Starting phenix.real_space_refine on Sun Oct 12 01:22:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ju6_36660/10_2025/8ju6_36660.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ju6_36660/10_2025/8ju6_36660.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ju6_36660/10_2025/8ju6_36660.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ju6_36660/10_2025/8ju6_36660.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ju6_36660/10_2025/8ju6_36660.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ju6_36660/10_2025/8ju6_36660.map" } resolution = 3.45 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= 0.001 sd= 0.082 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: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 12876 2.51 5 N 3256 2.21 5 O 3500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19732 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 4899 Classifications: {'peptide': 616} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 592} Chain breaks: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 3, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 4899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 4899 Classifications: {'peptide': 616} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 592} Chain breaks: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 3, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "D" Number of atoms: 4899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 4899 Classifications: {'peptide': 616} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 592} Chain breaks: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 3, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "C" Number of atoms: 4899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 4899 Classifications: {'peptide': 616} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 592} Chain breaks: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 3, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'XPW': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'XPW': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'XPW': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'XPW': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.25, per 1000 atoms: 0.27 Number of scatterers: 19732 At special positions: 0 Unit cell: (144.56, 142.48, 116.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 3500 8.00 N 3256 7.00 C 12876 6.00 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: 1.91 Conformation dependent library (CDL) restraints added in 890.5 milliseconds Enol-peptide restraints added in 1.2 microseconds 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4648 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 4 sheets defined 70.7% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 150 through 161 Processing helix chain 'A' and resid 162 through 167 removed outlier: 3.514A pdb=" N ASP A 167 " --> pdb=" O ALA A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 176 Processing helix chain 'A' and resid 182 through 186 Processing helix chain 'A' and resid 193 through 201 Processing helix chain 'A' and resid 208 through 220 removed outlier: 4.472A pdb=" N VAL A 212 " --> pdb=" O ASP A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 228 removed outlier: 3.551A pdb=" N PHE A 226 " --> pdb=" O ASN A 222 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASN A 228 " --> pdb=" O ARG A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 248 Processing helix chain 'A' and resid 250 through 259 Processing helix chain 'A' and resid 275 through 279 removed outlier: 3.872A pdb=" N GLY A 279 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'A' and resid 323 through 331 Processing helix chain 'A' and resid 335 through 357 removed outlier: 4.730A pdb=" N PHE A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS A 344 " --> pdb=" O LYS A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 365 removed outlier: 3.681A pdb=" N VAL A 365 " --> pdb=" O LEU A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 381 Processing helix chain 'A' and resid 382 through 391 removed outlier: 3.692A pdb=" N HIS A 388 " --> pdb=" O GLY A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 403 removed outlier: 3.727A pdb=" N ARG A 400 " --> pdb=" O GLU A 397 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N HIS A 401 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU A 402 " --> pdb=" O THR A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 440 Processing helix chain 'A' and resid 442 through 450 removed outlier: 4.486A pdb=" N HIS A 447 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N GLU A 448 " --> pdb=" O GLU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 466 removed outlier: 4.187A pdb=" N GLU A 457 " --> pdb=" O GLU A 453 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 458 " --> pdb=" O PRO A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 492 removed outlier: 3.679A pdb=" N SER A 470 " --> pdb=" O PHE A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 535 Processing helix chain 'A' and resid 546 through 570 removed outlier: 3.576A pdb=" N ALA A 569 " --> pdb=" O ALA A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 589 removed outlier: 4.258A pdb=" N VAL A 577 " --> pdb=" O ALA A 573 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL A 579 " --> pdb=" O LEU A 575 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N PHE A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 595 removed outlier: 3.745A pdb=" N GLY A 595 " --> pdb=" O PHE A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 612 removed outlier: 4.070A pdb=" N TYR A 602 " --> pdb=" O LEU A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 636 removed outlier: 3.616A pdb=" N LEU A 635 " --> pdb=" O ALA A 631 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 679 removed outlier: 3.537A pdb=" N THR A 668 " --> pdb=" O GLU A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 687 removed outlier: 3.681A pdb=" N SER A 687 " --> pdb=" O GLU A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 720 removed outlier: 3.680A pdb=" N PHE A 695 " --> pdb=" O TYR A 691 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE A 696 " --> pdb=" O PRO A 692 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 697 " --> pdb=" O VAL A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 748 removed outlier: 4.530A pdb=" N LYS A 727 " --> pdb=" O GLY A 723 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS A 730 " --> pdb=" O SER A 726 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N HIS A 731 " --> pdb=" O LYS A 727 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE A 748 " --> pdb=" O ILE A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 756 Processing helix chain 'B' and resid 150 through 161 Processing helix chain 'B' and resid 162 through 167 removed outlier: 3.625A pdb=" N ASP B 167 " --> pdb=" O ALA B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 177 Processing helix chain 'B' and resid 182 through 186 Processing helix chain 'B' and resid 193 through 201 Processing helix chain 'B' and resid 208 through 221 removed outlier: 4.520A pdb=" N VAL B 212 " --> pdb=" O ASP B 208 