Starting phenix.real_space_refine on Thu Feb 5 01:54:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uz6_64637/02_2026/9uz6_64637.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uz6_64637/02_2026/9uz6_64637.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uz6_64637/02_2026/9uz6_64637.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uz6_64637/02_2026/9uz6_64637.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uz6_64637/02_2026/9uz6_64637.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uz6_64637/02_2026/9uz6_64637.map" } resolution = 2.32 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.152 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 86 5.16 5 C 8952 2.51 5 N 2478 2.21 5 O 2676 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14192 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 933, 7096 Classifications: {'peptide': 933} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 45, 'TRANS': 885} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 7096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 933, 7096 Classifications: {'peptide': 933} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 45, 'TRANS': 885} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 3.25, per 1000 atoms: 0.23 Number of scatterers: 14192 At special positions: 0 Unit cell: (129.285, 112.385, 98.02, 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 86 16.00 O 2676 8.00 N 2478 7.00 C 8952 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: 1.41 Conformation dependent library (CDL) restraints added in 579.1 milliseconds 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3452 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 14 sheets defined 51.2% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 5 through 11 Processing helix chain 'A' and resid 13 through 20 removed outlier: 3.876A pdb=" N GLU A 17 " --> pdb=" O GLY A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 34 Processing helix chain 'A' and resid 38 through 47 Processing helix chain 'A' and resid 48 through 52 Processing helix chain 'A' and resid 64 through 77 Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 106 through 111 Processing helix chain 'A' and resid 117 through 120 Processing helix chain 'A' and resid 121 through 140 Processing helix chain 'A' and resid 150 through 166 Processing helix chain 'A' and resid 181 through 196 Processing helix chain 'A' and resid 203 through 209 removed outlier: 3.698A pdb=" N LEU A 208 " --> pdb=" O GLN A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 240 Processing helix chain 'A' and resid 251 through 256 removed outlier: 4.198A pdb=" N LEU A 255 " --> pdb=" O MET A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 263 Processing helix chain 'A' and resid 292 through 298 removed outlier: 5.287A pdb=" N ARG A 296 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET A 298 " --> pdb=" O LYS A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 379 Proline residue: A 355 - end of helix Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 430 through 443 Processing helix chain 'A' and resid 449 through 460 Processing helix chain 'A' and resid 465 through 469 removed outlier: 3.520A pdb=" N LEU A 469 " --> pdb=" O PRO A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 481 Processing helix chain 'A' and resid 485 through 499 removed outlier: 3.675A pdb=" N LYS A 499 " --> pdb=" O SER A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 524 Processing helix chain 'A' and resid 525 through 528 Processing helix chain 'A' and resid 539 through 542 Processing helix chain 'A' and resid 543 through 562 Processing helix chain 'A' and resid 572 through 591 Processing helix chain 'A' and resid 607 through 616 removed outlier: 3.751A pdb=" N ALA A 611 " --> pdb=" O GLY A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 644 Processing helix chain 'A' and resid 664 through 675 removed outlier: 3.916A pdb=" N PHE A 675 " --> pdb=" O VAL A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 689 removed outlier: 3.539A pdb=" N MET A 686 " --> pdb=" O GLY A 683 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ASN A 687 " --> pdb=" O ALA A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 699 Processing helix chain 'A' and resid 706 through 711 Processing helix chain 'A' and resid 731 through 735 removed outlier: 3.524A pdb=" N VAL A 735 " --> pdb=" O ALA A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 762 No H-bonds generated for 'chain 'A' and resid 760 through 762' Processing helix chain 'A' and resid 763 through 798 removed outlier: 3.969A pdb=" N SER A 767 " --> pdb=" O ILE A 763 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ALA A 776 " --> pdb=" O ARG A 772 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N GLU A 777 " --> pdb=" O MET A 773 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY A 778 " --> pdb=" O MET A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 828 Processing helix chain 'A' and resid 830 through 841 removed outlier: 3.825A pdb=" N ILE A 839 " --> pdb=" O ALA A 835 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP A 840 " --> pdb=" O LYS A 836 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR A 841 " --> pdb=" O ARG A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 888 Processing helix chain 'A' and resid 904 through 909 removed outlier: 3.976A pdb=" N LEU A 908 " --> pdb=" O ILE A 904 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL A 909 " --> pdb=" O GLN A 905 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 904 through 909' Processing helix chain 'A' and resid 917 through 923 Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 13 through 20 removed outlier: 3.899A pdb=" N GLU B 17 " --> pdb=" O GLY B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 34 Processing helix chain 'B' and resid 38 through 47 Processing helix chain 'B' and resid 48 through 52 Processing helix chain 'B' and resid 64 through 77 Processing helix chain 'B' and resid 96 through 103 Processing helix chain 'B' and resid 106 through 111 Processing helix chain 'B' and resid 117 through 120 Processing helix chain 'B' and resid 121 through 140 Processing helix chain 'B' and resid 150 through 166 Processing helix chain 'B' and resid 181 through 196 Processing helix chain 'B' and resid 203 through 209 removed outlier: 3.698A pdb=" N LEU B 208 " --> pdb=" O GLN B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 240 Processing helix chain 'B' and resid 251 through 256 removed