Starting phenix.real_space_refine on Fri Jul 3 07:21:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w51_65649/07_2026/9w51_65649.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w51_65649/07_2026/9w51_65649.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w51_65649/07_2026/9w51_65649.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w51_65649/07_2026/9w51_65649.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w51_65649/07_2026/9w51_65649.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w51_65649/07_2026/9w51_65649.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.061 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 44 5.16 5 C 8100 2.51 5 N 2146 2.21 5 O 2080 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12370 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6171 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 802, 6154 Classifications: {'peptide': 802} Link IDs: {'PTRANS': 43, 'TRANS': 758} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 802, 6154 Classifications: {'peptide': 802} Link IDs: {'PTRANS': 43, 'TRANS': 758} Chain breaks: 2 bond proxies already assigned to first conformer: 6274 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'PGT': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PGT:plan-1': 1, 'PGT:plan-2': 1} Unresolved non-hydrogen planarities: 7 Restraints were copied for chains: B Time building chain proxies: 6.58, per 1000 atoms: 0.53 Number of scatterers: 12370 At special positions: 0 Unit cell: (135.89, 80.25, 121.98, 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 44 16.00 O 2080 8.00 N 2146 7.00 C 8100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 867.1 milliseconds 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2984 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 4 sheets defined 65.3% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 33 through 56 removed outlier: 3.828A pdb=" N GLY A 37 " --> pdb=" O ARG A 33 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N VAL A 39 " --> pdb=" O PRO A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 70 Processing helix chain 'A' and resid 72 through 86 removed outlier: 4.171A pdb=" N ALA A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 85 " --> pdb=" O SER A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 101 removed outlier: 3.569A pdb=" N TRP A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 125 removed outlier: 4.133A pdb=" N THR A 112 " --> pdb=" O ARG A 108 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N GLY A 113 " --> pdb=" O SER A 109 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER A 116 " --> pdb=" O THR A 112 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ALA A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE A 120 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 140 Processing helix chain 'A' and resid 141 through 143 No H-bonds generated for 'chain 'A' and resid 141 through 143' Processing helix chain 'A' and resid 148 through 174 removed outlier: 3.792A pdb=" N LEU A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU A 160 " --> pdb=" O ALA A 156 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLY A 161 " --> pdb=" O SER A 157 " (cutoff:3.500A) Proline residue: A 165 - end of helix removed outlier: 5.154A pdb=" N ALA A 169 " --> pdb=" O PRO A 165 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 183 removed outlier: 3.995A pdb=" N ALA A 179 " --> pdb=" O ASP A 175 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER A 181 " --> pdb=" O ASP A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 211 removed outlier: 3.855A pdb=" N HIS A 211 " --> pdb=" O PHE A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 260 removed outlier: 4.667A pdb=" N LEU A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU A 258 " --> pdb=" O ALA A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 285 Processing helix chain 'A' and resid 292 through 302 Processing helix chain 'A' and resid 308 through 323 removed outlier: 3.568A pdb=" N VAL A 323 " --> pdb=" O ARG A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 345 Processing helix chain 'A' and resid 355 through 377 removed outlier: 3.817A pdb=" N ILE A 359 " --> pdb=" O PHE A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 387 Processing helix chain 'A' and resid 392 through 419 removed outlier: 3.649A pdb=" N ILE A 396 " --> pdb=" O PRO A 392 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP A 397 " --> pdb=" O HIS A 393 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA A 414 " --> pdb=" O CYS A 410 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N GLN A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLY A 416 " --> pdb=" O LEU A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 439 Processing helix chain 'A' and resid 446 through 462 removed outlier: 4.364A pdb=" N LEU A 452 " --> pdb=" O GLU A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 475 removed outlier: 3.657A pdb=" N VAL A 475 " --> pdb=" O LEU A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 500 removed outlier: 4.734A pdb=" N VAL A 493 " --> pdb=" O VAL A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 510 Processing helix chain 'A' and resid 518 through 542 Processing helix chain 'A' and resid 553 through 566 Processing helix chain 'A' and resid 570 through 576 removed outlier: 3.912A pdb=" N LEU A 576 " --> pdb=" O GLY A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 627 removed outlier: 3.782A pdb=" N GLU A 616 " --> pdb=" O MET A 612 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE A 618 " --> pdb=" O ARG A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 649 Processing helix chain 'A' and resid 672 through 689 Processing helix chain 'A' and resid 701 through 715 removed outlier: 3.904A