Starting phenix.real_space_refine on Tue May 20 08:17:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ju6_36660/05_2025/8ju6_36660.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ju6_36660/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ju6_36660/05_2025/8ju6_36660.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ju6_36660/05_2025/8ju6_36660.map" model { file = "/net/cci-nas-00/data/ceres_data/8ju6_36660/05_2025/8ju6_36660.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ju6_36660/05_2025/8ju6_36660.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'ARG:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 3} 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: {'ARG:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 3} 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: {'ARG:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 3} 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: {'ARG:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 3} 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: 10.42, per 1000 atoms: 0.53 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: 4.86 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 1.97 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: 5.79 Time building geometry restraints manager: 5.47 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: 0.04 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.680 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 40.780 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.050 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (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 TRP 0.014 0.002 TRP A 733 HIS 0.009 0.001 HIS A 252 PHE 0.017 0.002 PHE C 580 TYR 0.046 0.001 TYR B 621 ARG 0.007 0.001 ARG A 774 Details of bonding type rmsd hydrogen bonds : bond 0.17234 ( 1138) hydrogen bonds : angle 5.68398 ( 3297) covalent geometry : bond 0.00802 (20204) covalent geometry : angle 0.75223 (27452) *********************** 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 : 2.031 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: 0.7135 (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: 0.6860 (mt) REVERT: C 252 HIS cc_start: 0.7052 (p-80) cc_final: 0.6826 (p-80) REVERT: C 588 ASN cc_start: 0.8376 (m-40) cc_final: 0.7842 (m-40) REVERT: C 625 MET cc_start: 0.7400 (mtm) cc_final: 0.6932 (ttm) REVERT: C 718 MET cc_start: 0.7686 (ptt) cc_final: 0.6647 (ptp) outliers start: 2 outliers final: 1 residues processed: 376 average time/residue: 0.2935 time to fit residues: 172.9556 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 : 1.998 ------------------------------------------------------------------------------- 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 206 optimal weight: 1.9990 chunk 184 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 191 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 116 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 chunk 221 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 228 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.204009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.153386 restraints weight = 27697.923| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.44 r_work: 0.3471 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20204 Z= 0.155 Angle : 0.619 9.497 27452 Z= 0.312 Chirality : 0.040 0.185 3144 Planarity : 0.004 0.035 3420 Dihedral : 7.032 75.528 2878 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.38 % Allowed : 7.64 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.17), residues: 2448 helix: 1.09 (0.13), residues: 1528 sheet: -2.60 (0.59), residues: 84 loop : -0.21 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 733 HIS 0.004 0.001 HIS C 252 PHE 0.016 0.002 PHE C 485 TYR 0.035 0.001 TYR B 621 ARG 0.006 0.001 ARG A 219 Details of bonding type rmsd hydrogen bonds : bond 0.04260 ( 1138) hydrogen bonds : angle 4.11543 ( 3297) covalent geometry : bond 0.00352 (20204) covalent geometry : angle 0.61912 (27452) *********************** 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 358 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 329 time to evaluate : 1.943 Fit side-chains revert: symmetry clash REVERT: A 228 ASN cc_start: 0.9109 (OUTLIER) cc_final: 0.8660 (p0) REVERT: A 444 GLU cc_start: 0.8047 (mp0) cc_final: 0.7839 (pt0) REVERT: A 578 MET cc_start: 0.8317 (tpp) cc_final: 0.7601 (tpp) REVERT: A 588 ASN cc_start: 0.8556 (m-40) cc_final: 0.8059 (m-40) REVERT: