Starting phenix.real_space_refine on Sun May 3 22:25:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11sz_76027/05_2026/11sz_76027.cif Found real_map, /net/cci-nas-00/data/ceres_data/11sz_76027/05_2026/11sz_76027.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/11sz_76027/05_2026/11sz_76027.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11sz_76027/05_2026/11sz_76027.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/11sz_76027/05_2026/11sz_76027.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11sz_76027/05_2026/11sz_76027.map" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 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 64 5.16 5 C 9849 2.51 5 N 2800 2.21 5 O 3030 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15743 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 890, 6580 Classifications: {'peptide': 890} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 39, 'TRANS': 850} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 6595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 892, 6595 Classifications: {'peptide': 892} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 39, 'TRANS': 852} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 461 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "D" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 861 Classifications: {'peptide': 113} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 103} Chain: "H" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 888 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 114} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "L" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 358 Classifications: {'peptide': 44} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 39} Chain breaks: 1 Time building chain proxies: 4.15, per 1000 atoms: 0.26 Number of scatterers: 15743 At special positions: 0 Unit cell: (105.6, 135.3, 204.6, 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 64 16.00 O 3030 8.00 N 2800 7.00 C 9849 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 39 " - pdb=" SG CYS D 109 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 810.8 milliseconds 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3792 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 21 sheets defined 40.4% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 13 through 33 removed outlier: 4.054A pdb=" N ARG A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU A 29 " --> pdb=" O GLN A 25 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N LEU A 30 " --> pdb=" O ARG A 26 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N GLU A 31 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU A 32 " --> pdb=" O ARG A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 60 Processing helix chain 'A' and resid 105 through 110 removed outlier: 3.927A pdb=" N PHE A 109 " --> pdb=" O ASP A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 118 Processing helix chain 'A' and resid 120 through 137 Processing helix chain 'A' and resid 140 through 144 removed outlier: 3.979A pdb=" N LEU A 144 " --> pdb=" O PRO A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 166 removed outlier: 3.803A pdb=" N ARG A 163 " --> pdb=" O ASP A 159 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG A 166 " --> pdb=" O MET A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 178 Processing helix chain 'A' and resid 181 through 192 removed outlier: 3.729A pdb=" N GLY A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 205 through 220 Processing helix chain 'A' and resid 237 through 247 removed outlier: 3.647A pdb=" N VAL A 241 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 286 Processing helix chain 'A' and resid 311 through 327 Processing helix chain 'A' and resid 329 through 333 removed outlier: 4.158A pdb=" N VAL A 333 " --> pdb=" O THR A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 359 removed outlier: 3.686A pdb=" N ILE A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 380 No H-bonds generated for 'chain 'A' and resid 378 through 380' Processing helix chain 'A' and resid 381 through 397 removed outlier: 3.735A pdb=" N ALA A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 417 removed outlier: 3.684A pdb=" N ALA A 416 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLY A 417 " --> pdb=" O TRP A 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 413 through 417' Processing helix chain 'A' and resid 480 through 498 Processing helix chain 'A' and resid 502 through 513 Processing helix chain 'A' and resid 527 through 538 Processing helix chain 'A' and resid 567 through 574 Processing helix chain 'A' and resid 574 through 590 Processing helix chain 'A' and resid 596 through 604 removed outlier: 3.575A pdb=" N VAL A 600 " --> pdb=" O PRO A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 609 removed outlier: 3.593A pdb=" N ASP A 609 " --> pdb=" O ALA A 606 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 606 through 609' Processing helix chain 'A' and resid 610 through 632 Processing helix chain 'A' and resid 643 through 653 removed outlier: 4.094A pdb=" N LEU A 647 " --> pdb=" O SER A 643 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA A 648 " --> pdb=" O ILE A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 674 removed outlier: 3.717A pdb=" N ALA A 674 " --> pdb=" O ARG A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 692 Processing helix chain 'A' and resid 716 through 729 removed outlier: 3.862A pdb=" N ARG A 729 " --> pdb=" O GLU A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 748 Processing helix chain 'A' and resid 749 through 759 removed outlier: 4.806A pdb=" N ASP A 753 " --> pdb=" O PRO A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 793 Processing helix chain 'A' and resid 797 through 807 Processing helix chain 'A' and resid 819 through 830 removed outlier: 3.672A pdb=" N ALA A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 859 Processing helix chain 'A' and resid 865 through 869 removed outlier: 3.659A pdb=" N THR A 868 " --> pdb=" O ASP A 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 27 removed outlier: 4.671A pdb=" N LEU B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA B 22 " --> pdb=" O LEU B 18 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ALA B 23 " --> pdb=" O ASP B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 32 Processing helix chain 'B' and resid 50 through 60 Processing helix chain 'B' and resid 75 through 80 removed outlier: 3.765A pdb=" N LEU B 79 " --> pdb=" O ASP B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 118 