pdb=" N LEU A 705 " --> pdb=" O PRO A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 734 Processing helix chain 'A' and resid 776 through 793 Processing helix chain 'A' and resid 835 through 842 Processing helix chain 'A' and resid 861 through 870 Processing helix chain 'B' and resid 34 through 56 removed outlier: 4.996A pdb=" N VAL B 39 " --> pdb=" O PRO B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 70 Processing helix chain 'B' and resid 72 through 86 removed outlier: 4.171A pdb=" N ALA B 84 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 101 removed outlier: 3.569A pdb=" N TRP B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 125 removed outlier: 4.134A pdb=" N THR B 112 " --> pdb=" O ARG B 108 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N GLY B 113 " --> pdb=" O SER B 109 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER B 116 " --> pdb=" O THR B 112 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ALA B 117 " --> pdb=" O GLY B 113 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ILE B 120 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA B 123 " --> pdb=" O ALA B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 140 Processing helix chain 'B' and resid 141 through 143 No H-bonds generated for 'chain 'B' and resid 141 through 143' Processing helix chain 'B' and resid 148 through 174 removed outlier: 3.793A pdb=" N LEU B 154 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU B 160 " --> pdb=" O ALA B 156 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLY B 161 " --> pdb=" O SER B 157 " (cutoff:3.500A) Proline residue: B 165 - end of helix removed outlier: 5.154A pdb=" N ALA B 169 " --> pdb=" O PRO B 165 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS B 174 " --> pdb=" O LEU B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 183 removed outlier: 3.995A pdb=" N ALA B 179 " --> pdb=" O ASP B 175 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER B 181 " --> pdb=" O ASP B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 211 removed outlier: 3.854A pdb=" N HIS B 211 " --> pdb=" O PHE B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 260 removed outlier: 4.667A pdb=" N LEU B 244 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LEU B 258 " --> pdb=" O ALA B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 285 Processing helix chain 'B' and resid 292 through 302 Processing helix chain 'B' and resid 308 through 323 removed outlier: 3.568A pdb=" N VAL B 323 " --> pdb=" O ARG B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 345 Processing helix chain 'B' and resid 355 through 377 removed outlier: 3.817A pdb=" N ILE B 359 " --> pdb=" O PHE B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 387 Processing helix chain 'B' and resid 392 through 419 removed outlier: 3.650A pdb=" N ILE B 396 " --> pdb=" O PRO B 392 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP B 397 " --> pdb=" O HIS B 393 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA B 414 " --> pdb=" O CYS B 410 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N GLN B 415 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLY B 416 " --> pdb=" O LEU B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 439 Processing helix chain 'B' and resid 446 through 462 removed outlier: 4.364A pdb=" N LEU B 452 " --> pdb=" O GLU B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 475 removed outlier: 3.657A pdb=" N VAL B 475 " --> pdb=" O LEU B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 500 removed outlier: 4.735A pdb=" N VAL B 493 " --> pdb=" O VAL B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 510 Processing helix chain 'B' and resid 518 through 542 Processing helix chain 'B' and resid 553 through 566 Processing helix chain 'B' and resid 570 through 576 removed outlier: 3.912A pdb=" N LEU B 576 " --> pdb=" O GLY B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 627 removed outlier: 3.782A pdb=" N GLU B 616 " --> pdb=" O MET B 612 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE B 618 " --> pdb=" O ARG B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 649 Processing helix chain 'B' and resid 672 through 689 Processing helix chain 'B' and resid 701 through 715 removed outlier: 3.904A pdb=" N LEU B 705 " --> pdb=" O PRO B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 734 Processing helix chain 'B' and resid 776 through 793 Processing helix chain 'B' and resid 835 through 842 Processing helix chain 'B' and resid 861 through 870 Processing sheet with id=AA1, first strand: chain 'A' and resid 223 through 226 Processing sheet with id=AA2, first strand: chain 'A' and resid 581 through 584 removed outlier: 6.227A pdb=" N MET A 601 " --> pdb=" O VAL A 633 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N TYR A 635 " --> pdb=" O MET A 601 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ALA A 603 " --> pdb=" O TYR A 635 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL A 637 " --> pdb=" O ALA A 603 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N TYR A 851 " --> pdb=" O GLN A 636 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASP A 846 " --> pdb=" O ALA A 659 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ALA A 659 " --> pdb=" O ASP A 846 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N GLU A 848 " --> pdb=" O GLU A 657 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLU A 657 " --> pdb=" O GLU A 848 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ARG A 850 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY A 800 " --> pdb=" O ALA A 659 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL A 661 " --> pdb=" O SER A 798 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N SER A 798 " --> pdb=" O VAL A 661 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ALA