B 340 LYS cc_start: 0.8219 (mppt) cc_final: 0.7998 (mmtp) REVERT: B 550 GLN cc_start: 0.8721 (mp10) cc_final: 0.7869 (mp10) REVERT: B 605 MET cc_start: 0.7631 (mmp) cc_final: 0.7070 (mmp) REVERT: B 680 MET cc_start: 0.4724 (tmm) cc_final: 0.3835 (ptt) REVERT: D 340 LYS cc_start: 0.8212 (mppt) cc_final: 0.7956 (mmtp) REVERT: D 605 MET cc_start: 0.8008 (mmp) cc_final: 0.7288 (mmm) REVERT: C 252 HIS cc_start: 0.7632 (p-80) cc_final: 0.7327 (p-80) REVERT: C 340 LYS cc_start: 0.8293 (mppt) cc_final: 0.7987 (mmtp) REVERT: C 444 GLU cc_start: 0.8107 (mp0) cc_final: 0.7884 (pt0) REVERT: C 449 MET cc_start: 0.8841 (mtp) cc_final: 0.8515 (mtp) REVERT: C 473 ILE cc_start: 0.9291 (mt) cc_final: 0.8954 (mt) REVERT: C 588 ASN cc_start: 0.8454 (m-40) cc_final: 0.7954 (m-40) REVERT: C 680 MET cc_start: 0.4441 (tmm) cc_final: 0.3734 (ptt) REVERT: C 718 MET cc_start: 0.8035 (ptt) cc_final: 0.6820 (ptt) outliers start: 29 outliers final: 10 residues processed: 351 average time/residue: 0.2771 time to fit residues: 151.7569 Evaluate side-chains 312 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 301 time to evaluate : 2.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 228 ASN 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 139 optimal weight: 0.7980 chunk 172 optimal weight: 20.0000 chunk 87 optimal weight: 0.0060 chunk 196 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 204 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 110 optimal weight: 6.9990 overall best weight: 0.8998 ------------------------------------------------------------------------------- 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 ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4378 r_free = 0.4378 target = 0.207170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.149198 restraints weight = 27359.518| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 3.02 r_work: 0.3472 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1622 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= 0.124 Angle : 0.568 8.605 27452 Z= 0.283 Chirality : 0.038 0.147 3144 Planarity : 0.004 0.039 3420 Dihedral : 6.095 72.327 2876 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.38 % Allowed : 11.72 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.17), residues: 2448 helix: 1.29 (0.13), residues: 1512 sheet: -2.82 (0.61), residues: 76 loop : -0.17 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 733 HIS 0.003 0.001 HIS C 252 PHE 0.014 0.001 PHE A 341 TYR 0.026 0.001 TYR B 621 ARG 0.006 0.000 ARG A 219 Details of bonding type rmsd hydrogen bonds : bond 0.03784 ( 1138) hydrogen bonds : angle 3.84424 ( 3297) covalent geometry : bond 0.00278 (20204) covalent geometry : angle 0.56777 (27452) *********************** 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 354 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 325 time to evaluate : 2.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 578 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.7527 (tpp) REVERT: A 588 ASN cc_start: 0.8536 (m-40) cc_final: 0.8053 (m-40) REVERT: A 605 MET cc_start: 0.8080 (mmm) cc_final: 0.7360 (mtp) REVERT: A 685 MET cc_start: 0.7719 (tpp) cc_final: 0.7327 (mtt) REVERT: B 340 LYS cc_start: 0.8149 (mppt) cc_final: 0.7839 (mmtp) REVERT: B 550 GLN cc_start: 0.8734 (mp10) cc_final: 0.7776 (mp10) REVERT: B 605 MET cc_start: 0.7735 (mmp) cc_final: 0.6385 (mmm) REVERT: B 625 MET cc_start: 0.7843 (mpp) cc_final: 0.7597 (mpp) REVERT: D 340 LYS cc_start: 0.8145 (mppt) cc_final: 0.7851 (mmtp) REVERT: D 605 MET cc_start: 0.7945 (mmp) cc_final: 0.7435 (mmm) REVERT: D 718 MET cc_start: 0.7771 (tpt) cc_final: 0.7562 (mtt) REVERT: C 252 HIS cc_start: 0.7876 (p-80) cc_final: 0.7479 (p-80) REVERT: C 340 LYS cc_start: 0.8201 (mppt) cc_final: 0.7862 (mmtp) REVERT: C 449 MET cc_start: 0.8851 (mtp) cc_final: 0.8634 (mtp) REVERT: C 588 ASN cc_start: 0.8474 (m-40) cc_final: 0.8037 (m-40) REVERT: C 718 MET cc_start: 0.7830 (ptt) cc_final: 0.7625 (ptt) outliers start: 29 outliers final: 14 residues processed: 340 average time/residue: 0.2906 time to fit residues: 153.8949 Evaluate side-chains 321 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 306 time to evaluate : 1.