Processing helix chain 'B' and resid 120 through 137 removed outlier: 3.512A pdb=" N ARG B 124 " --> pdb=" O ASP B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 144 removed outlier: 3.983A pdb=" N LEU B 144 " --> pdb=" O PRO B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 165 removed outlier: 3.984A pdb=" N ARG B 163 " --> pdb=" O ASP B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 179 removed outlier: 3.824A pdb=" N GLY B 177 " --> pdb=" O PHE B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 192 removed outlier: 4.066A pdb=" N SER B 184 " --> pdb=" O ALA B 180 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL B 187 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 204 No H-bonds generated for 'chain 'B' and resid 202 through 204' Processing helix chain 'B' and resid 205 through 219 removed outlier: 3.614A pdb=" N LEU B 211 " --> pdb=" O SER B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 247 removed outlier: 3.630A pdb=" N VAL B 241 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN B 246 " --> pdb=" O GLU B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 286 Processing helix chain 'B' and resid 311 through 327 Processing helix chain 'B' and resid 329 through 333 removed outlier: 3.962A pdb=" N VAL B 333 " --> pdb=" O THR B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 359 removed outlier: 3.673A pdb=" N ILE B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 381 Processing helix chain 'B' and resid 382 through 397 Processing helix chain 'B' and resid 413 through 417 removed outlier: 3.753A pdb=" N ALA B 416 " --> pdb=" O ASP B 413 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLY B 417 " --> pdb=" O TRP B 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 413 through 417' Processing helix chain 'B' and resid 480 through 498 Processing helix chain 'B' and resid 502 through 513 Processing helix chain 'B' and resid 527 through 538 Processing helix chain 'B' and resid 567 through 574 Processing helix chain 'B' and resid 574 through 590 Processing helix chain 'B' and resid 596 through 603 Processing helix chain 'B' and resid 606 through 610 Processing helix chain 'B' and resid 611 through 632 removed outlier: 3.535A pdb=" N TRP B 632 " --> pdb=" O LEU B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 653 removed outlier: 4.143A pdb=" N LEU B 647 " --> pdb=" O SER B 643 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA B 648 " --> pdb=" O ILE B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 674 removed outlier: 3.872A pdb=" N ALA B 674 " --> pdb=" O ARG B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 692 Processing helix chain 'B' and resid 716 through 728 Processing helix chain 'B' and resid 744 through 749 Proline residue: B 749 - end of helix Processing helix chain 'B' and resid 750 through 759 removed outlier: 3.616A pdb=" N PHE B 754 " --> pdb=" O MET B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 793 Processing helix chain 'B' and resid 797 through 808 Processing helix chain 'B' and resid 819 through 830 removed outlier: 3.763A pdb=" N ALA B 823 " --> pdb=" O GLY B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 860 removed outlier: 3.593A pdb=" N ARG B 860 " --> pdb=" O GLU B 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 869 removed outlier: 3.878A pdb=" N THR B 868 " --> pdb=" O ASP B 865 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 69 removed outlier: 4.140A pdb=" N LYS C 69 " --> pdb=" O ALA C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 95 removed outlier: 3.563A pdb=" N ASP C 94 " --> pdb=" O LYS C 91 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR C 95 " --> pdb=" O THR C 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 91 through 95' Processing helix chain 'D' and resid 100 through 104 removed outlier: 3.870A pdb=" N ASP D 103 " --> pdb=" O GLU D 100 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL D 104 " --> pdb=" O ALA D 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 100 through 104' Processing helix chain 'H' and resid 65 through 69 removed outlier: 3.621A pdb=" N LYS H 69 " --> pdb=" O ALA H 66 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 419 through 421 removed outlier: 5.940A pdb=" N LEU A 366 " --> pdb=" O GLU A 420 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA A 335 " --> pdb=" O ARG A 436 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLY A 295 " --> pdb=" O VAL A 452 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLU A 454 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N VAL A 293 " --> pdb=" O GLU A 454 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA A 291 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ILE A 37 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N GLU A 277 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA A 39 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL A 231 " --> pdb=" O GLY A 154 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N VAL A 198 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL A 151 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N VAL A 200 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA A 153 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N THR A 199 " --> pdb=" O ASP B 201 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THR B 199 " --> pdb=" O ASP A 201 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N VAL B 198 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL B 151 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N VAL B 200 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ALA B 153 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY B 229 " --> pdb=" O PHE B 152 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 231 " --> pdb=" O GLY B 154 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA B 39 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N GLU B 277 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ILE B 37 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA B 291 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N VAL B 293 " --> pdb=" O GLU B 454 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLU B 454 " --> pdb=" O VAL B 293 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY B 295 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA B 335 " --> pdb=" O ARG B 436 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY B 369 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 67 Processing sheet with id=AA3, first strand: chain 'A' and resid 103 through 104 Processing sheet with id=AA4, first strand: chain 'A' and resid 398 