A 762 " --> pdb=" O SER A 798 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N GLY A 800 " --> pdb=" O ALA A 762 " (cutoff:3.500A) removed outlier: 9.126A pdb=" N LEU A 764 " --> pdb=" O GLY A 800 " (cutoff:3.500A) removed outlier: 11.081A pdb=" N VAL A 802 " --> pdb=" O LEU A 764 " (cutoff:3.500A) removed outlier: 16.278A pdb=" N LEU A 766 " --> pdb=" O VAL A 802 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASP A 765 " --> pdb=" O ASN A 752 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASN A 752 " --> pdb=" O ASP A 765 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N MET A 767 " --> pdb=" O PHE A 750 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N PHE A 750 " --> pdb=" O MET A 767 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N HIS A 743 " --> pdb=" O PRO A 747 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ARG A 737 " --> pdb=" O LEU A 753 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 223 through 226 Processing sheet with id=AA4, first strand: chain 'B' and resid 581 through 584 removed outlier: 6.227A pdb=" N MET B 601 " --> pdb=" O VAL B 633 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N TYR B 635 " --> pdb=" O MET B 601 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ALA B 603 " --> pdb=" O TYR B 635 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL B 637 " --> pdb=" O ALA B 603 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N TYR B 851 " --> pdb=" O GLN B 636 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASP B 846 " --> pdb=" O ALA B 659 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ALA B 659 " --> pdb=" O ASP B 846 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N GLU B 848 " --> pdb=" O GLU B 657 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLU B 657 " --> pdb=" O GLU B 848 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ARG B 850 " --> pdb=" O LEU B 655 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY B 800 " --> pdb=" O ALA B 659 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL B 661 " --> pdb=" O SER B 798 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N SER B 798 " --> pdb=" O VAL B 661 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ALA B 762 " --> pdb=" O SER B 798 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N GLY B 800 " --> pdb=" O ALA B 762 " (cutoff:3.500A) removed outlier: 9.126A pdb=" N LEU B 764 " --> pdb=" O GLY B 800 " (cutoff:3.500A) removed outlier: 11.081A pdb=" N VAL B 802 " --> pdb=" O LEU B 764 " (cutoff:3.500A) removed outlier: 16.278A pdb=" N LEU B 766 " --> pdb=" O VAL B 802 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASP B 765 " --> pdb=" O ASN B 752 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASN B 752 " --> pdb=" O ASP B 765 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N MET B 767 " --> pdb=" O PHE B 750 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N PHE B 750 " --> pdb=" O MET B 767 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N HIS B 743 " --> pdb=" O PRO B 747 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ARG B 737 " --> pdb=" O LEU B 753 " (cutoff:3.500A) 776 hydrogen bonds defined for protein. 2270 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.28 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3909 1.34 - 1.46: 2903 1.46 - 1.58: 5772 1.58 - 1.70: 0 1.70 - 1.81: 70 Bond restraints: 12654 Sorted by residual: bond pdb=" C LYS A 746 " pdb=" N PRO A 747 " ideal model delta sigma weight residual 1.333 1.356 -0.023 1.01e-02 9.80e+03 4.98e+00 bond pdb=" C LYS B 746 " pdb=" N PRO B 747 " ideal model delta sigma weight residual 1.333 1.356 -0.023 1.01e-02 9.80e+03 4.98e+00 bond pdb=" C ALA B 545 " pdb=" N PRO B 546 " ideal model delta sigma weight residual 1.329 1.355 -0.026 1.18e-02 7.18e+03 4.69e+00 bond pdb=" C ALA A 545 " pdb=" N PRO A 546 " ideal model delta sigma weight residual 1.329 1.355 -0.026 1.18e-02 7.18e+03 4.69e+00 bond pdb=" C THR A 265 " pdb=" N PRO A 266 " ideal model delta sigma weight residual 1.329 1.354 -0.025 1.18e-02 7.18e+03 4.58e+00 ... (remaining 12649 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 12695 1.21 - 2.42: 3888 2.42 - 3.63: 543 3.63 - 4.85: 86 4.85 - 6.06: 10 Bond angle restraints: 17222 Sorted by residual: angle pdb=" CA ASP B 647 " pdb=" CB ASP B 647 " pdb=" CG ASP B 647 " ideal model delta sigma weight residual 112.60 116.81 -4.21 1.00e+00 1.00e+00 1.77e+01 angle pdb=" CA ASP A 647 " pdb=" CB ASP A 647 " pdb=" CG ASP A 647 " ideal model delta sigma weight residual 112.60 116.81 -4.21 1.00e+00 1.00e+00 1.77e+01 angle pdb=" N ILE B 89 " pdb=" CA ILE B 89 " pdb=" C ILE B 89 " ideal model delta sigma weight residual 113.42 108.64 4.78 1.17e+00 7.31e-01 1.67e+01 angle pdb=" N ILE A 89 " pdb=" CA ILE A 89 " pdb=" C ILE A 89 " ideal model delta sigma weight residual 113.42 108.67 4.75 1.17e+00 7.31e-01 1.65e+01 angle pdb=" CA ASP B 757 " pdb=" CB ASP B 757 " pdb=" CG ASP B 757 " ideal model delta sigma weight residual 112.60 116.54 -3.94 1.00e+00 1.00e+00 1.55e+01 ... (remaining 17217 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.87: 6600 14.87 - 29.75: 658 29.75 - 44.62: 205 44.62 - 59.50: 47 59.50 - 74.37: 32 Dihedral angle restraints: 7542 sinusoidal: 2912 harmonic: 4630 Sorted by residual: dihedral pdb=" CA VAL A 88 " pdb=" C VAL A 88 " pdb=" N ILE A 89 " pdb=" CA ILE A 89 " ideal model delta harmonic sigma weight residual 180.00 155.41 24.59 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA VAL B 88 " pdb=" C VAL B 88 " pdb=" N ILE B 89 " pdb=" CA ILE B 89 " ideal model delta harmonic sigma weight residual 180.00 155.45 24.55 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA VAL B 489 " pdb=" C VAL B 489 " pdb=" N GLY B 490 " pdb=" CA GLY B 490 " ideal model delta harmonic sigma weight