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain B residue 395 THR 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 345 MET 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 18 optimal weight: 0.0770 chunk 52 optimal weight: 5.9990 chunk 243 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 70 optimal weight: 0.2980 chunk 124 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 203 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 118 optimal weight: 0.9980 overall best weight: 0.8742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 ASN A 228 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 = 0.4249 r_free = 0.4249 target = 0.198349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.141256 restraints weight = 26693.826| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.72 r_work: 0.3380 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1897 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= 0.117 Angle : 0.550 8.903 27452 Z= 0.273 Chirality : 0.037 0.125 3144 Planarity : 0.004 0.041 3420 Dihedral : 5.536 67.594 2876 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.76 % Allowed : 13.43 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.17), residues: 2448 helix: 1.47 (0.13), residues: 1504 sheet: -2.99 (0.60), residues: 76 loop : -0.17 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 733 HIS 0.002 0.001 HIS B 252 PHE 0.018 0.001 PHE A 554 TYR 0.021 0.001 TYR B 621 ARG 0.007 0.000 ARG A 219 Details of bonding type rmsd hydrogen bonds : bond 0.03492 ( 1138) hydrogen bonds : angle 3.71928 ( 3297) covalent geometry : bond 0.00264 (20204) covalent geometry : angle 0.54989 (27452) *********************** 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 362 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 325 time to evaluate : 2.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 ARG cc_start: 0.8897 (mmt90) cc_final: 0.8650 (mmt-90) REVERT: A 228 ASN cc_start: 0.9208 (OUTLIER) cc_final: 0.8831 (p0) REVERT: A 444 GLU cc_start: 0.8216 (mp0) cc_final: 0.7908 (pt0) REVERT: A 578 MET cc_start: 0.8359 (tpp) cc_final: 0.7602 (tpp) REVERT: A 588 ASN cc_start: 0.8506 (m-40) cc_final: 0.8059 (m-40) REVERT: A 605 MET cc_start: 0.8220 (mmm) cc_final: 0.7819 (mtm) REVERT: A 685 MET cc_start: 0.7670 (tpp) cc_final: 0.7308 (mtt) REVERT: B 255 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7390 (mp0) REVERT: B 340 LYS cc_start: 0.7984 (mppt) cc_final: 0.7742 (mmtt) REVERT: B 449 MET cc_start: 0.8930 (mtp) cc_final: 0.8680 (mtp) REVERT: B 605 MET cc_start: 0.7784 (mmp) cc_final: 0.7225 (mmp) REVERT: B 625 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7556 (mmm) REVERT: D 605 MET cc_start: 0.8037 (mmp) cc_final: 0.6979 (mtp) REVERT: C 252 HIS cc_start: 0.7895 (p-80) cc_final: 0.7548 (p-80) REVERT: C 340 LYS cc_start: 0.8077 (mppt) cc_final: 0.7876 (mmtt) REVERT: C 345 MET cc_start: 0.9160 (OUTLIER) cc_final: 0.8866 (tpp) REVERT: C 473 ILE cc_start: 0.9293 (mt) cc_final: 0.8985 (mt) REVERT: C 550 GLN cc_start: 0.8807 (mt0) cc_final: 0.8462 (mp10) REVERT: C 588 ASN cc_start: 0.8448 (m-40) cc_final: 0.8051 (m-40) REVERT: C 680 MET cc_start: 0.4761 (tmm) cc_final: 0.3465 (ptt) REVERT: C 718 MET cc_start: 0.8030 (ptt) cc_final: 0.7183 (ptt) outliers start: 37 outliers final: 18 residues processed: 347 average time/residue: 0.2960 time to fit residues: 160.2394 Evaluate side-chains 331 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 310 time to evaluate : 2.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain B residue 204 ASN 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 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 395 THR Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 781 ASP Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 551 LEU 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 167 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 174 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 160 optimal weight: 9.9990 chunk 143 optimal weight: 0.0980 chunk 78 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 205 optimal weight: 1.9990 chunk 61 optimal weight: 20.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN B 204 ASN ** 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 = 0.4365 r_free = 0.4365 target = 0.205864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.156025 restraints weight = 27763.584| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 2.49 r_work: 0.3483 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2011 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= 0.143 Angle : 0.568 8.505 27452 Z= 0.283 Chirality : 0.038 0.123 3144 Planarity : 0.004 0.041 3420 Dihedral : 5.390 65.251 2876 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.09 % Allowed : 14.56 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.17), residues: 2448 helix: 1.49 (0.13), residues: 1512 sheet: -3.12 (0.59), residues: 76 loop : -0.13 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 733 HIS 0.004 0.001 HIS B 243 PHE 0.016 0.001 PHE A 554 TYR 0.017 0.001 TYR A 702 ARG 0.004 0.000 ARG A 219 Details of bonding type rmsd hydrogen bonds : bond 0.03494 ( 1138) hydrogen bonds : angle 3.73765 ( 3297) covalent geometry : bond 0.00331 (20204) covalent geometry : angle 0.56839 (27452) *********************** 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 365 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 321 time to evaluate : 2.