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY B 221 " --> pdb=" O ALA B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 228 removed outlier: 3.569A pdb=" N PHE B 226 " --> pdb=" O ASN B 222 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASN B 228 " --> pdb=" O ARG B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 248 Processing helix chain 'B' and resid 250 through 259 Processing helix chain 'B' and resid 275 through 279 removed outlier: 3.734A pdb=" N GLY B 279 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 295 Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 323 through 331 Processing helix chain 'B' and resid 335 through 357 removed outlier: 4.661A pdb=" N PHE B 341 " --> pdb=" O GLU B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 365 removed outlier: 3.683A pdb=" N VAL B 365 " --> pdb=" O LEU B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 381 Processing helix chain 'B' and resid 382 through 391 removed outlier: 3.692A pdb=" N HIS B 388 " --> pdb=" O GLY B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 403 removed outlier: 3.503A pdb=" N THR B 399 " --> pdb=" O ASP B 396 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG B 400 " --> pdb=" O GLU B 397 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N HIS B 401 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU B 402 " --> pdb=" O THR B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 440 Processing helix chain 'B' and resid 442 through 450 removed outlier: 4.384A pdb=" N HIS B 447 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N GLU B 448 " --> pdb=" O GLU B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 492 removed outlier: 4.191A pdb=" N GLU B 457 " --> pdb=" O GLU B 453 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU B 458 " --> pdb=" O PRO B 454 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ALA B 468 " --> pdb=" O ARG B 464 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL B 469 " --> pdb=" O LYS B 465 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER B 470 " --> pdb=" O PHE B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 535 removed outlier: 3.588A pdb=" N ASP B 531 " --> pdb=" O THR B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 570 removed outlier: 3.884A pdb=" N GLN B 550 " --> pdb=" O ASP B 546 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU B 551 " --> pdb=" O GLY B 547 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA B 569 " --> pdb=" O ALA B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 589 removed outlier: 3.551A pdb=" N MET B 578 " --> pdb=" O TYR B 574 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL B 579 " --> pdb=" O LEU B 575 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE B 580 " --> pdb=" O ALA B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 595 removed outlier: 3.517A pdb=" N ARG B 594 " --> pdb=" O TYR B 591 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY B 595 " --> pdb=" O PHE B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 612 removed outlier: 3.827A pdb=" N TYR B 602 " --> pdb=" O LEU B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 636 removed outlier: 3.628A pdb=" N SER B 634 " --> pdb=" O SER B 630 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU B 635 " --> pdb=" O ALA B 631 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 636 " --> pdb=" O LEU B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 679 removed outlier: 3.526A pdb=" N THR B 668 " --> pdb=" O GLU B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 687 removed outlier: 4.499A pdb=" N MET B 685 " --> pdb=" O ASP B 682 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER B 687 " --> pdb=" O GLU B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 748 removed outlier: 3.673A pdb=" N PHE B 695 " --> pdb=" O TYR B 691 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 697 " --> pdb=" O VAL B 693 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N THR B 721 " --> pdb=" O LEU B 717 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL B 722 " --> pdb=" O MET B 718 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER B 726 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LYS B 727 " --> pdb=" O GLY B 723 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N HIS B 731 " --> pdb=" O LYS B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 756 Processing helix chain 'D' and resid 150 through 161 Processing helix chain 'D' and resid 163 through 167 removed outlier: 3.516A pdb=" N LEU D 166 " --> pdb=" O THR D 163 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP D 167 " --> pdb=" O ALA D 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 163 through 167' Processing helix chain 'D' and resid 168 through 176 Processing helix chain 'D' and resid 182 through 186 Processing helix chain 'D' and resid 193 through 201 Processing helix chain 'D' and resid 208 through 220 removed outlier: 4.442A pdb=" N VAL D 212 " --> pdb=" O ASP D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 228 removed outlier: 3.518A pdb=" N PHE D 226 " --> pdb=" O ASN D 222 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN D 228 " --> pdb=" O ARG D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 248 Processing helix chain 'D' and resid 250 through 259 Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.821A pdb=" N GLY D 279 " --> pdb=" O LYS D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 295 Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'D' and resid 323 through 332 removed outlier: 3.514A pdb=" N ALA D 332 " --> pdb=" O LEU D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 357 removed outlier: 4.662A pdb=" N PHE D 341 " --> pdb=" O GLU D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 365 removed outlier: 3.680A pdb=" N VAL D 365 " --> pdb=" O LEU D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 381 Processing helix chain 'D' and resid 382 through 391 removed outlier: 3.678A pdb=" N HIS D 388 " --> pdb=" O GLY D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 403 removed outlier: 3.732A pdb=" N LEU D 402 " --> pdb=" O THR D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 440 Processing helix chain 'D' and resid 442 through 450 removed outlier: 4.559A pdb=" N HIS D 447 " --> pdb=" O ILE D 443 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N GLU D 448 " --> pdb=" O GLU D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 492 removed outlier: 4.186A pdb=" N GLU D 457 " --> pdb=" O GLU D 453 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU D 458 " --> pdb=" O PRO D 454 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ALA D 468 " --> pdb=" O ARG D 464 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL D 469 " --> pdb=" O LYS D 465 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER D 470 " --> pdb=" O PHE D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 535 removed outlier: 3.633A pdb=" N ASP D 531 " --> pdb=" O THR D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 570 removed outlier: 4.044A pdb=" N GLN D 550 " --> pdb=" O ASP D 546 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU D 551 " --> pdb=" O GLY D 547 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA D 569 " --> pdb=" O ALA D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 589 removed outlier: 3.693A pdb=" N MET D 578 " --> pdb=" O TYR D 574 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL D 579 " --> pdb=" O LEU D 575 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE D 580 " --> pdb=" O ALA D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 595 removed outlier: 3.528A pdb=" N ARG D 594 " --> pdb=" O TYR D 591 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY D 595 " --> pdb=" O PHE D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 612 removed outlier: 3.758A pdb=" N TYR D 602 " --> pdb=" O LEU D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 613 through 636 removed outlier: 3.811A pdb=" N LEU D 635 " --> pdb=" O ALA D 631 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU D 636 " --> pdb=" O LEU D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 679 Processing helix chain 'D' and resid 683 through 687 removed outlier: 3.756A pdb=" N SER D 687 " --> pdb=" O GLU D 684 " (cutoff:3.500A) Processing helix chain 'D' and resid 691 through 748 removed outlier: 3.613A pdb=" N PHE D 695 " --> pdb=" O TYR D 691 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE D 697 " --> pdb=" O VAL D 693 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR D 721 " --> pdb=" O LEU D 717 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL D 722 " --> pdb=" O MET D 718 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER D 726 " --> pdb=" O VAL D 722 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N LYS D 727 " --> pdb=" O GLY D 723 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS D 730 " --> pdb=" O SER D 726 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS D 731 " --> pdb=" O LYS D 727 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE D 748 " --> pdb=" O ILE D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 756 Processing helix chain 'C' and resid 150 through 161 Processing helix chain 'C' and resid 162 through 167 removed outlier: 3.531A pdb=" N LEU C 166 " --> pdb=" O THR C 163 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP C 167 " --> pdb=" O ALA C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 176 Processing helix chain 'C' and resid 182 through 186 Processing helix chain 'C' and resid 193 through 201 removed outlier: 3.505A pdb=" N LYS C 197 " --> pdb=" O THR C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 220 removed outlier: 4.393A pdb=" N VAL C 212 " --> pdb=" O ASP C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 228 removed outlier: 3.500A pdb=" N PHE C 226 " --> pdb=" O ASN C 222 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN C 228 " --> pdb=" O ARG C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 248 Processing helix chain 'C' and resid 250 through 259 Processing helix chain 'C' and resid 275 through 279 removed outlier: 3.765A pdb=" N GLY C 279 " --> pdb=" O LYS C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 295 Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'C' and resid 323 through 332 removed outlier: 3.565A pdb=" N ALA C 332 " --> pdb=" O LEU C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 357 removed outlier: 4.449A pdb=" N PHE C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 365 removed outlier: 3.690A pdb=" N VAL C 365 " --> pdb=" O LEU C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 381 Processing helix chain 'C' and resid 382 through 391 removed outlier: 3.683A pdb=" N HIS C 388 " --> pdb=" O GLY C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 403 removed outlier: 3.831A pdb=" N LEU C 402 " --> pdb=" O THR C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 440 Processing helix chain 'C' and resid 442 through 450 removed outlier: 4.512A pdb=" N HIS C 447 " --> pdb=" O ILE C 443 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N GLU C 448 " --> pdb=" O GLU C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 466 removed outlier: 4.197A pdb=" N GLU C 457 " --> pdb=" O GLU C 453 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU C 458 " --> pdb=" O PRO C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 492 removed outlier: 3.615A pdb=" N SER C 470 " --> pdb=" O PHE C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 535 Processing helix chain 'C' and resid 546 through 570 removed outlier: 3.644A pdb=" N GLN C 550 " --> pdb=" O ASP C 546 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA C 569 " --> pdb=" O ALA C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 589 removed outlier: 4.237A pdb=" N VAL C 577 " --> pdb=" O ALA C 573 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL C 579 " --> pdb=" O LEU C 575 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N PHE C 580 " --> pdb=" O ALA C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 595 removed outlier: 3.563A pdb=" N ARG C 594 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY C 595 " --> pdb=" O PHE C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 612 removed outlier: 3.817A pdb=" N TYR C 602 " --> pdb=" O LEU C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 636 removed outlier: 3.731A pdb=" N LEU C 635 " --> pdb=" O ALA C 631 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C 636 " --> pdb=" O LEU C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 679 removed outlier: 3.602A pdb=" N THR C 668 " --> pdb=" O GLU C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 687 removed outlier: 3.761A pdb=" N SER C 687 " --> pdb=" O GLU C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 691 through 748 removed outlier: 3.723A pdb=" N PHE C 695 " --> pdb=" O TYR C 691 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE C 696 " --> pdb=" O PRO C 692 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR C 721 " --> pdb=" O LEU C 717 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N VAL C 722 " --> pdb=" O MET C 718 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER C 726 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N LYS C 727 " --> pdb=" O GLY C 723 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS C 730 " --> pdb=" O SER C 726 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N HIS C 731 " --> pdb=" O LYS C 727 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE C 748 " --> pdb=" O ILE C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 756 Processing sheet with id=AA1, first strand: chain 'A' and resid 405 through 410 removed outlier: 7.129A pdb=" N SER A 416 " --> pdb=" O ASP A 408 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER A 417 " --> pdb=" O VAL A 780 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 405 through 410 removed outlier: 7.126A pdb=" N SER B 416 " --> pdb=" O ASP B 408 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER B 417 " --> pdb=" O VAL B 780 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 405 through 410 removed outlier: 7.112A pdb=" N SER D 416 " --> pdb=" O ASP D 408 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER D 417 " --> pdb=" O VAL D 780 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 405 through 410 removed outlier: 7.127A pdb=" N SER C 416 " --> pdb=" O ASP C 408 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER C 417 " --> pdb=" O VAL C 780 " (cutoff:3.500A) 1138 hydrogen bonds defined for protein. 