through 399 Processing sheet with id=AA5, first strand: chain 'A' and resid 472 through 478 Processing sheet with id=AA6, first strand: chain 'A' and resid 770 through 771 removed outlier: 6.885A pdb=" N LEU A 639 " --> pdb=" O VAL A 771 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LYS A 551 " --> pdb=" O SER A 810 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N PHE A 812 " --> pdb=" O LYS A 551 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ALA A 553 " --> pdb=" O PHE A 812 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLU A 814 " --> pdb=" O ALA A 553 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU A 555 " --> pdb=" O GLU A 814 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 733 through 734 removed outlier: 6.299A pdb=" N SER A 713 " --> pdb=" O VAL A 701 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N VAL A 701 " --> pdb=" O SER A 713 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N THR A 715 " --> pdb=" O VAL A 699 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL A 699 " --> pdb=" O THR A 715 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 66 through 67 Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 104 Processing sheet with id=AB1, first strand: chain 'B' and resid 398 through 399 Processing sheet with id=AB2, first strand: chain 'B' and resid 472 through 478 Processing sheet with id=AB3, first strand: chain 'B' and resid 638 through 641 removed outlier: 6.938A pdb=" N LEU B 552 " --> pdb=" O LEU B 638 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N ALA B 640 " --> pdb=" O LEU B 552 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N VAL B 554 " --> pdb=" O ALA B 640 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LYS B 551 " --> pdb=" O ALA B 809 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N VAL B 837 " --> pdb=" O SER B 810 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N PHE B 812 " --> pdb=" O VAL B 837 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 733 through 734 removed outlier: 5.559A pdb=" N SER B 713 " --> pdb=" O VAL B 701 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL B 701 " --> pdb=" O SER B 713 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N THR B 715 " --> pdb=" O VAL B 699 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL B 699 " --> pdb=" O THR B 715 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 72 through 75 Processing sheet with id=AB6, first strand: chain 'C' and resid 96 through 98 Processing sheet with id=AB7, first strand: chain 'D' and resid 35 through 40 Processing sheet with id=AB8, first strand: chain 'D' and resid 66 through 69 removed outlier: 6.706A pdb=" N TRP D 56 " --> pdb=" O LEU D 68 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 5 through 9 removed outlier: 3.697A pdb=" N LEU H 22 " --> pdb=" O LEU H 85 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 47 through 53 removed outlier: 3.696A pdb=" N VAL H 50 " --> pdb=" O TRP H 38 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N TRP H 38 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N PHE H 52 " --> pdb=" O MET H 36 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N MET H 36 " --> pdb=" O PHE H 52 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 55 through 58 Processing sheet with id=AC3, first strand: chain 'L' and resid 69 through 70 704 hydrogen bonds defined for protein. 1965 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.21 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4624 1.33 - 1.45: 2627 1.45 - 1.57: 8697 1.57 - 1.69: 0 1.69 - 1.82: 106 Bond restraints: 16054 Sorted by residual: bond pdb=" N VAL A 200 " pdb=" CA VAL A 200 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.15e-02 7.56e+03 1.04e+01 bond pdb=" CA SER A 207 " pdb=" CB SER A 207 " ideal model delta sigma weight residual 1.530 1.488 0.041 1.56e-02 4.11e+03 7.07e+00 bond pdb=" N THR A 202 " pdb=" CA THR A 202 " ideal model delta sigma weight residual 1.458 1.489 -0.032 1.22e-02 6.72e+03 6.71e+00 bond pdb=" N GLU B 833 " pdb=" CA GLU B 833 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.17e-02 7.31e+03 6.17e+00 bond pdb=" N GLY B 831 " pdb=" CA GLY B 831 " ideal model delta sigma weight residual 1.443 1.476 -0.033 1.37e-02 5.33e+03 5.77e+00 ... (remaining 16049 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 21583 2.15 - 4.31: 218 4.31 - 6.46: 37 6.46 - 8.61: 8 8.61 - 10.77: 6 Bond angle restraints: 21852 Sorted by residual: angle pdb=" C ALA A 203 " pdb=" CA ALA A 203 " pdb=" CB ALA A 203 " ideal model delta sigma weight residual 117.23 111.54 5.69 1.36e+00 5.41e-01 1.75e+01 angle pdb=" CB LYS A 732 " pdb=" CG LYS A 732 " pdb=" CD LYS A 732 " ideal model delta sigma weight residual 111.30 120.42 -9.12 2.30e+00 1.89e-01 1.57e+01 angle pdb=" N GLY B 830 " pdb=" CA GLY B 830 " pdb=" C GLY B 830 " ideal model delta sigma weight residual 115.30 110.06 5.24 1.44e+00 4.82e-01 1.33e+01 angle pdb=" CB MET A 750 " pdb=" CG MET A 750 " pdb=" SD MET A 750 " ideal model delta sigma weight residual 112.70 123.47 -10.77 3.00e+00 1.11e-01 1.29e+01 angle pdb=" CB MET D 110 " pdb=" CG MET D 110 " pdb=" SD MET D 110 " ideal model delta sigma weight residual 112.70 123.18 -10.48 3.00e+00 1.11e-01 1.22e+01 ... (remaining 21847 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 8197 17.98 - 35.96: 943 35.96 - 53.94: 274 53.94 - 71.92: 41 71.92 - 89.90: 15 Dihedral angle restraints: 9470 sinusoidal: 3525 harmonic: 5945 Sorted by residual: dihedral pdb=" CA ILE B 27 " pdb=" C ILE B 27 " pdb=" N ARG B 28 " pdb=" CA ARG B 28 " ideal model delta harmonic sigma weight residual 180.00 -160.03 -19.97 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CG ARG B 124 " pdb=" CD ARG B 124 " pdb=" NE ARG B 124 " pdb=" CZ ARG B 124 " ideal model delta sinusoidal sigma weight residual 180.00 135.23 44.77 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CG ARG A 56 " pdb=" CD ARG A 56 " pdb=" NE ARG A 56 " pdb=" CZ ARG A 56 " ideal model delta sinusoidal sigma weight residual 90.00 134.18 -44.18 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 9467 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1694 0.033 - 0.066: 555 0.066 - 0.099: 142 0.099 - 0.131: 100 0.131 - 0.164: 2 Chirality restraints: 2493 Sorted by residual: chirality pdb=" CA VAL A 200 " pdb=" N VAL A 200 " pdb=" C VAL A 200 " pdb=" CB VAL A 200 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.16 2.00e-01 2.50e+01 6.75e-01 chirality pdb=" CA PRO A 749 " pdb=" N PRO A 749 " pdb=" C PRO A 749 " pdb=" CB PRO A 749 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.34e-01 chirality pdb=" CA