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 578 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.7585 (tpp) REVERT: A 588 ASN cc_start: 0.8465 (m-40) cc_final: 0.8118 (m-40) REVERT: A 605 MET cc_start: 0.8291 (mmm) cc_final: 0.7963 (mtm) REVERT: A 685 MET cc_start: 0.7673 (tpp) cc_final: 0.7396 (mtt) REVERT: B 605 MET cc_start: 0.7834 (mmp) cc_final: 0.6943 (mmm) REVERT: B 625 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7680 (mpp) REVERT: D 605 MET cc_start: 0.8079 (mmp) cc_final: 0.7117 (mtp) REVERT: C 252 HIS cc_start: 0.7661 (p-80) cc_final: 0.7416 (p-80) REVERT: C 345 MET cc_start: 0.9116 (OUTLIER) cc_final: 0.8839 (tpp) REVERT: C 550 GLN cc_start: 0.8796 (mt0) cc_final: 0.8487 (mp10) REVERT: C 588 ASN cc_start: 0.8389 (m-40) cc_final: 0.8024 (m-40) outliers start: 44 outliers final: 27 residues processed: 348 average time/residue: 0.2984 time to fit residues: 160.8829 Evaluate side-chains 334 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 304 time to evaluate : 2.087 ------------------------------------------------------------------------------- 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 379 LYS 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 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 395 THR 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 250 CYS Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 345 MET 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 551 LEU 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 213 optimal weight: 0.5980 chunk 137 optimal weight: 1.9990 chunk 18 optimal weight: 0.2980 chunk 0 optimal weight: 20.0000 chunk 243 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 219 optimal weight: 8.9990 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 228 ASN ** 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 = 0.4365 r_free = 0.4365 target = 0.206097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.155888 restraints weight = 27665.044| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.48 r_work: 0.3522 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2173 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= 0.120 Angle : 0.563 8.823 27452 Z= 0.279 Chirality : 0.037 0.148 3144 Planarity : 0.004 0.041 3420 Dihedral : 5.222 63.891 2876 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.09 % Allowed : 15.46 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.17), residues: 2448 helix: 1.53 (0.13), residues: 1512 sheet: -3.24 (0.58), residues: 76 loop : -0.12 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 733 HIS 0.003 0.001 HIS C 326 PHE 0.017 0.001 PHE A 554 TYR 0.017 0.001 TYR A 702 ARG 0.007 0.000 ARG B 186 Details of bonding type rmsd hydrogen bonds : bond 0.03375 ( 1138) hydrogen bonds : angle 3.70282 ( 3297) covalent geometry : bond 0.00274 (20204) covalent geometry : angle 0.56274 (27452) *********************** 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 369 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 325 time to evaluate : 2.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 GLU cc_start: 0.8025 (mp0) cc_final: 0.7824 (pm20) REVERT: A 578 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.7606 (tpp) REVERT: A 588 ASN cc_start: 0.8459 (m-40) cc_final: 0.8129 (m-40) REVERT: A 605 MET cc_start: 0.8325 (mmm) cc_final: 0.8017 (mtm) REVERT: A 685 MET cc_start: 0.7624 (tpp) cc_final: 0.7306 (mtt) REVERT: B 255 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7334 (mt-10) REVERT: B 383 ILE cc_start: 0.9173 (OUTLIER) cc_final: 0.8901 (mt) REVERT: B 605 MET cc_start: 0.7860 (mmp) cc_final: 0.7061 (mmm) REVERT: B 625 MET cc_start: 0.7984 (OUTLIER) cc_final: 0.7488 (mmm) REVERT: D 383 ILE cc_start: 0.9193 (OUTLIER) cc_final: 0.8865 (mt) REVERT: D 550 GLN cc_start: 0.8888 (mp10) cc_final: 0.7947 (mp10) REVERT: D 605 MET cc_start: 