residual 180.00 160.27 19.73 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 7539 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1147 0.038 - 0.076: 487 0.076 - 0.114: 265 0.114 - 0.152: 93 0.152 - 0.190: 32 Chirality restraints: 2024 Sorted by residual: chirality pdb=" CA PRO A 288 " pdb=" N PRO A 288 " pdb=" C PRO A 288 " pdb=" CB PRO A 288 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 9.07e-01 chirality pdb=" CA PRO B 288 " pdb=" N PRO B 288 " pdb=" C PRO B 288 " pdb=" CB PRO B 288 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 9.07e-01 chirality pdb=" CA PRO B 643 " pdb=" N PRO B 643 " pdb=" C PRO B 643 " pdb=" CB PRO B 643 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 9.05e-01 ... (remaining 2021 not shown) Planarity restraints: 2172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 850 " -0.179 9.50e-02 1.11e+02 8.03e-02 4.16e+00 pdb=" NE ARG A 850 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 850 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG A 850 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 850 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 850 " -0.179 9.50e-02 1.11e+02 8.03e-02 4.15e+00 pdb=" NE ARG B 850 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG B 850 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG B 850 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 850 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 151 " -0.110 9.50e-02 1.11e+02 4.99e-02 2.05e+00 pdb=" NE ARG B 151 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG B 151 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG B 151 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 151 " 0.000 2.00e-02 2.50e+03 ... (remaining 2169 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 4342 2.89 - 3.39: 12401 3.39 - 3.89: 19878 3.89 - 4.40: 22546 4.40 - 4.90: 38044 Nonbonded interactions: 97211 Sorted by model distance: nonbonded pdb=" O PHE A 723 " pdb=" OG SER A 724 " model vdw 2.386 3.040 nonbonded pdb=" O PHE B 723 " pdb=" OG SER B 724 " model vdw 2.386 3.040 nonbonded pdb=" O LEU A 604 " pdb=" O TYR A 635 " model vdw 2.491 3.040 nonbonded pdb=" O LEU B 604 " pdb=" O TYR B 635 " model vdw 2.492 3.040 nonbonded pdb=" NE BARG B 559 " pdb=" OD2 ASP B 588 " model vdw 2.580 3.120 ... (remaining 97206 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 2.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 16.620 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.032 12654 Z= 0.465 Angle : 1.140 6.057 17222 Z= 0.809 Chirality : 0.058 0.190 2024 Planarity : 0.006 0.080 2172 Dihedral : 14.441 74.374 4558 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.90 % Favored : 93.97 % Rotamer: Outliers : 0.80 % Allowed : 9.41 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.18), residues: 1596 helix: -1.11 (0.14), residues: 1020 sheet: -0.99 (0.35), residues: 154 loop : -2.46 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG B 151 TYR 0.017 0.003 TYR A 594 PHE 0.019 0.002 PHE B 355 TRP 0.018 0.002 TRP A 619 HIS 0.005 0.002 HIS A 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00722 / 0.46 (12654) covalent geometry : angle 1.14004 / 0.81 (17222) hydrogen bonds : bond 0.19161 / 13.07 ( 776) hydrogen bonds : angle 7.57043 / 5.44 ( 2270) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 146 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 LEU cc_start: 0.9608 (OUTLIER) cc_final: 0.9365 (pp) REVERT: A 540 TRP cc_start: 0.8413 (OUTLIER) cc_final: 0.7618 (t60) REVERT: A 670 ASN cc_start: 0.8126 (t0) cc_final: 0.7223 (t0) REVERT: A 675 MET cc_start: 0.8487 (tpt) cc_final: 0.6974 (tpt) REVERT: A 683 ASN cc_start: 0.9332 (t0) cc_final: 0.8846 (p0) REVERT: B 273 LEU cc_start: 0.9608 (OUTLIER) cc_final: 0.9365 (pp) REVERT: B 540 TRP cc_start: 0.8414 (OUTLIER) cc_final: 0.7618 (t60) REVERT: B 670 ASN cc_start: 0.8126 (t0) cc_final: 0.7222 (t0) REVERT: B 675 MET cc_start: 0.8487 (tpt) cc_final: 0.6974 (tpt) REVERT: B 683 ASN cc_start: 0.9332 (t0) cc_final: 0.8846 (p0) outliers start: 10 outliers final: 2 residues processed: 156 average time/residue: 0.1032 time to fit residues: 23.4161 Evaluate side-chains 94 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 540 TRP Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 540 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.5980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 ASN A 744 GLN ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 ASN B 744 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.081726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.062650 restraints weight = 63929.437| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 5.22 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3171 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12654 Z= 0.144 Angle : 0.648 9.823 17222 Z= 0.314 Chirality : 0.038 0.132 2024 Planarity : 0.004 0.034 2172 Dihedral : 5.299 52.872 1802 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.59 % Allowed : 13.72 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.21), residues: 1596 helix: 1.09 (0.16), residues: 1026 sheet: -0.51 (0.35), residues: 146 loop : -1.63 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 238 TYR 0.018 0.002 TYR A 605 PHE 0.012 0.001 PHE A 294 TRP 0.010 0.001 TRP B 510 HIS 0.003 0.001 HIS A 400 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (12654) covalent geometry : angle 0.64753 / 0.31 (17222) hydrogen bonds : bond 0.04175 / 2.83 ( 776) hydrogen bonds : angle 4.42717 / 3.17 ( 2270) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 670 ASN cc_start: 0.8612 (t0) cc_final: 0.8213 (t0) REVERT: A 683 ASN cc_start: 0.9215 (t0) cc_final: 0.8752 (p0) REVERT: B 670 ASN cc_start: 0.8612 (t0) cc_final: 0.8214 (t0) REVERT: B 683 ASN cc_start: 0.9213 (t0) cc_final: 