final: 0.8108 (t80) REVERT: A 304 THR cc_start: 0.9092 (m) cc_final: 0.8839 (p) REVERT: A 500 GLN cc_start: 0.7525 (mp10) cc_final: 0.7027 (mp10) REVERT: A 501 ARG cc_start: 0.7653 (mmp-170) cc_final: 0.7337 (mmp80) REVERT: A 653 GLU cc_start: 0.7124 (mt-10) cc_final: 0.6862 (tm-30) REVERT: A 657 PHE cc_start: 0.8802 (m-80) cc_final: 0.8560 (m-80) REVERT: A 750 ASN cc_start: 0.8753 (t0) cc_final: 0.8232 (t0) REVERT: A 761 ILE cc_start: 0.8962 (mp) cc_final: 0.8753 (mp) REVERT: A 773 ARG cc_start: 0.6471 (ptt90) cc_final: 0.6145 (ptm-80) REVERT: B 116 ARG cc_start: 0.8830 (pmt170) cc_final: 0.8304 (tmm-80) REVERT: B 236 ASP cc_start: 0.8098 (m-30) cc_final: 0.7788 (m-30) REVERT: B 268 PHE cc_start: 0.8615 (t80) cc_final: 0.8120 (t80) REVERT: B 304 THR cc_start: 0.9220 (m) cc_final: 0.8969 (p) REVERT: B 313 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8326 (mm-30) REVERT: B 495 ILE cc_start: 0.9071 (tp) cc_final: 0.8323 (tt) REVERT: B 500 GLN cc_start: 0.7813 (mp-120) cc_final: 0.7437 (mp10) REVERT: B 501 ARG cc_start: 0.7573 (mmp-170) cc_final: 0.6844 (ptt180) REVERT: B 523 LEU cc_start: 0.9613 (mp) cc_final: 0.9356 (mm) REVERT: B 631 SER cc_start: 0.8631 (t) cc_final: 0.8048 (p) REVERT: B 657 PHE cc_start: 0.8740 (m-80) cc_final: 0.8463 (m-80) REVERT: B 750 ASN cc_start: 0.8820 (t0) cc_final: 0.8188 (t0) REVERT: B 753 THR cc_start: 0.8691 (m) cc_final: 0.8236 (m) REVERT: B 773 ARG cc_start: 0.6285 (ppt170) cc_final: 0.5899 (ptm-80) REVERT: C 116 ARG cc_start: 0.8855 (pmt170) cc_final: 0.8301 (tmm160) REVERT: C 236 ASP cc_start: 0.8135 (m-30) cc_final: 0.7817 (m-30) REVERT: C 237 PHE cc_start: 0.8599 (t80) cc_final: 0.8170 (t80) REVERT: C 304 THR cc_start: 0.9241 (m) cc_final: 0.8991 (p) REVERT: C 348 ILE cc_start: 0.9072 (pt) cc_final: 0.8860 (mt) REVERT: C 407 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8171 (tm-30) REVERT: C 415 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8906 (mp) REVERT: C 500 GLN cc_start: 0.7497 (mp10) cc_final: 0.7125 (mp10) REVERT: C 501 ARG cc_start: 0.7599 (mmp-170) cc_final: 0.6863 (ptt180) REVERT: C 523 LEU cc_start: 0.9623 (mp) cc_final: 0.9357 (mm) REVERT: C 631 SER cc_start: 0.8601 (t) cc_final: 0.8033 (p) REVERT: C 657 PHE cc_start: 0.8763 (m-80) cc_final: 0.8430 (m-80) REVERT: C 684 MET cc_start: 0.6765 (mtm) cc_final: 0.5677 (mtt) REVERT: C 750 ASN cc_start: 0.8810 (t0) cc_final: 0.8183 (t0) REVERT: C 753 THR cc_start: 0.8719 (m) cc_final: 0.8291 (m) REVERT: C 773 ARG cc_start: 0.6253 (ppt170) cc_final: 0.5880 (ptm-80) REVERT: D 116 ARG cc_start: 0.8842 (pmt170) cc_final: 0.8319 (tmm160) REVERT: D 236 ASP cc_start: 0.8156 (m-30) cc_final: 0.7838 (m-30) REVERT: D 237 PHE cc_start: 0.8593 (t80) cc_final: 0.8177 (t80) REVERT: D 304 THR cc_start: 0.9239 (m) cc_final: 0.8990 (p) REVERT: D 500 GLN cc_start: 0.7512 (mp10) cc_final: 0.7095 (mp10) REVERT: D 501 ARG cc_start: 0.7737 (mmp-170) cc_final: 0.6994 (ptt180) REVERT: D 657 PHE cc_start: 0.8815 (m-80) cc_final: 0.8541 (m-80) REVERT: D 750 ASN cc_start: 0.8645 (t0) cc_final: 0.8071 (t0) REVERT: D 761 ILE cc_start: 0.9070 (mp) cc_final: 0.8843 (mp) REVERT: D 773 ARG cc_start: 0.5924 (ppt170) cc_final: 0.5609 (ptm-80) outliers start: 44 outliers final: 39 residues processed: 418 average time/residue: 0.3297 time to fit residues: 213.6041 Evaluate side-chains 430 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 390 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 709 ASP Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 709 ASP Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 473 ASP Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 473 ASP Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 722 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 238 optimal weight: 2.9990 chunk 232 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 191 optimal weight: 0.2980 chunk 32 optimal weight: 2.9990 chunk 252 optimal weight: 8.9990 chunk 228 optimal weight: 2.9990 chunk 233 optimal weight: 2.9990 chunk 253 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 137 optimal weight: 9.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 678 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.159744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.119827 restraints weight = 89354.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.123511 restraints weight = 39947.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.123895 restraints weight = 28766.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.124426 restraints weight = 24314.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.125218 restraints weight = 22335.804| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3233 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3233 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.6429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22340 Z= 0.122 Angle : 0.579 12.181 30028 Z= 0.298 Chirality : 0.036 0.149 3272 Planarity : 0.003 0.046 3688 Dihedral : 13.476 87.245 3644 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.62 % Favored : 90.34 % Rotamer: Outliers : 1.84 % Allowed : 17.44 % Favored : 80.73 % 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: -0.80 (0.17), residues: 2568 helix: 1.00 (0.14), residues: 1508 sheet: -2.46 (0.70), residues: 48 loop : -2.97 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 723 TYR 0.012 0.001 TYR B 655 PHE 0.024 0.001 PHE B 582 TRP 0.012 0.001 TRP B 274 HIS 0.008 0.001 HIS B 380 Details of bonding type rmsd covalent geometry : bond 0.00275 (22340) covalent geometry : angle 0.57892 (30028) hydrogen bonds : bond 0.03665 ( 1034) hydrogen bonds : angle 4.21626 ( 3042) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7922.89 seconds wall clock time: 136 minutes 6.54 seconds (8166.54 seconds total)