0.8113 (mmt) cc_final: 0.7283 (mtp) REVERT: C 345 MET cc_start: 0.9099 (OUTLIER) cc_final: 0.8852 (tpp) REVERT: C 379 LYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8782 (ttmt) REVERT: C 383 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8834 (mt) REVERT: C 473 ILE cc_start: 0.9382 (mt) cc_final: 0.9106 (mt) REVERT: C 550 GLN cc_start: 0.8852 (mt0) cc_final: 0.8336 (mp10) REVERT: C 588 ASN cc_start: 0.8395 (m-40) cc_final: 0.8046 (m-40) REVERT: C 718 MET cc_start: 0.7938 (ptt) cc_final: 0.7226 (ptt) outliers start: 44 outliers final: 30 residues processed: 349 average time/residue: 0.2879 time to fit residues: 156.3947 Evaluate side-chains 345 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 308 time to evaluate : 1.966 ------------------------------------------------------------------------------- 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 328 LEU Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 486 THR 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 554 PHE 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 356 LEU Chi-restraints excluded: chain D residue 383 ILE 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 153 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 345 MET 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 551 LEU Chi-restraints excluded: chain C residue 609 ILE 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 126 optimal weight: 5.9990 chunk 187 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 185 optimal weight: 7.9990 chunk 169 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 194 optimal weight: 0.6980 chunk 188 optimal weight: 0.9980 chunk 49 optimal weight: 0.0040 chunk 121 optimal weight: 0.9980 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.206718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.156392 restraints weight = 27528.157| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 2.46 r_work: 0.3503 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20204 Z= 0.113 Angle : 0.570 10.571 27452 Z= 0.280 Chirality : 0.037 0.154 3144 Planarity : 0.003 0.041 3420 Dihedral : 5.079 61.903 2876 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.28 % Allowed : 16.03 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.17), residues: 2448 helix: 1.58 (0.13), residues: 1512 sheet: -3.24 (0.58), residues: 76 loop : -0.13 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 409 HIS 0.011 0.001 HIS C 252 PHE 0.017 0.001 PHE A 554 TYR 0.019 0.001 TYR C 253 ARG 0.005 0.000 ARG B 186 Details of bonding type rmsd hydrogen bonds : bond 0.03273 ( 1138) hydrogen bonds : angle 3.68075 ( 3297) covalent geometry : bond 0.00255 (20204) covalent geometry : angle 0.56981 (27452) *********************** 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 370 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 322 time to evaluate : 2.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 383 ILE cc_start: 0.9191 (OUTLIER) cc_final: 0.8897 (mt) REVERT: A 578 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.7729 (tpp) REVERT: A 588 ASN cc_start: 0.8410 (m-40) cc_final: 0.8115 (m-40) REVERT: A 605 MET cc_start: 0.8325 (mmm) cc_final: 0.8049 (mtm) REVERT: A 607 GLN cc_start: 0.7983 (mm110) cc_final: 0.7506 (mt0) REVERT: A 685 MET cc_start: 0.7649 (tpp) cc_final: 0.7331 (mtt) REVERT: B 255 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7336 (mt-10) REVERT: B 383 ILE cc_start: 0.9184 (OUTLIER) cc_final: 0.8913 (mt) REVERT: B 605 MET cc_start: 0.7768 (mmp) cc_final: 0.7054 (mmm) REVERT: B 625 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7699 (mpp) REVERT: D 383 ILE cc_start: 0.9201 (OUTLIER) cc_final: 0.8839 (mt) REVERT: D 550 GLN cc_start: 0.8930 (mp10) cc_final: 0.8028 (mp10) REVERT: D 605 MET cc_start: 0.8117 (mmt) cc_final: 0.7304 (mtp) REVERT: C 345 MET cc_start: 0.9141 (OUTLIER) cc_final: 0.8914 (tpp) REVERT: C 379 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8714 (ttmt) REVERT: C 473 ILE cc_start: 0.9389 (mt) cc_final: 0.9105 (mt) REVERT: C 550 GLN cc_start: 0.8780 (mt0) cc_final: 0.8475 (mp10) REVERT: C 588 ASN cc_start: 0.8397 (m-40) cc_final: 0.8163 (m-40) REVERT: C 718 MET cc_start: 0.7770 (ptt) cc_final: 0.7520 (ptt) outliers start: 48 outliers final: 33 residues processed: 352 average time/residue: 0.2821 time to fit residues: 156.0401 Evaluate side-chains 352 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 312 time to evaluate : 1.981 ------------------------------------------------------------------------------- 