0.8752 (p0) outliers start: 20 outliers final: 12 residues processed: 116 average time/residue: 0.0955 time to fit residues: 16.7992 Evaluate side-chains 96 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 540 TRP Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 679 ARG Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 540 TRP Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 679 ARG Chi-restraints excluded: chain B residue 787 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 32 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 156 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 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 = 0.3638 r_free = 0.3638 target = 0.081612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.062354 restraints weight = 70498.712| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 5.62 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12654 Z= 0.121 Angle : 0.619 14.310 17222 Z= 0.286 Chirality : 0.037 0.162 2024 Planarity : 0.004 0.032 2172 Dihedral : 4.543 48.515 1794 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.55 % Allowed : 13.72 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.22), residues: 1596 helix: 1.70 (0.16), residues: 1028 sheet: -0.12 (0.34), residues: 156 loop : -1.29 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 687 TYR 0.013 0.001 TYR A 605 PHE 0.010 0.001 PHE B 621 TRP 0.011 0.001 TRP A 510 HIS 0.002 0.001 HIS A 386 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (12654) covalent geometry : angle 0.61876 / 0.29 (17222) hydrogen bonds : bond 0.03638 / 2.48 ( 776) hydrogen bonds : angle 4.06689 / 2.93 ( 2270) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 CYS cc_start: 0.8796 (m) cc_final: 0.8478 (m) REVERT: A 675 MET cc_start: 0.8576 (tpt) cc_final: 0.8046 (tpt) REVERT: A 683 ASN cc_start: 0.9249 (t0) cc_final: 0.8777 (p0) REVERT: A 770 HIS cc_start: 0.8156 (OUTLIER) cc_final: 0.7576 (t-90) REVERT: B 331 CYS cc_start: 0.8793 (m) cc_final: 0.8501 (m) REVERT: B 675 MET cc_start: 0.8579 (tpt) cc_final: 0.8048 (tpt) REVERT: B 683 ASN cc_start: 0.9250 (t0) cc_final: 0.8782 (p0) REVERT: B 770 HIS cc_start: 0.8164 (OUTLIER) cc_final: 0.7582 (t-90) outliers start: 32 outliers final: 14 residues processed: 124 average time/residue: 0.1044 time to fit residues: 19.6141 Evaluate side-chains 109 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain A residue 540 TRP Chi-restraints excluded: chain A residue 703 ASP Chi-restraints excluded: chain A residue 770 HIS Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 487 CYS Chi-restraints excluded: chain B residue 540 TRP Chi-restraints excluded: chain B residue 703 ASP Chi-restraints excluded: chain B residue 770 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 11 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 133 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 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 = 0.3637 r_free = 0.3637 target = 0.081457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.062188 restraints weight = 77177.622| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 5.76 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3163 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12654 Z= 0.124 Angle : 0.611 10.484 17222 Z= 0.284 Chirality : 0.037 0.171 2024 Planarity : 0.004 0.060 2172 Dihedral : 4.470 47.583 1794 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.07 % Allowed : 14.83 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.22), residues: 1596 helix: 1.84 (0.17), residues: 1030 sheet: -0.11 (0.34), residues: 156 loop : -1.16 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 679 TYR 0.013 0.001 TYR A 635 PHE 0.011 0.001 PHE B 621 TRP 0.009 0.001 TRP B 510 HIS 0.002 0.000 HIS B 386 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (12654) covalent geometry : angle 0.61057 / 0.28 (17222) hydrogen bonds : bond 0.03419 / 2.32 ( 776) hydrogen bonds : angle 3.97836 / 2.87 ( 2270) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 CYS cc_start: 0.8730 (m) cc_final: 0.8400 (m) REVERT: A 683 ASN cc_start: 0.9259 (t0) cc_final: 0.8776 (p0) REVERT: A 770 HIS cc_start: 0.8172 (OUTLIER) cc_final: 0.7595 (t-90) REVERT: B 331 CYS cc_start: 0.8733 (m) cc_final: 0.8403 (m) REVERT: B 683 ASN cc_start: 0.9263 (t0) cc_final: 0.8785 (p0) REVERT: B 770 HIS cc_start: 0.8175 (OUTLIER) cc_final: 0.7597 (t-90) outliers start: 26 outliers final: 20 residues processed: 121 average time/residue: 0.0981 time to fit residues: 18.2178 Evaluate side-chains 120 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 540 TRP Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 703 ASP Chi-restraints excluded: chain A residue 770 HIS Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 487 CYS Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 540 TRP Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 703 ASP Chi-restraints excluded: chain B residue 770 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 40 optimal weight: 3.9990 chunk 71 optimal weight: 0.0050 chunk 0 optimal weight: 8.9990 chunk 145 optimal weight: 0.2980 chunk 114 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 76 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 GLN ** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.082503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.062672 restraints weight = 97054.787| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 6.60 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3176 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3176 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12654 Z= 0.104 Angle : 0.580 9.674 17222 Z= 0.268 Chirality : 0.036 0.157 2024 Planarity : 0.004 0.040 2172 Dihedral : 4.330 48.008 1794 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.47 % Allowed : 14.99 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.22), residues: 1596 helix: 1.94 (0.17), residues: 1032 sheet: 0.03 (0.34), residues: 156 loop : -1.07 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 679 TYR 0.010 0.001 TYR B 635 PHE 0.008 0.001 PHE A 294 TRP 0.009 0.001 TRP B 510 HIS 0.001 0.000 HIS A 386 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 (12654) covalent geometry : angle 0.57979 / 0.27 (17222) hydrogen bonds : bond 0.03120 / 2.12 ( 776) hydrogen bonds : angle 3.81584 / 2.74 ( 2270) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 103 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 CYS cc_start: 0.8671 (m) cc_final: 0.8393 (m) REVERT: A 417 LEU cc_start: 0.9464 (tp) cc_final: 0.9083 (tp) REVERT: A 625 CYS cc_start: 0.7530 (m) cc_final: 0.7133 (m) REVERT: A 683 ASN cc_start: 0.9269 (t0) cc_final: 0.8794 (p0) REVERT: A 770 HIS cc_start: 0.8151 (OUTLIER) cc_final: 0.7586 (t-90) REVERT: B 331 CYS cc_start: 0.8662 (m) cc_final: 0.8384 (m) REVERT: B 417 LEU cc_start: 0.9460 (tp) cc_final: 0.9086 (tp) REVERT: B 625 CYS cc_start: 0.7544 (m) cc_final: 0.7149 (m) REVERT: B 683 ASN cc_start: 0.9271 (t0) cc_final: 0.8798 (p0) REVERT: B 770 HIS cc_start: 0.8159 (OUTLIER) cc_final: 0.7591 (t-90) outliers start: 31 outliers final: 22 residues processed: 128 average time/residue: 0.0922 time to fit residues: 17.9873 Evaluate side-chains 116 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 540 TRP Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 636 GLN Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 770 HIS Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 487 CYS Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 540 TRP Chi-restraints excluded: chain B residue 601 MET Chi-restraints excluded: chain B residue 636 GLN Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 770 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 154 optimal weight: 0.7980 chunk 105 optimal weight: 0.0870 chunk 41 optimal weight: 0.0010 chunk 92 optimal weight: 0.9980 chunk 150 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 chunk 131 optimal weight: 2.9990 chunk 133 optimal weight: 0.6980 chunk 47 optimal weight: 0.4980 chunk 36 optimal weight: 2.9990 chunk 142 optimal weight: 7.9990 overall best weight: 0.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 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 = 0.3663 r_free = 0.3663 target = 0.082848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.063368 restraints weight = 87287.023| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 6.32 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3191 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3191 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12654 Z= 0.103 Angle : 0.594 9.093 17222 Z= 0.271 Chirality : 0.037 0.222 2024 Planarity : 0.004 0.042 2172 Dihedral : 4.274 47.791 1794 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.55 % Allowed : 15.95 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.22), residues: 1596 helix: 1.99 (0.17), residues: 1032 sheet: 0.17 (0.34), residues: 156 loop : -0.98 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 665 TYR 0.017 0.001 TYR A 635 PHE 0.008 0.001 PHE A 294 TRP 0.007 0.001 TRP B 510 HIS 0.001 0.000 HIS A 400 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.10 (12654) covalent geometry : angle 0.59436 / 0.27 (17222) hydrogen bonds : bond 0.03039 / 2.07 ( 776) hydrogen bonds : angle 3.76545 / 2.70 ( 2270) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 96 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 CYS cc_start: 0.8668 (m) cc_final: 0.8399 (m) REVERT: A 534 LEU cc_start: 0.8866 (tt) cc_final: 0.8640 (mm) REVERT: A 683 ASN cc_start: 0.9255 (t0) cc_final: 0.8778 (p0) REVERT: A 770 HIS cc_start: 0.8134 (OUTLIER) cc_final: 0.7566 (t-90) REVERT: B 331 CYS cc_start: 0.8657 (m) cc_final: 0.8390 (m) REVERT: B 534 LEU cc_start: 0.8859 (tt) cc_final: 0.8634 (mm) REVERT: B 683 ASN cc_start: 0.9251 (t0) cc_final: 0.8776 (p0) REVERT: B 770 HIS cc_start: 0.8146 (OUTLIER) cc_final: 0.7576 (t-90) outliers start: 32 outliers final: 20 residues processed: 122 average time/residue: 0.0991 time to fit residues: 18.4727 Evaluate side-chains 116 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 540 TRP Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 770 HIS Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 487 CYS Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 540 TRP Chi-restraints excluded: chain B residue 601 MET Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 770 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 139 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 chunk 103 optimal weight: 0.0870 chunk 141 optimal weight: 0.2980 chunk 28 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 13 optimal weight: 0.0040 chunk 3 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 135 optimal weight: 4.9990 overall best weight: 0.3970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 636 GLN B 636 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.083203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.063701 restraints weight = 86339.472| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 6.26 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12654 Z= 0.099 Angle : 0.587 8.744 17222 Z= 0.265 Chirality : 0.036 0.156 2024 Planarity : 0.004 0.043 2172 Dihedral : 4.147 47.297 1794 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.23 % Allowed : 16.43 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.22), residues: 1596 helix: 2.10 (0.16), residues: 1032 sheet: 0.37 (0.34), residues: 156 loop : -0.94 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 665 TYR 0.010 0.001 TYR A 635 PHE 0.008 