ARG B 26 " pdb=" N ARG B 26 " pdb=" C ARG B 26 " pdb=" CB ARG B 26 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.32e-01 ... (remaining 2490 not shown) Planarity restraints: 2889 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 312 " 0.031 5.00e-02 4.00e+02 4.70e-02 3.54e+00 pdb=" N PRO B 313 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 313 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 313 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 91 " -0.010 2.00e-02 2.50e+03 1.28e-02 3.30e+00 pdb=" CG TYR B 91 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR B 91 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR B 91 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR B 91 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 91 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 91 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 91 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 312 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.26e+00 pdb=" N PRO A 313 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 313 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 313 " 0.025 5.00e-02 4.00e+02 ... (remaining 2886 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2945 2.77 - 3.30: 14169 3.30 - 3.84: 25319 3.84 - 4.37: 27835 4.37 - 4.90: 50846 Nonbonded interactions: 121114 Sorted by model distance: nonbonded pdb=" O LEU A 126 " pdb=" OG SER A 130 " model vdw 2.238 3.040 nonbonded pdb=" OG SER B 207 " pdb=" O ALA B 380 " model vdw 2.244 3.040 nonbonded pdb=" NH2 ARG L 75 " pdb=" O PRO L 80 " model vdw 2.252 3.120 nonbonded pdb=" O ASP D 17 " pdb=" NE2 GLN D 114 " model vdw 2.275 3.120 nonbonded pdb=" O ALA B 587 " pdb=" OG1 THR B 590 " model vdw 2.277 3.040 ... (remaining 121109 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 8 through 897) } 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: 8.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.890 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 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 : 0.002 0.042 16055 Z= 0.119 Angle : 0.557 10.766 21854 Z= 0.287 Chirality : 0.040 0.164 2493 Planarity : 0.004 0.047 2889 Dihedral : 16.789 89.900 5675 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 6.85 % Allowed : 25.48 % Favored : 67.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.19), residues: 2101 helix: 1.80 (0.20), residues: 695 sheet: 0.34 (0.28), residues: 358 loop : -0.21 (0.20), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 54 TYR 0.031 0.001 TYR B 91 PHE 0.005 0.001 PHE A 577 TRP 0.010 0.001 TRP H 38 HIS 0.005 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00226 (16054) covalent geometry : angle 0.55734 (21852) SS BOND : bond 0.00331 ( 1) SS BOND : angle 0.45448 ( 2) hydrogen bonds : bond 0.17152 ( 704) hydrogen bonds : angle 6.27850 ( 1965) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 115 time to evaluate : 0.675 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 689 ASP cc_start: 0.9241 (m-30) cc_final: 0.9000 (p0) REVERT: B 726 LEU cc_start: 0.8773 (mm) cc_final: 0.8526 (mm) outliers start: 110 outliers final: 96 residues processed: 222 average time/residue: 0.4632 time to fit residues: 117.0365 Evaluate side-chains 189 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 93 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 256 LYS Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 785 ASP Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 834 GLN Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 836 CYS Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 256 LYS Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 334 ASP Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 615 GLN Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 767 SER Chi-restraints excluded: chain B residue 783 SER Chi-restraints excluded: chain B residue 785 ASP Chi-restraints excluded: chain B residue 826 LEU Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 836 CYS Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain C residue 64 TYR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain L residue 109 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 0.0670 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.0020 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.0010 overall best weight: 0.2532 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN A 834 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.086683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.052021 restraints weight = 47206.100| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 3.27 r_work: 0.2699 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16055 Z= 0.100 Angle : 0.531 7.902 21854 Z= 0.267 Chirality : 0.040 0.161 2493 Planarity : 0.004 0.047 2889 Dihedral : 7.810 77.271 2434 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 5.36 % Allowed : 25.86 % Favored : 68.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.19), residues: 2101 helix: 2.27 (0.20), residues: 709 sheet: 0.49 (0.28), residues: 362 loop : -0.24 (0.20), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 40 TYR 0.013 0.001 TYR B 91 PHE 0.018 0.001 PHE H 31 TRP 0.007 0.001 TRP A 55 HIS 0.004 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00218 (16054) covalent geometry : angle 0.53084 (21852) SS BOND : bond 0.00284 ( 1) SS BOND : angle 0.65334 ( 2) hydrogen bonds : bond 0.03793 ( 704) hydrogen bonds : angle 4.63706 ( 1965) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 103 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 612 MET cc_start: 0.7296 (pmm) cc_final: 0.6769 (ptp) REVERT: A 622 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8783 (mp0) REVERT: B 726 LEU cc_start: 0.8848 (mm) cc_final: 0.8570 (mm) REVERT: B 768 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8595 (pp) REVERT: C 64 TYR cc_start: 0.6160 (OUTLIER) cc_final: 0.5710 (p90) REVERT: D 110 MET cc_start: 0.6752 (ppp) cc_final: 0.6518 (ppp) REVERT: D 111 GLN cc_start: 0.6388 (pm20) cc_final: 0.5708 (pm20) REVERT: H 41 GLN cc_start: 0.9396 (pp30) cc_final: 0.9094 (pm20) outliers start: 86 outliers final: 48 residues processed: 179 average time/residue: 0.5165 time to fit residues: 103.4128 Evaluate side-chains 147 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 96 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 615 GLN Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain B residue 785 ASP Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain C residue 64 TYR Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain L residue 63 GLN Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 109 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 71 optimal weight: 0.9990 chunk 96 optimal weight: 0.0570 chunk 182 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 208 optimal weight: 20.0000 chunk 132 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 overall best weight: 0.