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 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 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 551 LEU 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 356 LEU Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 444 GLU Chi-restraints excluded: chain D residue 543 LEU 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 622 LEU Chi-restraints excluded: chain D residue 781 ASP Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 345 MET 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 551 LEU Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 717 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 106 optimal weight: 3.9990 chunk 196 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 161 optimal weight: 0.0870 chunk 112 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 205 optimal weight: 0.9980 chunk 100 optimal weight: 10.0000 chunk 195 optimal weight: 3.9990 chunk 229 optimal weight: 0.9980 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN ** 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 = 0.4365 r_free = 0.4365 target = 0.205945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.156961 restraints weight = 28029.107| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.39 r_work: 0.3516 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2418 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= 0.123 Angle : 0.585 11.254 27452 Z= 0.284 Chirality : 0.038 0.162 3144 Planarity : 0.003 0.041 3420 Dihedral : 5.025 61.040 2876 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.23 % Allowed : 16.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.17), residues: 2448 helix: 1.69 (0.13), residues: 1476 sheet: -3.31 (0.58), residues: 76 loop : -0.24 (0.22), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 463 HIS 0.005 0.001 HIS C 252 PHE 0.018 0.001 PHE A 554 TYR 0.016 0.001 TYR C 253 ARG 0.003 0.000 ARG B 186 Details of bonding type rmsd hydrogen bonds : bond 0.03254 ( 1138) hydrogen bonds : angle 3.71062 ( 3297) covalent geometry : bond 0.00285 (20204) covalent geometry : angle 0.58488 (27452) *********************** 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 367 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 320 time to evaluate : 2.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 ARG cc_start: 0.8483 (mpt90) cc_final: 0.8236 (mpt90) REVERT: A 383 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.8947 (mt) REVERT: A 578 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.7765 (tpp) REVERT: A 588 ASN cc_start: 0.8415 (m-40) cc_final: 0.8102 (m-40) REVERT: A 605 MET cc_start: 0.8330 (mmm) cc_final: 0.8113 (mtm) REVERT: A 607 GLN cc_start: 0.7914 (mm110) cc_final: 0.7514 (mt0) REVERT: A 685 MET cc_start: 0.7649 (tpp) cc_final: 0.7333 (mtt) REVERT: B 255 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7335 (mt-10) REVERT: B 383 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.8935 (mt) REVERT: B 605 MET cc_start: 0.7812 (mmp) cc_final: 0.7148 (mmm) REVERT: B 625 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7695 (mpp) REVERT: D 383 ILE cc_start: 0.9231 (OUTLIER) cc_final: 0.8994 (mt) REVERT: D 605 MET cc_start: 0.8189 (mmt) cc_final: 0.7392 (mtp) REVERT: C 345 MET cc_start: 0.9106 (OUTLIER) cc_final: 0.8877 (tpp) REVERT: C 379 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8903 (ttmt) REVERT: C 383 ILE cc_start: 0.9173 (OUTLIER) cc_final: 0.8916 (mt) REVERT: C 473 ILE cc_start: 0.9391 (mt) cc_final: 0.9087 (mt) REVERT: C 550 GLN cc_start: 0.8753 (mt0) cc_final: 0.8441 (mp10) REVERT: C 588 ASN cc_start: 0.8368 (m-40) cc_final: 0.8035 (m-40) outliers start: 47 outliers final: 36 residues processed: 350 average time/residue: 0.2904 time to fit residues: 159.4605 Evaluate side-chains 354 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 310 time to evaluate : 2.123 ------------------------------------------------------------------------------- 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 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 551 LEU Chi-restraints excluded: chain B residue 625 MET Chi-restraints excluded: chain D residue 153 ILE 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 444 GLU Chi-restraints excluded: chain D residue 543 LEU 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 153 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 345 MET 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 551 LEU