0.001 PHE A 294 TRP 0.008 0.001 TRP A 510 HIS 0.001 0.000 HIS A 386 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (12654) covalent geometry : angle 0.58680 / 0.27 (17222) hydrogen bonds : bond 0.02923 / 1.99 ( 776) hydrogen bonds : angle 3.70470 / 2.66 ( 2270) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 CYS cc_start: 0.8643 (m) cc_final: 0.8378 (m) REVERT: A 534 LEU cc_start: 0.8840 (tt) cc_final: 0.8638 (mm) REVERT: A 683 ASN cc_start: 0.9260 (t0) cc_final: 0.8805 (p0) REVERT: A 770 HIS cc_start: 0.8130 (OUTLIER) cc_final: 0.7565 (t-90) REVERT: B 331 CYS cc_start: 0.8634 (m) cc_final: 0.8366 (m) REVERT: B 534 LEU cc_start: 0.8823 (tt) cc_final: 0.8622 (mm) REVERT: B 683 ASN cc_start: 0.9255 (t0) cc_final: 0.8798 (p0) REVERT: B 770 HIS cc_start: 0.8139 (OUTLIER) cc_final: 0.7570 (t-90) outliers start: 28 outliers final: 22 residues processed: 128 average time/residue: 0.0973 time to fit residues: 18.9705 Evaluate side-chains 119 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 540 TRP Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 636 GLN Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 770 HIS Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 487 CYS Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 540 TRP Chi-restraints excluded: chain B residue 601 MET Chi-restraints excluded: chain B residue 636 GLN Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 770 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 147 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 107 optimal weight: 0.0060 chunk 93 optimal weight: 1.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 415 GLN B 415 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.082468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.062294 restraints weight = 114661.963| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 7.18 r_work: 0.2990 rms_B_bonded: 7.11 restraints_weight: 2.0000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12654 Z= 0.118 Angle : 0.604 9.715 17222 Z= 0.271 Chirality : 0.036 0.141 2024 Planarity : 0.004 0.045 2172 Dihedral : 4.147 46.398 1794 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.15 % Allowed : 17.30 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.22), residues: 1596 helix: 2.16 (0.16), residues: 1032 sheet: 0.45 (0.34), residues: 156 loop : -0.91 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 665 TYR 0.016 0.001 TYR B 605 PHE 0.013 0.001 PHE A 118 TRP 0.007 0.001 TRP B 510 HIS 0.002 0.000 HIS B 386 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (12654) covalent geometry : angle 0.60351 / 0.27 (17222) hydrogen bonds : bond 0.03041 / 2.08 ( 776) hydrogen bonds : angle 3.72689 / 2.67 ( 2270) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8242 (mm110) REVERT: A 534 LEU cc_start: 0.8946 (tt) cc_final: 0.8678 (mm) REVERT: A 612 MET cc_start: 0.9183 (tmm) cc_final: 0.8946 (tmm) REVERT: A 683 ASN cc_start: 0.9278 (t0) cc_final: 0.8817 (p0) REVERT: A 770 HIS cc_start: 0.8295 (OUTLIER) cc_final: 0.7696 (t-90) REVERT: B 415 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8234 (mm110) REVERT: B 534 LEU cc_start: 0.8948 (tt) cc_final: 0.8681 (mm) REVERT: B 612 MET cc_start: 0.9172 (tmm) cc_final: 0.8936 (tmm) REVERT: B 683 ASN cc_start: 0.9278 (t0) cc_final: 0.8813 (p0) REVERT: B 770 HIS cc_start: 0.8306 (OUTLIER) cc_final: 0.7704 (t-90) outliers start: 27 outliers final: 20 residues processed: 118 average time/residue: 0.0956 time to fit residues: 17.2306 Evaluate side-chains 115 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 415 GLN Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 540 TRP Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 770 HIS Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 487 CYS Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 540 TRP Chi-restraints excluded: chain B residue 601 MET Chi-restraints excluded: chain B residue 646 MET Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 770 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 155 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 65 optimal weight: 9.9990 chunk 27 optimal weight: 0.8980 chunk 55 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 102 optimal weight: 6.9990 chunk 107 optimal weight: 0.6980 chunk 96 optimal weight: 6.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 636 GLN B 636 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.081759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.061910 restraints weight = 94306.879| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 6.41 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12654 Z= 0.133 Angle : 0.616 9.473 17222 Z= 0.277 Chirality : 0.037 0.142 2024 Planarity : 0.004 0.044 2172 Dihedral : 4.176 45.360 1794 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.31 % Allowed : 17.22 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.22), residues: 1596 helix: 2.20 (0.16), residues: 1032 sheet: 0.47 (0.34), residues: 156 loop : -0.90 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 665 TYR 0.011 0.001 TYR B 605 PHE 0.016 0.001 PHE B 843 TRP 0.008 0.001 TRP B 510 HIS 0.003 0.001 HIS B 386 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (12654) covalent geometry : angle 0.61618 / 0.28 (17222) hydrogen bonds : bond 0.03163 / 2.17 ( 776) hydrogen bonds : angle 3.78698 / 2.72 ( 2270) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 93 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 LEU cc_start: 0.8906 (tt) cc_final: 0.8662 (mm) REVERT: A 612 MET cc_start: 0.8694 (tmm) cc_final: 0.8452 (tmm) REVERT: A 625 CYS cc_start: 0.7641 (m) cc_final: 0.7303 (m) REVERT: A 683 ASN cc_start: 0.9254 (t0) cc_final: 0.8792 (p0) REVERT: A 770 HIS cc_start: 0.8171 (OUTLIER) cc_final: 0.7585 (t-90) REVERT: A 782 MET cc_start: 0.9215 (ptm) cc_final: 0.8927 (ppp) REVERT: A 801 MET cc_start: 0.8468 (mtp) cc_final: 0.8209 (mtm) REVERT: B 534 LEU cc_start: 0.8900 (tt) cc_final: 0.8654 (mm) REVERT: B 612 MET cc_start: 0.8685 (tmm) cc_final: 0.8447 (tmm) REVERT: B 625 CYS cc_start: 0.7650 (m) cc_final: 0.7318 (m) REVERT: B 683 ASN cc_start: 0.9251 (t0) cc_final: 0.8788 (p0) REVERT: B 770 HIS cc_start: 0.8178 (OUTLIER) cc_final: 0.7591 (t-90) REVERT: B 782 MET cc_start: 0.9220 (ptm) cc_final: 0.8928 (ppp) REVERT: B 801 MET cc_start: 0.8472 (mtp) cc_final: 0.8211 (mtm) outliers start: 29 outliers final: 24 residues processed: 114 average time/residue: 0.0905 time to fit residues: 15.7895 Evaluate side-chains 115 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 540 TRP Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 770 HIS Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 487 CYS Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 540 TRP Chi-restraints excluded: chain B residue 601 MET Chi-restraints excluded: chain B residue 646 MET Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 770 HIS Chi-restraints excluded: chain B residue 781 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 88 optimal weight: 0.8980 chunk 154 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 124 optimal weight: 0.0980 chunk 46 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 52 optimal weight: 0.0000 chunk 6 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.082740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.063244 restraints weight = 81011.052| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 5.99 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3191 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3191 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12654 Z= 0.103 Angle : 0.601 10.035 17222 Z= 0.267 Chirality : 0.036 0.137 2024 Planarity : 0.004 0.045 2172 Dihedral : 4.145 45.561 1794 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.07 % Allowed : 17.78 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.22), residues: 1596 helix: 2.29 (0.16), residues: 1032 sheet: 0.53 (0.34), residues: 156 loop : -0.86 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 679 TYR 0.012 0.001 TYR A 605 PHE 0.021 0.001 PHE B 118 TRP 0.009 0.001 TRP B 510 HIS 0.002 0.000 HIS A 386 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.10 (12654) covalent geometry : angle 0.60095 / 0.27 (17222) hydrogen bonds : bond 0.02911 / 1.99 ( 776) hydrogen bonds : angle 3.69981 / 2.66 ( 2270) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ASN cc_start: 0.9019 (m-40) cc_final: 0.8747 (m110) REVERT: A 534 LEU cc_start: 0.8880 (tt) cc_final: 0.8643 (mm) REVERT: A 612 MET cc_start: 0.8667 (tmm) cc_final: 0.8415 (tmm) REVERT: A 625 CYS cc_start: 0.7554 (m) cc_final: 0.7257 (m) REVERT: A 683 ASN cc_start: 0.9244 (t0) cc_final: 0.8769 (p0) REVERT: A 770 HIS cc_start: 0.8133 (OUTLIER) cc_final: 0.7578 (t-90) REVERT: A 782 MET cc_start: 0.9166 (ptm) cc_final: 0.8761 (ppp) REVERT: B 122 ASN cc_start: 0.9015 (m-40) cc_final: 0.8739 (m110) REVERT: B 534 LEU cc_start: 0.8872 (tt) cc_final: 0.8635 (mm) REVERT: B 541 LEU cc_start: 0.9065 (mt) cc_final: 0.8852 (mt) REVERT: B 612 MET cc_start: 0.8651 (tmm) cc_final: 0.8399 (tmm) REVERT: B 625 CYS cc_start: 0.7576 (m) cc_final: 0.7282 (m) REVERT: B 683 ASN cc_start: 0.9249 (t0) cc_final: 0.8782 (p0) REVERT: B 770 HIS cc_start: 0.8134 (OUTLIER) cc_final: 0.7579 (t-90) REVERT: B 782 MET cc_start: 0.9181 (ptm) cc_final: 0.8762 (ppp) outliers start: 26 outliers final: 21 residues processed: 125 average time/residue: 0.0905 time to fit residues: 17.2474 Evaluate side-chains 117 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 540 TRP Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 636 GLN Chi-restraints excluded: chain A residue 770 HIS Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 487 CYS Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 540 TRP Chi-restraints excluded: chain B residue 601 MET Chi-restraints excluded: chain B residue 636 GLN Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 770 HIS Chi-restraints excluded: chain B residue 781 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 148 optimal weight: 5.9990 chunk 85 optimal weight: 0.4980 chunk 74 optimal weight: 0.8980 chunk 155 optimal weight: 0.0770 chunk 37 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 133 optimal weight: 0.9980 chunk 102 optimal weight: 0.0980 chunk 143 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 44 optimal weight: 0.2980 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.083201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.063298 restraints weight = 102787.726| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 6.75 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3196 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3196 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12654 Z= 0.104 Angle : 0.641 10.513 17222 Z= 0.282 Chirality : 0.037 0.178 2024 Planarity : 0.004 0.045 2172 Dihedral : 4.154 45.638 1794 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.75 % Allowed : 18.42 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.22), residues: 1596 helix: 2.31 (0.16), residues: 1038 sheet: 0.62 (0.36), residues: 146 loop : -0.92 (0.33), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 838 TYR 0.045 0.002 TYR A 605 PHE 0.012 0.001 PHE B 118 TRP 0.009 0.001 TRP B 510 HIS 0.001 0.000 HIS B 386 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.10 (12654) covalent geometry : angle 0.64068 / 0.28 (17222) hydrogen bonds : bond 0.02877 / 1.97 ( 776) hydrogen bonds : angle 3.68698 / 2.65 ( 2270) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2537.35 seconds wall clock time: 44 minutes 17.52 seconds (2657.52 seconds total)