3297 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.39 Time building geometry restraints manager: 2.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 3084 1.27 - 1.40: 5224 1.40 - 1.54: 11670 1.54 - 1.68: 58 1.68 - 1.82: 168 Bond restraints: 20204 Sorted by residual: bond pdb=" C27 XPW C1201 " pdb=" C28 XPW C1201 " ideal model delta sigma weight residual 1.385 1.579 -0.194 2.00e-02 2.50e+03 9.39e+01 bond pdb=" C27 XPW A1201 " pdb=" C28 XPW A1201 " ideal model delta sigma weight residual 1.385 1.579 -0.194 2.00e-02 2.50e+03 9.36e+01 bond pdb=" C27 XPW B1201 " pdb=" C28 XPW B1201 " ideal model delta sigma weight residual 1.385 1.578 -0.193 2.00e-02 2.50e+03 9.31e+01 bond pdb=" C27 XPW D1201 " pdb=" C28 XPW D1201 " ideal model delta sigma weight residual 1.385 1.578 -0.193 2.00e-02 2.50e+03 9.30e+01 bond pdb=" C23 XPW B1201 " pdb=" C24 XPW B1201 " ideal model delta sigma weight residual 1.395 1.579 -0.184 2.00e-02 2.50e+03 8.43e+01 ... (remaining 20199 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 27001 2.45 - 4.90: 366 4.90 - 7.35: 56 7.35 - 9.79: 20 9.79 - 12.24: 9 Bond angle restraints: 27452 Sorted by residual: angle pdb=" CA GLU C 278 " pdb=" CB GLU C 278 " pdb=" CG GLU C 278 " ideal model delta sigma weight residual 114.10 122.52 -8.42 2.00e+00 2.50e-01 1.77e+01 angle pdb=" CB MET C 718 " pdb=" CG MET C 718 " pdb=" SD MET C 718 " ideal model delta sigma weight residual 112.70 100.46 12.24 3.00e+00 1.11e-01 1.67e+01 angle pdb=" C31 XPW D1201 " pdb=" C13 XPW D1201 " pdb=" O32 XPW D1201 " ideal model delta sigma weight residual 109.85 121.89 -12.04 3.00e+00 1.11e-01 1.61e+01 angle pdb=" C31 XPW A1201 " pdb=" C13 XPW A1201 " pdb=" O32 XPW A1201 " ideal model delta sigma weight residual 109.85 121.88 -12.03 3.00e+00 1.11e-01 1.61e+01 angle pdb=" C31 XPW B1201 " pdb=" C13 XPW B1201 " pdb=" O32 XPW B1201 " ideal model delta sigma weight residual 109.85 121.86 -12.01 3.00e+00 1.11e-01 1.60e+01 ... (remaining 27447 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 10903 17.94 - 35.87: 877 35.87 - 53.81: 186 53.81 - 71.75: 51 71.75 - 89.68: 27 Dihedral angle restraints: 12044 sinusoidal: 4828 harmonic: 7216 Sorted by residual: dihedral pdb=" CA VAL D 577 " pdb=" C VAL D 577 " pdb=" N MET D 578 " pdb=" CA MET D 578 " ideal model delta harmonic sigma weight residual 180.00 151.11 28.89 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA VAL B 577 " pdb=" C VAL B 577 " pdb=" N MET B 578 " pdb=" CA MET B 578 " ideal model delta harmonic sigma weight residual 180.00 156.20 23.80 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA MET C 718 " pdb=" C MET C 718 " pdb=" N GLY C 719 " pdb=" CA GLY C 719 " ideal model delta harmonic sigma weight residual 180.00 161.03 18.97 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 12041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2366 0.045 - 0.090: 677 0.090 - 0.136: 89 0.136 - 0.181: 3 0.181 - 0.226: 9 Chirality restraints: 3144 Sorted by residual: chirality pdb=" C17 XPW D1201 " pdb=" C16 XPW D1201 " pdb=" C19 XPW D1201 " pdb=" C31 XPW D1201 " both_signs ideal model delta sigma weight residual False 2.94 2.71 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" C17 XPW A1201 " pdb=" C16 XPW A1201 " pdb=" C19 XPW A1201 " pdb=" C31 XPW A1201 " both_signs ideal model delta sigma weight residual False 2.94 2.71 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" C17 XPW C1201 " pdb=" C16 XPW C1201 " pdb=" C19 XPW C1201 " pdb=" C31 XPW C1201 " both_signs ideal model delta sigma weight residual False 2.94 2.72 0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 3141 not shown) Planarity restraints: 3420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 621 " -0.018 2.00e-02 2.50e+03 1.85e-02 6.87e+00 pdb=" CG TYR B 621 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR B 621 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR B 621 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR B 621 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 621 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 621 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 621 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 546 " -0.011 2.00e-02 2.50e+03 2.14e-02 4.58e+00 pdb=" C ASP D 546 " 0.037 2.00e-02 2.50e+03 pdb=" O ASP D 546 " -0.014 2.00e-02 2.50e+03 pdb=" N GLY D 547 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 546 " 0.011 2.00e-02 2.50e+03 2.11e-02 4.44e+00 pdb=" C ASP B 546 " -0.036 2.00e-02 2.50e+03 pdb=" O ASP B 546 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY B 547 " 0.012 2.00e-02 2.50e+03 ... (remaining 3417 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 194 2.65 - 3.21: 19146 3.21 - 3.77: 30647 3.77 - 4.34: 41200 4.34 - 4.90: 67560 Nonbonded interactions: 158747 Sorted by model distance: nonbonded pdb=" O VAL B 722 " pdb=" OG SER B 726 " model vdw 2.087 3.040 nonbonded pdb=" O VAL A 722 " pdb=" OG SER A 726 " model vdw 2.093 3.040 nonbonded pdb=" NZ LYS B 462 " pdb=" OE2 GLU B 745 " model vdw 2.098 3.120 nonbonded pdb=" NZ LYS A 462 " pdb=" OE2 GLU A 745 " model vdw 2.127 3.120 nonbonded pdb=" O VAL D 722 " pdb=" OG SER D 726 " model vdw 2.127 3.040 ... (remaining 158742 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.910 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 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 : 0.008 0.194 20204 Z= 0.391 Angle : 0.752 12.243 27452 Z= 0.369 Chirality : 0.041 0.226 3144 Planarity : 0.004 0.040 3420 Dihedral : 14.618 89.683 7396 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.09 % Allowed : 0.52 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.43 (0.17), residues: 2448 helix: 0.89 (0.13), residues: 1480 sheet: -2.51 (0.62), residues: 76 loop : -0.32 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 774 TYR 0.046 0.001 TYR B 621 PHE 0.017 0.002 PHE C 580 TRP 0.014 0.002 TRP A 733 HIS 0.009 0.001 HIS A 252 Details of bonding type rmsd covalent geometry : bond 0.00802 (20204) covalent geometry : angle 0.75223 (27452) hydrogen bonds : bond 0.17234 ( 1138) hydrogen bonds : angle 5.68398 ( 3297) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 374 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 ILE cc_start: 0.7930 (mt) cc_final: 0.7052 (mt) REVERT: A 588 ASN cc_start: 0.8438 (m-40) cc_final: 0.7899 (m-40) REVERT: A 685 MET cc_start: 0.7533 (tpp) cc_final: 0.7136 (mtt) REVERT: D 219 ARG cc_start: 0.8478 (mpt180) cc_final: 0.8225 (mpt90) REVERT: C 157 ILE cc_start: 0.7877 (mt) cc_final: 0.6859 (mt) REVERT: C 252 HIS cc_start: 0.7052 (p-80) cc_final: 0.6825 (p-80) REVERT: C 588 ASN cc_start: 0.8376 (m-40) cc_final: 0.7841 (m-40) REVERT: C 625 MET cc_start: 0.7400 (mtm) cc_final: 0.6931 (ttm) REVERT: C 718 MET cc_start: 0.7686 (ptt) cc_final: 0.6646 (ptp) outliers start: 2 outliers final: 1 residues processed: 376 average time/residue: 0.1342 time to fit residues: 79.6635 Evaluate side-chains 309 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 308 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 204 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 235 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 