Chi-restraints excluded: chain C residue 609 ILE 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 60 optimal weight: 0.5980 chunk 193 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 148 optimal weight: 0.8980 chunk 229 optimal weight: 0.9990 chunk 111 optimal weight: 8.9990 chunk 211 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 49 optimal weight: 0.0670 chunk 48 optimal weight: 0.7980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN A 239 GLN A 252 HIS ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.207217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.157953 restraints weight = 27687.643| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.37 r_work: 0.3532 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20204 Z= 0.109 Angle : 0.586 10.633 27452 Z= 0.284 Chirality : 0.038 0.232 3144 Planarity : 0.003 0.040 3420 Dihedral : 4.907 58.728 2876 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.85 % Allowed : 17.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.17), residues: 2448 helix: 1.74 (0.13), residues: 1480 sheet: -3.30 (0.57), residues: 76 loop : -0.22 (0.22), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 409 HIS 0.005 0.001 HIS A 252 PHE 0.018 0.001 PHE A 554 TYR 0.014 0.001 TYR C 253 ARG 0.003 0.000 ARG B 186 Details of bonding type rmsd hydrogen bonds : bond 0.03154 ( 1138) hydrogen bonds : angle 3.70247 ( 3297) covalent geometry : bond 0.00246 (20204) covalent geometry : angle 0.58562 (27452) *********************** 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 360 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 321 time to evaluate : 2.031 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 228 ASN cc_start: 0.9217 (OUTLIER) cc_final: 0.8969 (p0) REVERT: A 379 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8717 (ttmt) REVERT: A 383 ILE cc_start: 0.9202 (OUTLIER) cc_final: 0.8846 (mt) REVERT: A 578 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.7824 (tpp) REVERT: A 588 ASN cc_start: 0.8379 (m-40) cc_final: 0.8059 (m-40) REVERT: A 605 MET cc_start: 0.8051 (mmm) cc_final: 0.7702 (mtm) REVERT: A 685 MET cc_start: 0.7663 (tpp) cc_final: 0.7352 (mtt) REVERT: B 383 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8907 (mt) REVERT: B 605 MET cc_start: 0.7842 (mmp) cc_final: 0.7143 (mmm) REVERT: B 625 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7684 (mpp) REVERT: D 383 ILE cc_start: 0.9203 (OUTLIER) cc_final: 0.8833 (mt) REVERT: D 605 MET cc_start: 0.8180 (mmt) cc_final: 0.7409 (mtp) REVERT: C 345 MET cc_start: 0.9086 (OUTLIER) cc_final: 0.8871 (tpp) REVERT: C 379 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8830 (ttmt) REVERT: C 383 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8916 (mt) REVERT: C 473 ILE cc_start: 0.9369 (mt) cc_final: 0.9073 (mt) REVERT: C 550 GLN cc_start: 0.8710 (mt0) cc_final: 0.8407 (mp10) REVERT: C 588 ASN cc_start: 0.8396 (m-40) cc_final: 0.8154 (m-40) REVERT: C 713 MET cc_start: 0.8381 (tmm) cc_final: 0.7986 (mmt) outliers start: 39 outliers final: 28 residues processed: 346 average time/residue: 0.2914 time to fit residues: 158.1962 Evaluate side-chains 348 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 310 time to evaluate : 2.297 ------------------------------------------------------------------------------- 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 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 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 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 444 GLU Chi-restraints excluded: chain D residue 543 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 345 MET 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 551 LEU Chi-restraints excluded: chain C residue 717 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 179 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 67 optimal weight: 0.0040 chunk 143 optimal weight: 4.9990 chunk 224 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 215 optimal weight: 0.9980 chunk 87 optimal weight: 0.0030 chunk 64 optimal weight: 9.9990 overall best weight: 0.