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 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 = 0.3656 r_free = 0.3656 target = 0.084601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.049448 restraints weight = 47529.029| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 3.26 r_work: 0.2624 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16055 Z= 0.157 Angle : 0.562 8.347 21854 Z= 0.282 Chirality : 0.041 0.142 2493 Planarity : 0.004 0.046 2889 Dihedral : 6.226 58.896 2351 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.92 % Allowed : 25.86 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.19), residues: 2101 helix: 2.32 (0.20), residues: 714 sheet: 0.45 (0.28), residues: 360 loop : -0.37 (0.20), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 40 TYR 0.015 0.001 TYR B 91 PHE 0.021 0.001 PHE H 31 TRP 0.008 0.001 TRP A 55 HIS 0.006 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00375 (16054) covalent geometry : angle 0.56211 (21852) SS BOND : bond 0.00170 ( 1) SS BOND : angle 0.35879 ( 2) hydrogen bonds : bond 0.04986 ( 704) hydrogen bonds : angle 4.54357 ( 1965) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 96 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 615 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.7532 (mp10) REVERT: C 64 TYR cc_start: 0.6143 (OUTLIER) cc_final: 0.5625 (p90) REVERT: C 85 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6222 (mp) REVERT: C 107 PHE cc_start: 0.1554 (OUTLIER) cc_final: 0.0921 (p90) REVERT: D 25 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9001 (pp) REVERT: D 45 LEU cc_start: 0.7839 (mt) cc_final: 0.7543 (mt) REVERT: D 110 MET cc_start: 0.7019 (ppp) cc_final: 0.5567 (ppp) REVERT: D 111 GLN cc_start: 0.6464 (pm20) cc_final: 0.4865 (tt0) REVERT: H 41 GLN cc_start: 0.9394 (pp30) cc_final: 0.9026 (pm20) REVERT: L 58 LEU cc_start: 0.9171 (pt) cc_final: 0.8551 (tm) outliers start: 79 outliers final: 46 residues processed: 166 average time/residue: 0.5025 time to fit residues: 93.7752 Evaluate side-chains 139 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 88 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 615 GLN Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 747 MET Chi-restraints excluded: chain B residue 826 LEU Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain C residue 64 TYR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain L residue 106 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 60 optimal weight: 0.9980 chunk 202 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 94 optimal weight: 0.4980 chunk 84 optimal weight: 0.8980 chunk 13 optimal weight: 0.0070 chunk 105 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 199 optimal weight: 0.9980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.085386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.050429 restraints weight = 47594.231| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 3.27 r_work: 0.2648 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16055 Z= 0.116 Angle : 0.538 9.751 21854 Z= 0.265 Chirality : 0.041 0.177 2493 Planarity : 0.004 0.046 2889 Dihedral : 5.840 59.024 2337 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 5.05 % Allowed : 25.48 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.19), residues: 2101 helix: 2.36 (0.20), residues: 714 sheet: 0.42 (0.28), residues: 360 loop : -0.39 (0.20), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 21 TYR 0.021 0.001 TYR H 84 PHE 0.013 0.001 PHE H 31 TRP 0.009 0.001 TRP H 49 HIS 0.006 0.000 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00271 (16054) covalent geometry : angle 0.53810 (21852) SS BOND : bond 0.00198 ( 1) SS BOND : angle 0.41257 ( 2) hydrogen bonds : bond 0.03915 ( 704) hydrogen bonds : angle 4.36281 ( 1965) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 94 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 646 GLU cc_start: 0.9203 (OUTLIER) cc_final: 0.8916 (mt-10) REVERT: A 689 ASP cc_start: 0.9264 (m-30) cc_final: 0.8957 (p0) REVERT: B 615 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.7505 (mp10) REVERT: C 64 TYR cc_start: 0.5986 (OUTLIER) cc_final: 0.5447 (p90) REVERT: C 85 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6211 (mp) REVERT: C 107 PHE cc_start: 0.1402 (OUTLIER) cc_final: 0.0842 (p90) REVERT: D 25 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9028 (pp) REVERT: D 45 LEU cc_start: 0.7823 (mt) cc_final: 0.7573 (mt) REVERT: D 110 MET cc_start: 0.6731 (ppp) cc_final: 0.5371 (ppp) REVERT: D 111 GLN cc_start: 0.6274 (pm20) cc_final: 0.4737 (tt0) REVERT: H 40 ARG cc_start: 0.7507 (ttm-80) cc_final: 0.7242 (ttp-170) REVERT: H 41 GLN cc_start: 0.9357 (pp30) cc_final: 0.8955 (pm20) REVERT: L 58 LEU cc_start: 0.9195 (pt) cc_final: 0.8599 (tm) outliers start: 81 outliers final: 47 residues processed: 167 average time/residue: 0.4801 time to fit residues: 90.6643 Evaluate side-chains 145 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 92 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 646 GLU Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 593 ARG Chi-restraints excluded: chain B residue 615 GLN Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 747 MET Chi-restraints excluded: chain B residue 826 LEU Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain C residue 64 TYR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain L residue 63 GLN Chi-restraints excluded: chain L residue 106 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 189 optimal weight: 10.0000 chunk 153 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 chunk 193 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 94 optimal weight: 0.1980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN B 843 ASN ** D 66 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 = 0.3664 r_free = 0.3664 target = 0.084926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.049933 restraints weight = 47329.354| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 3.26 r_work: 0.2635 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16055 Z= 0.128 Angle : 0.546 10.134 21854 Z= 0.269 Chirality : 0.041 0.170 2493 Planarity : 0.004 0.045 2889 Dihedral : 5.681 56.579 2335 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.67 % Allowed : 25.92 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.19), residues: 2101 helix: 2.37 (0.20), residues: 716 sheet: 0.46 (0.28), residues: 356 loop : -0.41 (0.20), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 26 TYR 0.017 0.001 TYR B 91 PHE 0.014 0.001 PHE H 31 TRP 0.008 0.001 TRP A 55 HIS 0.006 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00307 (16054) covalent geometry : angle 0.54633 (21852) SS BOND : bond 0.00164 ( 1) SS BOND : angle 0.45644 ( 2) hydrogen bonds : bond 0.04201 ( 704) hydrogen bonds : angle 4.34512 ( 1965) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 92 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 622 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8757 (mp0) REVERT: A 646 GLU cc_start: 0.9234 (OUTLIER) cc_final: 0.8948 (mt-10) REVERT: A 689 ASP cc_start: 0.9268 (m-30) cc_final: 0.8982 (p0) REVERT: C 64 TYR cc_start: 0.5898 (OUTLIER) cc_final: 0.5405 (p90) REVERT: C 85 LEU cc_start: 0.7133 (OUTLIER) cc_final: 0.6225 (mp) REVERT: C 107 PHE cc_start: 0.1168 (OUTLIER) cc_final: 0.0783 (p90) REVERT: D 25 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9072 (pp) REVERT: D 45 LEU cc_start: 0.7821 (mt) cc_final: 0.7604 (mt) REVERT: D 110 MET cc_start: 0.6616 (ppp) cc_final: 0.5186 (ppp) REVERT: D 111 GLN cc_start: 0.6312 (pm20) cc_final: 0.4703 (tt0) REVERT: L 58 LEU cc_start: 0.9228 (pt) cc_final: 0.8684 (tm) REVERT: L 63 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8201 (pp30) outliers start: 75 outliers final: 46 residues processed: 157 average time/residue: 0.5212 time to fit residues: 92.7738 Evaluate side-chains 143 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 90 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 646 GLU Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 593 ARG Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 747 MET Chi-restraints excluded: chain B residue 826 LEU Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain C residue 64 TYR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain H residue 41 GLN Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain L residue 63 GLN Chi-restraints excluded: chain L residue 106 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 24 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 139 optimal weight: 0.9980 chunk 156 optimal weight: 8.9990 chunk 31 optimal weight: 0.8980 chunk 166 optimal weight: 2.9990 chunk 3 optimal weight: 0.0060 chunk 104 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 122 optimal weight: 0.5980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 66 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 = 0.3667 r_free = 0.3667 target = 0.085092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.050238 restraints weight = 47063.490| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 3.25 r_work: 0.2649 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16055 Z= 0.116 Angle : 0.542 10.889 21854 Z= 0.266 Chirality : 0.041 0.152 2493 Planarity : 0.004 0.045 2889 Dihedral : 5.273 55.805 2327 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.49 % Allowed : 25.79 % Favored : 69.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.19), residues: 2101 helix: 2.40 (0.20), residues: 716 sheet: 0.46 (0.28), residues: 350 loop : -0.43 (0.20), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 247 TYR 0.019 0.001 TYR H 84 PHE 0.009 0.001 PHE C 72 TRP 0.007 0.001 TRP A 55 HIS 0.006 0.000 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00277 (16054) covalent geometry : angle 0.54242 (21852) SS BOND : bond 0.00189 ( 1) SS BOND : angle 0.48808 ( 2) hydrogen bonds : bond 0.03871 ( 704) hydrogen bonds : angle 4.28124 ( 1965) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 93 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 646 GLU cc_start: 0.9212 (OUTLIER) cc_final: 0.8922 (mt-10) REVERT: A 689 ASP cc_start: 0.9262 (m-30) cc_final: 0.8976 (p0) REVERT: B 750 MET cc_start: 0.8461 (pmm) cc_final: 0.7843 (ppp) REVERT: C 64 TYR cc_start: 0.5984 (OUTLIER) cc_final: 0.5453 (p90) REVERT: C 85 LEU cc_start: 0.7186 (OUTLIER) cc_final: 0.6269 (mp) REVERT: C 107 PHE cc_start: 0.1100 (OUTLIER) cc_final: 0.0679 (p90) REVERT: D 25 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9084 (pp) REVERT: D 45 LEU cc_start: 0.7795 (mt) cc_final: 0.7557 (mt) REVERT: D 110 MET cc_start: 0.6667 (ppp) cc_final: 0.5598 (ppp) REVERT: D 111 GLN cc_start: 0.6410 (pm20) cc_final: 0.5029 (tt0) REVERT: H 34 TYR cc_start: 0.4722 (OUTLIER) cc_final: 0.4364 (t80) REVERT: H 41 GLN cc_start: 0.9350 (OUTLIER) cc_final: 0.8936 (pm20) REVERT: L 58 LEU cc_start: 0.9238 (pt) cc_final: 0.8742 (tm) REVERT: L 63 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8152 (pp30) outliers start: 72 outliers final: 46 residues processed: 158 average time/residue: 0.5344 time to fit residues: 95.0092 Evaluate side-chains 142 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 88 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 646 GLU Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 593 ARG Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 747 MET Chi-restraints excluded: chain B residue 826 LEU Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain C residue 64 TYR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain H residue 34 TYR Chi-restraints excluded: chain H residue 41 GLN Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain L residue 63 GLN Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain L residue 106 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 8 optimal weight: 0.0970 chunk 119 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 142 optimal weight: 0.3980 chunk 109 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 66 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 = 0.3667 r_free = 0.3667 target = 0.085042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.050187 restraints weight = 46974.688| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 3.25 r_work: 0.2644 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16055 Z= 0.117 Angle : 0.545 10.831 21854 Z= 0.267 Chirality : 0.041 0.141 2493 Planarity : 0.004 0.044 2889 Dihedral : 5.053 55.706 2323 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.99 % Allowed : 26.79 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.19), residues: 2101 helix: 2.39 (0.20), residues: 717 sheet: 0.42 (0.28), residues: 356 loop : -0.43 (0.20), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 71 TYR 0.024 0.001 TYR B 91 PHE 0.008 0.001 PHE H 29 TRP 0.007 0.001 TRP H 38 HIS 0.006 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00279 (16054) covalent geometry : angle 0.54501 (21852) SS BOND : bond 0.00172 ( 1) SS BOND : angle 0.50646 ( 2) hydrogen bonds : bond 0.03913 ( 704) hydrogen bonds : angle 4.25797 ( 1965) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 94 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 646 GLU cc_start: 0.9231 (OUTLIER) cc_final: 0.8933 (mt-10) REVERT: A 689 ASP cc_start: 0.9258 (m-30) cc_final: 0.8970 (p0) REVERT: B 612 MET cc_start: 0.8414 (pmm) cc_final: 0.7991 (mpp) REVERT: C 64 TYR cc_start: 0.6063 (OUTLIER) cc_final: 0.5549 (p90) REVERT: C 85 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.6289 (mp) REVERT: C 107 PHE cc_start: 0.1089 (OUTLIER) cc_final: 0.0687 (p90) REVERT: D 25 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.8997 (pp) REVERT: D 45 LEU cc_start: 0.7793 (mt) cc_final: 0.7592 (mt) REVERT: D 110 MET cc_start: 0.6604 (ppp) cc_final: 0.5252 (ppp) REVERT: D 111 GLN cc_start: 0.6144 (pm20) cc_final: 0.4423 (tt0) REVERT: H 41 GLN cc_start: 0.9348 (OUTLIER) cc_final: 0.8936 (pm20) REVERT: L 58 LEU cc_start: 0.9286 (pt) cc_final: 0.8860 (tm) REVERT: L 63 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8186 (pp30) outliers start: 64 outliers final: 49 residues processed: 151 average time/residue: 0.5387 time to fit residues: 91.5791 Evaluate side-chains 148 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 92 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 646 GLU Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 593 ARG Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 826 LEU Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain C residue 64 TYR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain H residue 41 GLN Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain L residue 63 GLN Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain L residue 106 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 60 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 151 optimal weight: 0.9990 chunk 128 optimal weight: 0.8980 chunk 178 optimal weight: 0.3980 chunk 184 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 66 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 = 0.3659 r_free = 0.3659 target = 0.084724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.049799 restraints weight = 47190.252| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 3.26 r_work: 0.2637 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16055 Z= 0.129 Angle : 0.558 8.846 21854 Z= 0.274 Chirality : 0.041 0.136 2493 Planarity : 0.004 0.044 2889 Dihedral : 5.037 55.380 2320 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.24 % Allowed : 26.79 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.19), residues: 2101 helix: 2.40 (0.20), residues: 717 sheet: 0.42 (0.28), residues: 350 loop : -0.43 (0.20), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 247 TYR 0.030 0.001 TYR B 91 PHE 0.008 0.001 PHE H 29 TRP 0.007 0.001 TRP A 55 HIS 0.006 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00311 (16054) covalent geometry : angle 0.55795 (21852) SS BOND : bond 0.00191 ( 1) SS BOND : angle 0.52998 ( 2) hydrogen bonds : bond 0.04083 ( 704) hydrogen bonds : angle 4.27586 ( 1965) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 95 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 646 GLU cc_start: 0.9244 (OUTLIER) cc_final: 0.8937 (mt-10) REVERT: A 689 ASP cc_start: 0.9258 (m-30) cc_final: 0.8971 (p0) REVERT: B 612 MET cc_start: 0.8450 (pmm) cc_final: 0.8113 (mpp) REVERT: B 750 MET cc_start: 0.8346 (pmm) cc_final: 0.7501 (ppp) REVERT: C 64 TYR cc_start: 0.6172 (OUTLIER) cc_final: 0.5625 (p90) REVERT: C 85 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.6315 (mp) REVERT: C 107 PHE cc_start: 0.1111 (OUTLIER) cc_final: 0.0707 (p90) REVERT: D 25 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8935 (pp) REVERT: D 45 LEU cc_start: 0.7847 (mt) cc_final: 0.7626 (mt) REVERT: D 110 MET cc_start: 0.6618 (ppp) cc_final: 0.5164 (ppp) REVERT: D 111 GLN cc_start: 0.5886 (pm20) cc_final: 0.4552 (tt0) REVERT: H 41 GLN cc_start: 0.9341 (OUTLIER) cc_final: 0.8916 (pm20) REVERT: L 58 LEU cc_start: 0.9291 (pt) cc_final: 0.8809 (tm) REVERT: L 63 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8203 (pp30) outliers start: 68 outliers final: 50 residues processed: 157 average time/residue: 0.5277 time to fit residues: 93.8721 Evaluate side-chains 149 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 92 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 646 GLU Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 593 ARG Chi-restraints excluded: chain B residue 615 GLN Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 826 LEU Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain C residue 64 TYR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain H residue 41 GLN Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain L residue 63 GLN Chi-restraints excluded: chain L residue 106 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 91 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 43 optimal weight: 0.0670 chunk 148 optimal weight: 0.8980 chunk 167 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 24 optimal weight: 0.1980 chunk 169 optimal weight: 0.9980 chunk 196 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.085212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.050467 restraints weight = 47118.765| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 3.25 r_work: 0.2652 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16055 Z= 0.109 Angle : 0.553 9.577 21854 Z= 0.270 Chirality : 0.041 0.157 2493 Planarity : 0.004 0.045 2889 Dihedral : 4.975 55.622 2320 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.86 % Allowed : 27.17 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.19), residues: 2101 helix: 2.42 (0.20), residues: 717 sheet: 0.42 (0.28), residues: 353 loop : -0.41 (0.20), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 26 TYR 0.007 0.001 TYR A 91 PHE 0.008 0.001 PHE H 29 TRP 0.007 0.001 TRP A 55 HIS 0.006 0.000 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00260 (16054) covalent geometry : angle 0.55286 (21852) SS BOND : bond 0.00202 ( 1) SS BOND : angle 0.53188 ( 2) hydrogen bonds : bond 0.03696 ( 704) hydrogen bonds : angle 4.20979 ( 1965) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 99 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ARG cc_start: 0.8635 (ppt170) cc_final: 0.8331 (pmt170) REVERT: A 646 GLU cc_start: 0.9241 (OUTLIER) cc_final: 0.8933 (mt-10) REVERT: A 689 ASP cc_start: 0.9268 (m-30) cc_final: 0.8975 (p0) REVERT: B 