ASN A 204 ASN ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 ASN B 260 GLN B 736 GLN ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.204039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.153427 restraints weight = 27659.725| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.44 r_work: 0.3467 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20204 Z= 0.154 Angle : 0.618 9.244 27452 Z= 0.311 Chirality : 0.040 0.185 3144 Planarity : 0.004 0.036 3420 Dihedral : 6.985 75.453 2878 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.23 % Allowed : 7.69 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.71 (0.17), residues: 2448 helix: 1.10 (0.13), residues: 1528 sheet: -2.58 (0.60), residues: 84 loop : -0.21 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 219 TYR 0.035 0.001 TYR B 621 PHE 0.016 0.002 PHE C 485 TRP 0.011 0.002 TRP D 733 HIS 0.004 0.001 HIS C 252 Details of bonding type rmsd covalent geometry : bond 0.00349 (20204) covalent geometry : angle 0.61798 (27452) hydrogen bonds : bond 0.04285 ( 1138) hydrogen bonds : angle 4.10723 ( 3297) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 328 time to evaluate : 0.766 Fit side-chains revert: symmetry clash REVERT: A 578 MET cc_start: 0.8378 (tpp) cc_final: 0.7622 (tpp) REVERT: A 588 ASN cc_start: 0.8561 (m-40) cc_final: 0.8064 (m-40) REVERT: B 340 LYS cc_start: 0.8217 (mppt) cc_final: 0.8001 (mmtp) REVERT: B 550 GLN cc_start: 0.8725 (mp10) cc_final: 0.7867 (mp10) REVERT: B 605 MET cc_start: 0.7641 (mmp) cc_final: 0.7077 (mmp) REVERT: B 680 MET cc_start: 0.4830 (tmm) cc_final: 0.3928 (ptt) REVERT: D 340 LYS cc_start: 0.8213 (mppt) cc_final: 0.7957 (mmtp) REVERT: D 605 MET cc_start: 0.8011 (mmp) cc_final: 0.7291 (mmm) REVERT: C 252 HIS cc_start: 0.7634 (p-80) cc_final: 0.7327 (p-80) REVERT: C 340 LYS cc_start: 0.8298 (mppt) cc_final: 0.7996 (mmtp) REVERT: C 444 GLU cc_start: 0.8096 (mp0) cc_final: 0.7875 (pt0) REVERT: C 449 MET cc_start: 0.8836 (mtp) cc_final: 0.8512 (mtp) REVERT: C 473 ILE cc_start: 0.9295 (mt) cc_final: 0.8958 (mt) REVERT: C 588 ASN cc_start: 0.8454 (m-40) cc_final: 0.7951 (m-40) REVERT: C 680 MET cc_start: 0.4432 (tmm) cc_final: 0.3723 (ptt) REVERT: C 718 MET cc_start: 0.8017 (ptt) cc_final: 0.6776 (ptp) outliers start: 26 outliers final: 9 residues processed: 347 average time/residue: 0.1369 time to fit residues: 74.9652 Evaluate side-chains 310 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 301 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 781 ASP Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 781 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 186 optimal weight: 0.1980 chunk 32 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 182 optimal weight: 0.7980 chunk 6 optimal weight: 0.1980 chunk 224 optimal weight: 1.9990 chunk 96 optimal weight: 9.9990 chunk 234 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 169 optimal weight: 6.9990 chunk 160 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 HIS B 204 ASN D 243 HIS C 243 HIS ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.207825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.151394 restraints weight = 27810.353| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 3.10 r_work: 0.3492 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20204 Z= 0.119 Angle : 0.556 8.926 27452 Z= 0.278 Chirality : 0.038 0.145 3144 Planarity : 0.004 0.039 3420 Dihedral : 5.913 71.252 2876 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.42 % Allowed : 11.72 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.97 (0.17), residues: 2448 helix: 1.36 (0.13), residues: 1504 sheet: -2.80 (0.61), residues: 76 loop : -0.18 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 219 TYR 0.026 0.001 TYR B 621 PHE 0.014 0.001 PHE A 341 TRP 0.009 0.001 TRP D 733 HIS 0.003 0.001 HIS B 252 Details of bonding type rmsd covalent geometry : bond 0.00265 (20204) covalent geometry : angle 0.55630 (27452) hydrogen bonds : bond 0.03697 ( 1138) hydrogen bonds : angle 3.80451 ( 3297) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 325 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 578 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.7555 (tpp) REVERT: A 588 ASN cc_start: 0.8491 (m-40) cc_final: 0.8026 (m-40) REVERT: A 605 MET cc_start: 0.8085 (mmm) cc_final: 0.7391 (mtp) REVERT: A 685 MET cc_start: 0.7681 (tpp) cc_final: 0.7303 (mtt) REVERT: B 186 ARG cc_start: 0.7822 (mtt-85) cc_final: 0.7508 (mtt-85) REVERT: B 340 LYS cc_start: 0.8113 (mppt) cc_final: 0.7811 (mmtp) REVERT: B 449 MET cc_start: 0.8940 (mtp) cc_final: 0.8711 (mtp) REVERT: B 550 GLN cc_start: 0.8736 (mp10) cc_final: 0.7863 (mp10) REVERT: B 605 MET cc_start: 0.7754 (mmp) cc_final: 0.6418 (mmm) REVERT: D 340 LYS cc_start: 0.8133 (mppt) cc_final: 0.7817 (mmtp) REVERT: D 449 MET cc_start: 0.8879 (mtp) cc_final: 0.8647 (mtp) REVERT: D 605 MET cc_start: 0.7956 (mmp) cc_final: 0.7477 (mmm) REVERT: C 252 HIS cc_start: 0.7867 (p-80) cc_final: 0.7504 (p-80) REVERT: C 340 LYS cc_start: 0.8183 (mppt) cc_final: 0.7946 (mmtt) REVERT: C 588 ASN cc_start: 0.8440 (m-40) cc_final: 0.8020 (m-40) REVERT: C 718 MET cc_start: 0.7878 (ptt) cc_final: 0.7269 (ptt) outliers start: 30 outliers final: 12 residues processed: 341 average time/residue: 0.1408 time to fit residues: 75.3576 Evaluate side-chains 318 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 305 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 781 ASP Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 781 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 0 optimal weight: 20.0000 chunk 6 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 126 optimal weight: 0.9980 chunk 171 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 42 optimal weight: 0.0670 chunk 29 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 ASN A 204 ASN B 204 ASN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.207978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.151200 restraints weight = 27851.317| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 3.15 r_work: 0.3490 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20204 Z= 0.112 Angle : 0.549 8.572 27452 Z= 0.273 Chirality : 0.037 0.120 3144 Planarity : 0.004 0.039 3420 Dihedral : 5.468 64.703 2876 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.66 % Allowed : 13.66 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.17), residues: 2448 helix: 1.49 (0.13), residues: 1504 sheet: -3.01 (0.59), residues: 76 loop : -0.16 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 219 TYR 0.019 0.001 TYR B 621 PHE 0.017 0.001 PHE A 554 TRP 0.007 0.001 TRP B 737 HIS 0.002 0.001 HIS B 252 Details of bonding type rmsd covalent geometry : bond 0.00251 (20204) covalent geometry : angle 0.54862 (27452) hydrogen bonds : bond 0.03475 ( 1138) hydrogen bonds : angle 3.72110 ( 3297) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 331 time to evaluate : 0.746 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: A 219 ARG cc_start: 0.8863 (mmt90) cc_final: 0.8618 (mmt-90) REVERT: A 578 MET cc_start: 0.8364 (tpp) cc_final: 0.7595 (tpp) REVERT: A 588 ASN cc_start: 0.8484 (m-40) cc_final: 0.8103 (m-40) REVERT: A 