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN ** 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 = 0.4378 r_free = 0.4378 target = 0.207445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.157595 restraints weight = 27781.799| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 2.43 r_work: 0.3542 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20204 Z= 0.112 Angle : 0.600 10.649 27452 Z= 0.290 Chirality : 0.038 0.186 3144 Planarity : 0.003 0.039 3420 Dihedral : 4.849 57.848 2876 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.94 % Allowed : 17.46 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.17), residues: 2448 helix: 1.76 (0.13), residues: 1476 sheet: -3.34 (0.57), residues: 76 loop : -0.26 (0.22), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 409 HIS 0.005 0.001 HIS C 252 PHE 0.018 0.001 PHE A 554 TYR 0.014 0.001 TYR C 253 ARG 0.003 0.000 ARG B 186 Details of bonding type rmsd hydrogen bonds : bond 0.03140 ( 1138) hydrogen bonds : angle 3.70029 ( 3297) covalent geometry : bond 0.00253 (20204) covalent geometry : angle 0.60048 (27452) ********************** 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 360 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 319 time to evaluate : 2.121 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: 0.9199 (OUTLIER) cc_final: 0.8927 (p0) REVERT: A 379 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8678 (ttmt) REVERT: A 578 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.7829 (tpp) REVERT: A 588 ASN cc_start: 0.8377 (m-40) cc_final: 0.8093 (m-40) REVERT: A 605 MET cc_start: 0.7994 (mmm) cc_final: 0.7634 (mtm) REVERT: A 685 MET cc_start: 0.7662 (tpp) cc_final: 0.7354 (mtt) REVERT: B 383 ILE cc_start: 0.9181 (OUTLIER) cc_final: 0.8909 (mt) REVERT: B 588 ASN cc_start: 0.8460 (m-40) cc_final: 0.8093 (m-40) REVERT: B 605 MET cc_start: 0.7856 (mmp) cc_final: 0.7184 (mmm) REVERT: B 625 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7735 (mpp) REVERT: D 383 ILE cc_start: 0.9208 (OUTLIER) cc_final: 0.8948 (mt) REVERT: D 605 MET cc_start: 0.8186 (mmt) cc_final: 0.7432 (mtp) REVERT: C 379 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8789 (ttmt) REVERT: C 383 ILE cc_start: 0.9180 (OUTLIER) cc_final: 0.8930 (mt) REVERT: C 473 ILE cc_start: 0.9382 (mt) cc_final: 0.9092 (mt) REVERT: C 550 GLN cc_start: 0.8713 (mt0) cc_final: 0.8432 (mp10) REVERT: C 588 ASN cc_start: 0.8401 (m-40) cc_final: 0.8144 (m-40) REVERT: C 713 MET cc_start: 0.8357 (tmm) cc_final: 0.7841 (tpp) outliers start: 41 outliers final: 29 residues processed: 345 average time/residue: 0.2839 time to fit residues: 153.7310 Evaluate side-chains 350 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 313 time to evaluate : 2.038 ------------------------------------------------------------------------------- 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 227 ILE Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 328 LEU 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 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 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 356 LEU Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 444 GLU Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain D residue 781 ASP Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 341 PHE 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 551 LEU Chi-restraints excluded: chain C residue 717 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 120 optimal weight: 0.3980 chunk 241 optimal weight: 0.8980 chunk 2 optimal weight: 10.0000 chunk 23 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 chunk 226 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 201 optimal weight: 0.8980 chunk 15 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.207449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.157498 restraints weight = 27958.598| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.44 r_work: 0.3533 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.174 20204 Z= 0.142 Angle : 0.754 59.178 27452 Z= 0.402 Chirality : 0.038 0.336 3144 Planarity : 0.004 0.063 3420 Dihedral : 4.879 57.239 2876 Min Nonbonded Distance : 1.617 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.04 % Allowed : 17.50 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.17), residues: 2448 helix: 1.76 (0.13), residues: 1476 sheet: -3.34 (0.57), residues: 76 loop : -0.27 (0.22), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 409 HIS 0.005 0.001 HIS C 252 PHE 0.017 0.001 PHE A 554 TYR 0.014 0.001 TYR C 253 ARG 0.010 0.000 ARG A 219 Details of bonding type rmsd hydrogen bonds : bond 0.03140 ( 1138) hydrogen bonds : angle 3.70137 ( 3297) covalent geometry : bond 0.00314 (20204) covalent geometry : angle 0.75367 (27452) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9084.25 seconds wall clock time: 157 minutes 57.85 seconds (9477.85 seconds total)