612 MET cc_start: 0.8410 (pmm) cc_final: 0.8083 (mpp) REVERT: B 750 MET cc_start: 0.8500 (pmm) cc_final: 0.7648 (ppp) REVERT: C 64 TYR cc_start: 0.6076 (OUTLIER) cc_final: 0.5406 (p90) REVERT: C 77 ASP cc_start: 0.6457 (m-30) cc_final: 0.5898 (p0) REVERT: C 85 LEU cc_start: 0.7263 (OUTLIER) cc_final: 0.6305 (mp) REVERT: C 107 PHE cc_start: 0.1569 (OUTLIER) cc_final: 0.1086 (p90) REVERT: D 25 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9059 (pp) REVERT: D 45 LEU cc_start: 0.7729 (mt) cc_final: 0.7493 (mt) REVERT: D 110 MET cc_start: 0.6582 (ppp) cc_final: 0.5575 (ppp) REVERT: D 111 GLN cc_start: 0.5829 (pm20) cc_final: 0.4657 (tt0) REVERT: H 34 TYR cc_start: 0.4523 (OUTLIER) cc_final: 0.4288 (t80) REVERT: H 41 GLN cc_start: 0.9339 (OUTLIER) cc_final: 0.8917 (pm20) REVERT: L 58 LEU cc_start: 0.9288 (pt) cc_final: 0.8776 (tm) REVERT: L 63 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8228 (pp30) outliers start: 62 outliers final: 49 residues processed: 154 average time/residue: 0.5349 time to fit residues: 93.2456 Evaluate side-chains 153 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 96 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 646 GLU Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 593 ARG Chi-restraints excluded: chain B residue 615 GLN Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 826 LEU Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain C residue 64 TYR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain H residue 34 TYR Chi-restraints excluded: chain H residue 41 GLN Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain L residue 63 GLN Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain L residue 106 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 184 optimal weight: 40.0000 chunk 178 optimal weight: 1.9990 chunk 176 optimal weight: 0.3980 chunk 25 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 155 optimal weight: 0.6980 chunk 52 optimal weight: 0.0980 chunk 19 optimal weight: 0.9990 chunk 195 optimal weight: 0.6980 chunk 96 optimal weight: 0.0770 chunk 71 optimal weight: 0.6980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.085786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.051088 restraints weight = 47136.966| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 3.26 r_work: 0.2670 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16055 Z= 0.098 Angle : 0.571 11.653 21854 Z= 0.275 Chirality : 0.040 0.150 2493 Planarity : 0.004 0.045 2889 Dihedral : 4.915 55.931 2320 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.55 % Allowed : 27.66 % Favored : 68.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.19), residues: 2101 helix: 2.49 (0.20), residues: 711 sheet: 0.39 (0.28), residues: 358 loop : -0.34 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 26 TYR 0.024 0.001 TYR L 57 PHE 0.013 0.001 PHE C 72 TRP 0.007 0.001 TRP A 55 HIS 0.006 0.000 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00228 (16054) covalent geometry : angle 0.57146 (21852) SS BOND : bond 0.00224 ( 1) SS BOND : angle 0.51366 ( 2) hydrogen bonds : bond 0.03331 ( 704) hydrogen bonds : angle 4.11667 ( 1965) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 99 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ARG cc_start: 0.8622 (ppt170) cc_final: 0.8411 (pmt170) REVERT: A 622 GLU cc_start: 0.8993 (OUTLIER) cc_final: 0.8752 (mp0) REVERT: A 646 GLU cc_start: 0.9224 (OUTLIER) cc_final: 0.8900 (mt-10) REVERT: A 689 ASP cc_start: 0.9243 (m-30) cc_final: 0.8954 (p0) REVERT: B 612 MET cc_start: 0.8501 (pmm) cc_final: 0.8174 (mpp) REVERT: C 64 TYR cc_start: 0.6107 (OUTLIER) cc_final: 0.5496 (p90) REVERT: C 77 ASP cc_start: 0.6212 (m-30) cc_final: 0.5641 (p0) REVERT: C 85 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.6301 (mp) REVERT: C 107 PHE cc_start: 0.1597 (OUTLIER) cc_final: 0.1109 (p90) REVERT: D 25 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9040 (pp) REVERT: D 45 LEU cc_start: 0.7749 (mt) cc_final: 0.7507 (mt) REVERT: D 110 MET cc_start: 0.6461 (ppp) cc_final: 0.5496 (ppp) REVERT: D 111 GLN cc_start: 0.5590 (pm20) cc_final: 0.4309 (tt0) REVERT: H 34 TYR cc_start: 0.4409 (OUTLIER) cc_final: 0.4193 (t80) REVERT: H 41 GLN cc_start: 0.9331 (OUTLIER) cc_final: 0.8913 (pm20) REVERT: L 58 LEU cc_start: 0.9261 (pt) cc_final: 0.8722 (tm) REVERT: L 63 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8250 (pp30) outliers start: 57 outliers final: 41 residues processed: 150 average time/residue: 0.5384 time to fit residues: 91.2650 Evaluate side-chains 146 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 96 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 646 GLU Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 593 ARG Chi-restraints excluded: chain B residue 615 GLN Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 826 LEU Chi-restraints excluded: chain C residue 64 TYR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain H residue 34 TYR Chi-restraints excluded: chain H residue 41 GLN Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain L residue 63 GLN Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain L residue 106 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 156 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 103 optimal weight: 0.2980 chunk 71 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 52 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 114 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 = 0.3667 r_free = 0.3667 target = 0.085047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.050253 restraints weight = 47143.859| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 3.25 r_work: 0.2643 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16055 Z= 0.122 Angle : 0.575 10.880 21854 Z= 0.281 Chirality : 0.041 0.137 2493 Planarity : 0.004 0.045 2889 Dihedral : 4.906 55.448 2317 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.43 % Allowed : 27.98 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.19), residues: 2101 helix: 2.45 (0.20), residues: 718 sheet: 0.40 (0.28), residues: 348 loop : -0.39 (0.20), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 26 TYR 0.036 0.001 TYR B 91 PHE 0.013 0.001 PHE H 72 TRP 0.008 0.001 TRP H 38 HIS 0.006 0.000 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00292 (16054) covalent geometry : angle 0.57513 (21852) SS BOND : bond 0.00193 ( 1) SS BOND : angle 0.51114 ( 2) hydrogen bonds : bond 0.03864 ( 704) hydrogen bonds : angle 4.17919 ( 1965) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5548.44 seconds wall clock time: 95 minutes 7.88 seconds (5707.88 seconds total)