605 MET cc_start: 0.8226 (mmm) cc_final: 0.7829 (mtm) REVERT: A 685 MET cc_start: 0.7658 (tpp) cc_final: 0.7297 (mtt) REVERT: B 340 LYS cc_start: 0.8011 (mppt) cc_final: 0.7780 (mmtt) REVERT: B 449 MET cc_start: 0.8887 (mtp) cc_final: 0.8672 (mtp) REVERT: B 605 MET cc_start: 0.7801 (mmp) cc_final: 0.7248 (mmp) REVERT: B 625 MET cc_start: 0.8156 (mpp) cc_final: 0.7935 (mpp) REVERT: D 449 MET cc_start: 0.8880 (mtp) cc_final: 0.8668 (mtp) REVERT: D 605 MET cc_start: 0.8024 (mmp) cc_final: 0.6989 (mtp) REVERT: D 718 MET cc_start: 0.7722 (tpt) cc_final: 0.7105 (mtt) REVERT: C 252 HIS cc_start: 0.7820 (p-80) cc_final: 0.7477 (p-80) REVERT: C 340 LYS cc_start: 0.8128 (mppt) cc_final: 0.7916 (mmtp) REVERT: C 390 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8543 (mm) REVERT: C 473 ILE cc_start: 0.9368 (mt) cc_final: 0.9080 (mt) REVERT: C 588 ASN cc_start: 0.8418 (m-40) cc_final: 0.8058 (m-40) REVERT: C 680 MET cc_start: 0.4556 (tmm) cc_final: 0.3188 (ptt) outliers start: 35 outliers final: 18 residues processed: 352 average time/residue: 0.1403 time to fit residues: 77.8820 Evaluate side-chains 330 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 311 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 444 GLU Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 781 ASP Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 550 GLN Chi-restraints excluded: chain C residue 781 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 78 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 chunk 213 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 100 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 220 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 HIS ** C 260 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 = 0.4353 r_free = 0.4353 target = 0.204610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.154159 restraints weight = 27603.541| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.36 r_work: 0.3450 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20204 Z= 0.169 Angle : 0.593 10.549 27452 Z= 0.294 Chirality : 0.039 0.139 3144 Planarity : 0.004 0.042 3420 Dihedral : 5.435 68.027 2876 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.37 % Allowed : 14.23 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.17), residues: 2448 helix: 1.49 (0.13), residues: 1504 sheet: -3.19 (0.59), residues: 76 loop : -0.14 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 186 TYR 0.016 0.001 TYR A 702 PHE 0.016 0.001 PHE A 554 TRP 0.008 0.001 TRP C 463 HIS 0.004 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00392 (20204) covalent geometry : angle 0.59286 (27452) hydrogen bonds : bond 0.03598 ( 1138) hydrogen bonds : angle 3.77890 ( 3297) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 318 time to evaluate : 0.777 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: A 578 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.7543 (tpp) REVERT: A 588 ASN cc_start: 0.8454 (m-40) cc_final: 0.8023 (m-40) REVERT: A 605 MET cc_start: 0.8345 (mmm) cc_final: 0.7987 (mtm) REVERT: A 685 MET cc_start: 0.7662 (tpp) cc_final: 0.7392 (mtt) REVERT: B 605 MET cc_start: 0.7909 (mmp) cc_final: 0.7042 (mmm) REVERT: B 625 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7872 (mpp) REVERT: D 383 ILE cc_start: 0.9251 (OUTLIER) cc_final: 0.8992 (mt) REVERT: D 605 MET cc_start: 0.8077 (mmp) cc_final: 0.7225 (mtp) REVERT: C 252 HIS cc_start: 0.7738 (p-80) cc_final: 0.7498 (p-80) REVERT: C 383 ILE cc_start: 0.9130 (OUTLIER) cc_final: 0.8847 (mt) REVERT: C 588 ASN cc_start: 0.8405 (m-40) cc_final: 0.8047 (m-40) outliers start: 50 outliers final: 31 residues processed: 346 average time/residue: 0.1394 time to fit residues: 75.6934 Evaluate side-chains 343 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 308 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 625 MET Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain D residue 781 ASP Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 379 LYS Chi-restraints excluded: chain C residue 383 ILE Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 444 GLU Chi-restraints excluded: chain C residue 550 GLN Chi-restraints excluded: chain C residue 781 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 139 optimal weight: 0.9990 chunk 168 optimal weight: 0.9990 chunk 240 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 151 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 147 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 ASN ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 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 = 0.4365 r_free = 0.4365 target = 0.206074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.155975 restraints weight = 27657.879| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.43 r_work: 0.3522 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20204 Z= 0.119 Angle : 0.563 8.872 27452 Z= 0.280 Chirality : 0.037 0.153 3144 Planarity : 0.004 0.041 3420 Dihedral : 5.174 63.865 2876 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.85 % Allowed : 15.99 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.18 (0.17), residues: 2448 helix: 1.65 (0.13), residues: 1476 sheet: -3.23 (0.59), residues: 76 loop : -0.23 (0.22), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 186 TYR 0.017 0.001 TYR A 702 PHE 0.017 0.001 PHE A 554 TRP 0.010 0.001 TRP C 733 HIS 0.003 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00273 (20204) covalent geometry : angle 0.56253 (27452) hydrogen bonds : bond 0.03315 ( 1138) hydrogen bonds : angle 3.68417 ( 3297) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 323 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 578 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.7635 (tpp) REVERT: A 588 ASN cc_start: 0.8456 (m-40) cc_final: 0.8124 (m-40) REVERT: A 605 MET cc_start: 0.8360 (mmm) cc_final: 0.8097 (mtm) REVERT: A 607 GLN cc_start: 0.7859 (mm110) cc_final: 0.7220 (mt0) REVERT: A 685 MET cc_start: 0.7633 (tpp) cc_final: 0.7310 (mtt) REVERT: B 383 ILE cc_start: 0.9187 (OUTLIER) cc_final: 0.8920 (mt) REVERT: B 605 MET cc_start: 0.7752 (mmp) cc_final: 0.6985 (mmm) REVERT: B 625 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7872 (mpp) REVERT: D 550 GLN cc_start: 0.8899 (mp10) cc_final: 0.7963 (mp10) REVERT: D 605 MET cc_start: 0.8130 (mmt) cc_final: 0.7306 (mtp) REVERT: C 252 HIS cc_start: 0.7695 (p-80) cc_final: 0.7480 (p-80) REVERT: C 473 ILE cc_start: 0.9389 (mt) cc_final: 0.9115 (mt) REVERT: C 588 ASN cc_start: 0.8416 (m-40) cc_final: 0.8085 (m-40) REVERT: C 718 MET cc_start: 0.7884 (ptt) cc_final: 0.7538 (ptt) outliers start: 39 outliers final: 26 residues processed: 346 average time/residue: 0.1395 time to fit residues: 76.1278 Evaluate side-chains 335 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 306 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 625 MET Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 781 ASP Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 379 LYS Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 444 GLU Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 781 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 101 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 chunk 196 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 171 optimal weight: 5.9990 chunk 185 optimal weight: 1.9990 chunk 223 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 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 = 0.4354 r_free = 0.4354 target = 0.204865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.155879 restraints weight = 27703.998| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.46 r_work: 0.3482 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20204 Z= 0.137 Angle : 0.582 10.436 27452 Z= 0.288 Chirality : 0.038 0.155 3144 Planarity : 0.004 0.041 3420 Dihedral : 5.140 63.091 2876 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.99 % Allowed : 16.27 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.20 (0.17), residues: 2448 helix: 1.59 (0.13), residues: 1500 sheet: -3.30 (0.59), residues: 76 loop : -0.10 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 219 TYR 0.014 0.001 TYR A 702 PHE 0.018 0.001 PHE B 172 TRP 0.007 0.001 TRP D 733 HIS 0.008 0.001 HIS A 252 Details of bonding type rmsd covalent geometry : bond 0.00320 (20204) covalent geometry : angle 0.58177 (27452) hydrogen bonds : bond 0.03392 ( 1138) hydrogen bonds : angle 3.71105 ( 3297) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 322 time to evaluate : 0.770 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: A 219 ARG cc_start: 0.8704 (mmt90) cc_final: 0.8501 (mmt90) REVERT: A 228 ASN cc_start: 0.9197 (OUTLIER) cc_final: 0.8823 (p0) REVERT: A 383 ILE cc_start: 0.9260 (OUTLIER) cc_final: 0.9028 (mt) REVERT: A 578 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.7699 (tpp) REVERT: A 588 ASN cc_start: 0.8417 (m-40) cc_final: 0.8100 (m-40) REVERT: A 605 MET cc_start: 0.8400 (mmm) cc_final: 0.8164 (mtm) REVERT: A 607 GLN cc_start: 0.7875 (mm110) cc_final: 0.7203 (mt0) REVERT: A 685 MET cc_start: 0.7630 (tpp) cc_final: 0.7263 (mtt) REVERT: B 383 ILE cc_start: 0.9234 (OUTLIER) cc_final: 0.8959 (mt) REVERT: B 605 MET cc_start: 0.7814 (mmp) cc_final: 0.7102 (mmm) REVERT: B 625 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7867 (mpp) REVERT: D 383 ILE cc_start: 0.9265 (OUTLIER) cc_final: 0.8923 (mt) REVERT: D 605 MET cc_start: 0.8142 (mmt) cc_final: 0.7322 (mtp) REVERT: C 219 ARG cc_start: 0.9016 (mmt-90) cc_final: 0.8797 (mmt180) REVERT: C 252 HIS cc_start: 0.7749 (p-80) cc_final: 0.7545 (p-80) REVERT: C 473 ILE cc_start: 0.9407 (mt) cc_final: 0.9103 (mt) REVERT: C 588 ASN cc_start: 0.8414 (m-40) cc_final: 0.8088 (m-40) outliers start: 42 outliers final: 29 residues processed: 347 average time/residue: 0.1386 time to fit residues: 76.0692 Evaluate side-chains 343 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 308 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 625 MET Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 781 ASP Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 379 LYS Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 444 GLU Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 781 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 167 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 170 optimal weight: 2.9990 chunk 194 optimal weight: 0.6980 chunk 143 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 151 optimal weight: 0.1980 chunk 77 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 35 optimal weight: 20.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 252 HIS ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.205935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.155577 restraints weight = 27734.347| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 2.42 r_work: 0.3513 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20204 Z= 0.118 Angle : 0.588 10.597 27452 Z= 0.287 Chirality : 0.038 0.142 3144 Planarity : 0.004 0.041 3420 Dihedral : 5.037 60.920 2876 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.85 % Allowed : 16.98 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.22 (0.17), residues: 2448 helix: 1.68 (0.13), residues: 1472 sheet: -3.34 (0.58), residues: 76 loop : -0.18 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 219 TYR 0.015 0.001 TYR A 702 PHE 0.033 0.001 PHE B 172 TRP 0.009 0.001 TRP D 733 HIS 0.003 0.001 HIS A 252 Details of bonding type rmsd covalent geometry : bond 0.00270 (20204) covalent geometry : angle 0.58819 (27452) hydrogen bonds : bond 0.03295 ( 1138) hydrogen bonds : angle 3.70304 ( 3297) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 321 time to evaluate : 0.782 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: A 219 ARG cc_start: 0.8677 (mmt90) cc_final: 0.8350 (mmp80) REVERT: A 383 ILE cc_start: 0.9242 (OUTLIER) cc_final: 0.9019 (mt) REVERT: A 578 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.7694 (tpp) REVERT: A 588 ASN cc_start: 0.8405 (m-40) cc_final: 0.8075 (m-40) REVERT: A 605 MET cc_start: 0.8102 (mmm) cc_final: 0.7759 (mtm) REVERT: A 685 MET cc_start: 0.7665 (tpp) cc_final: 0.7328 (mtt) REVERT: B 383 ILE cc_start: 0.9227 (OUTLIER) cc_final: 0.8966 (mt) REVERT: B 605 MET cc_start: 0.7848 (mmp) cc_final: 0.7144 (mmm) REVERT: B 625 MET cc_start: 0.8147 (OUTLIER) cc_final: 0.7856 (mpp) REVERT: D 383 ILE cc_start: 0.9257 (OUTLIER) cc_final: 0.8945 (mt) REVERT: D 605 MET cc_start: 0.8195 (mmt) cc_final: 0.7410 (mtp) REVERT: C 219 ARG cc_start: 0.9000 (mmt-90) cc_final: 0.8796 (mmt180) REVERT: C 383 ILE cc_start: 0.9198 (OUTLIER) cc_final: 0.8948 (mt) REVERT: C 473 ILE cc_start: 0.9398 (mt) cc_final: 0.9095 (mt) REVERT: C 588 ASN cc_start: 0.8417 (m-40) cc_final: 0.8080 (m-40) REVERT: C 713 MET cc_start: 0.8362 (tmm) cc_final: 0.8088 (mmp) outliers start: 39 outliers final: 28 residues processed: 346 average time/residue: 0.1379 time to fit residues: 75.6347 Evaluate side-chains 343 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 309 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 625 MET Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 781 ASP Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 379 LYS Chi-restraints excluded: chain C residue 383 ILE Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 444 GLU Chi-restraints excluded: chain C residue 781 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 33 optimal weight: 3.9990 chunk 227 optimal weight: 4.9990 chunk 230 optimal weight: 6.9990 chunk 152 optimal weight: 2.9990 chunk 222 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 148 optimal weight: 0.8980 chunk 164 optimal weight: 2.9990 chunk 225 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 60 optimal weight: 0.7980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 ASN ** B 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.194191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.136241 restraints weight = 26410.024| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.56 r_work: 0.3345 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 20204 Z= 0.191 Angle : 0.649 13.337 27452 Z= 0.317 Chirality : 0.040 0.239 3144 Planarity : 0.004 0.040 3420 Dihedral : 5.294 64.031 2876 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.28 % Allowed : 16.46 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.08 (0.17), residues: 2448 helix: 1.52 (0.13), residues: 1472 sheet: -3.42 (0.54), residues: 84 loop : -0.11 (0.22), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 219 TYR 0.019 0.001 TYR C 253 PHE 0.033 0.001 PHE B 172 TRP 0.009 0.002 TRP C 463 HIS 0.011 0.001 HIS C 252 Details of bonding type rmsd covalent geometry : bond 0.00451 (20204) covalent geometry : angle 0.64886 (27452) hydrogen bonds : bond 0.03642 ( 1138) hydrogen bonds : angle 3.85221 ( 3297) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 314 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 ASN cc_start: 0.9230 (OUTLIER) cc_final: 0.8882 (p0) REVERT: A 383 ILE cc_start: 0.9331 (OUTLIER) cc_final: 0.9068 (mt) REVERT: A 578 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.7632 (tpp) REVERT: A 588 ASN cc_start: 0.8467 (m-40) cc_final: 0.8166 (m-40) REVERT: A 605 MET cc_start: 0.8110 (mmm) cc_final: 0.7703 (mtm) REVERT: A 685 MET cc_start: 0.7729 (tpp) cc_final: 0.7345 (mtt) REVERT: A 761 MET cc_start: 0.8436 (tpt) cc_final: 0.8186 (tpt) REVERT: B 228 ASN cc_start: 0.9198 (OUTLIER) cc_final: 0.8890 (p0) REVERT: B 383 ILE cc_start: 0.9333 (OUTLIER) cc_final: 0.9044 (mt) REVERT: B 605 MET cc_start: 0.7959 (mmp) cc_final: 0.7254 (mmm) REVERT: B 625 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7817 (mpp) REVERT: D 383 ILE cc_start: 0.9342 (OUTLIER) cc_final: 0.8981 (mt) REVERT: D 605 MET cc_start: 0.8205 (mmt) cc_final: 0.7387 (mtp) REVERT: C 347 ASP cc_start: 0.8761 (m-30) cc_final: 0.8440 (m-30) REVERT: C 383 ILE cc_start: 0.9260 (OUTLIER) cc_final: 0.8971 (mt) REVERT: C 588 ASN cc_start: 0.8492 (m-40) cc_final: 0.8143 (m-40) outliers start: 48 outliers final: 35 residues processed: 344 average time/residue: 0.1365 time to fit residues: 74.3122 Evaluate side-chains 347 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 304 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 194 CYS Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 228 ASN Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 625 MET Chi-restraints excluded: chain B residue 781 ASP Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain D residue 781 ASP Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 379 LYS Chi-restraints excluded: chain C residue 383 ILE Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 444 GLU Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 781 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 86 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 173 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 201 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 129 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 157 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 ASN ** B 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 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 = 0.4213 r_free = 0.4213 target = 0.194194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.136254 restraints weight = 26673.331| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.38 r_work: 0.3357 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.175 20204 Z= 0.234 Angle : 0.915 59.200 27452 Z= 0.511 Chirality : 0.041 0.308 3144 Planarity : 0.004 0.041 3420 Dihedral : 5.337 64.035 2876 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.99 % Allowed : 16.84 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 2448 helix: 1.49 (0.13), residues: 1472 sheet: -3.42 (0.54), residues: 84 loop : -0.11 (0.22), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 186 TYR 0.017 0.001 TYR A 702 PHE 0.027 0.001 PHE B 172 TRP 0.009 0.002 TRP C 463 HIS 0.008 0.001 HIS C 252 Details of bonding type rmsd covalent geometry : bond 0.00533 (20204) covalent geometry : angle 0.91451 (27452) hydrogen bonds : bond 0.03639 ( 1138) hydrogen bonds : angle 3.85382 ( 3297) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 304 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 ASN cc_start: 0.9318 (OUTLIER) cc_final: 0.9004 (p0) REVERT: A 383 ILE cc_start: 0.9326 (OUTLIER) cc_final: 0.9066 (mt) REVERT: A 578 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.7636 (tpp) REVERT: A 588 ASN cc_start: 0.8508 (m-40) cc_final: 0.8170 (m-40) REVERT: A 605 MET cc_start: 0.8100 (mmm) cc_final: 0.7697 (mtm) REVERT: A 685 MET cc_start: 0.7714 (tpp) cc_final: 0.7335 (mtt) REVERT: B 228 ASN cc_start: 0.8911 (OUTLIER) cc_final: 0.8482 (p0) REVERT: B 383 ILE cc_start: 0.9332 (OUTLIER) cc_final: 0.9044 (mt) REVERT: B 605 MET cc_start: 0.7959 (mmp) cc_final: 0.7257 (mmm) REVERT: B 625 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7817 (mpp) REVERT: D 383 ILE cc_start: 0.9342 (OUTLIER) cc_final: 0.8981 (mt) REVERT: D 605 MET cc_start: 0.8199 (mmt) cc_final: 0.7391 (mtp) REVERT: C 347 ASP cc_start: 0.8741 (m-30) cc_final: 0.8423 (m-30) REVERT: C 383 ILE cc_start: 0.9259 (OUTLIER) cc_final: 0.8972 (mt) REVERT: C 588 ASN cc_start: 0.8486 (m-40) cc_final: 0.8135 (m-40) outliers start: 42 outliers final: 34 residues processed: 330 average time/residue: 0.1389 time to fit residues: 72.4861 Evaluate side-chains 344 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 302 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 228 ASN Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 625 MET Chi-restraints excluded: chain B residue 781 ASP Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 781 ASP Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 379 LYS Chi-restraints excluded: chain C residue 383 ILE Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 444 GLU Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 781 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 58 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 235 optimal weight: 9.9990 chunk 203 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 168 optimal weight: 5.9990 chunk 182 optimal weight: 0.8980 chunk 206 optimal weight: 0.8980 chunk 122 optimal weight: 20.0000 chunk 108 optimal weight: 0.0470 chunk 112 optimal weight: 0.1980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 ASN ** B 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 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 = 0.4214 r_free = 0.4214 target = 0.194358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.136278 restraints weight = 26663.647| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.39 r_work: 0.3359 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.175 20204 Z= 0.230 Angle : 0.843 56.441 27452 Z= 0.474 Chirality : 0.040 0.308 3144 Planarity : 0.004 0.114 3420 Dihedral : 5.337 64.035 2876 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.99 % Allowed : 16.94 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 2448 helix: 1.49 (0.13), residues: 1472 sheet: -3.42 (0.54), residues: 84 loop : -0.11 (0.22), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 186 TYR 0.017 0.001 TYR A 702 PHE 0.027 0.001 PHE B 172 TRP 0.009 0.002 TRP C 463 HIS 0.008 0.001 HIS C 252 Details of bonding type rmsd covalent geometry : bond 0.00531 (20204) covalent geometry : angle 0.84262 (27452) hydrogen bonds : bond 0.03639 ( 1138) hydrogen bonds : angle 3.85382 ( 3297) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4909.43 seconds wall clock time: 84 minutes 55.83 seconds (5095.83 seconds total)