outlier: 4.196A pdb=" N LEU B 255 " --> pdb=" O MET B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 263 Processing helix chain 'B' and resid 292 through 298 removed outlier: 5.307A pdb=" N ARG B 296 " --> pdb=" O GLU B 293 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET B 298 " --> pdb=" O LYS B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 379 Proline residue: B 355 - end of helix Processing helix chain 'B' and resid 398 through 409 Processing helix chain 'B' and resid 430 through 443 Processing helix chain 'B' and resid 449 through 460 Processing helix chain 'B' and resid 465 through 469 removed outlier: 3.520A pdb=" N LEU B 469 " --> pdb=" O PRO B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 481 Processing helix chain 'B' and resid 485 through 499 removed outlier: 3.672A pdb=" N LYS B 499 " --> pdb=" O SER B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 524 Processing helix chain 'B' and resid 525 through 528 Processing helix chain 'B' and resid 539 through 542 Processing helix chain 'B' and resid 543 through 562 Processing helix chain 'B' and resid 572 through 591 Processing helix chain 'B' and resid 607 through 616 removed outlier: 3.761A pdb=" N ALA B 611 " --> pdb=" O GLY B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 644 Processing helix chain 'B' and resid 664 through 675 removed outlier: 3.916A pdb=" N PHE B 675 " --> pdb=" O VAL B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 689 removed outlier: 3.539A pdb=" N MET B 686 " --> pdb=" O GLY B 683 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ASN B 687 " --> pdb=" O ALA B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 699 Processing helix chain 'B' and resid 706 through 711 Processing helix chain 'B' and resid 731 through 735 removed outlier: 3.537A pdb=" N VAL B 735 " --> pdb=" O ALA B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 762 No H-bonds generated for 'chain 'B' and resid 760 through 762' Processing helix chain 'B' and resid 763 through 798 removed outlier: 3.964A pdb=" N SER B 767 " --> pdb=" O ILE B 763 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ALA B 776 " --> pdb=" O ARG B 772 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N GLU B 777 " --> pdb=" O MET B 773 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY B 778 " --> pdb=" O MET B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 820 through 828 Processing helix chain 'B' and resid 830 through 841 removed outlier: 3.839A pdb=" N ILE B 839 " --> pdb=" O ALA B 835 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASP B 840 " --> pdb=" O LYS B 836 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR B 841 " --> pdb=" O ARG B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 888 Processing helix chain 'B' and resid 904 through 909 removed outlier: 3.976A pdb=" N LEU B 908 " --> pdb=" O ILE B 904 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL B 909 " --> pdb=" O GLN B 905 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 904 through 909' Processing helix chain 'B' and resid 917 through 923 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.478A pdb=" N THR A 83 " --> pdb=" O ASN A 412 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 143 through 144 removed outlier: 6.786A pdb=" N PHE A 214 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N SER A 245 " --> pdb=" O PHE A 214 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N VAL A 216 " --> pdb=" O SER A 245 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N ALA A 247 " --> pdb=" O VAL A 216 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU A 218 " --> pdb=" O ALA A 247 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ARG A 173 " --> pdb=" O GLY A 215 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N LEU A 217 " --> pdb=" O ARG A 173 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N PHE A 175 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N GLN A 219 " --> pdb=" O PHE A 175 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N ALA A 177 " --> pdb=" O GLN A 219 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 303 through 307 Processing sheet with id=AA4, first strand: chain 'A' and resid 382 through 383 removed outlier: 4.506A pdb=" N LYS A 382 " --> pdb=" O GLU A 395 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 565 through 567 removed outlier: 4.067A pdb=" N HIS A 704 " --> pdb=" O LEU A 681 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N SER A 648 " --> pdb=" O GLN A 678 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N TYR A 680 " --> pdb=" O SER A 648 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ILE A 650 " --> pdb=" O TYR A 680 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASP A 682 " --> pdb=" O ILE A 650 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL A 652 " --> pdb=" O ASP A 682 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE A 598 " --> pdb=" O SER A 648 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ILE A 650 " --> pdb=" O ILE A 598 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LEU A 600 " --> pdb=" O ILE A 650 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N VAL A 652 " --> pdb=" O LEU A 600 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 625 through 627 removed outlier: 3.946A pdb=" N LYS A 627 " --> pdb=" O ASN A 630 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 803 through 804 removed outlier: 4.622A pdb=" N ILE A 817 " --> pdb=" O LEU A 804 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.481A pdb=" N THR B 83 " --> pdb=" O ASN B 412 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 143 through 144 removed outlier: 6.785A pdb=" N PHE B 214 " --> pdb=" O VAL B 243 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N SER B 245 " --> pdb=" O PHE B 214 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N VAL B 216 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ALA B 247 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU B 218 " --> pdb=" O ALA B 247 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ARG B 173 " --> pdb=" O GLY B 215 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N LEU B 217 " --> pdb=" O ARG B 173 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N PHE B 175 " --> pdb=" O LEU B 217 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N GLN B 219 " --> pdb=" O PHE B 175 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N ALA B 177 " --> pdb=" O GLN B 219 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 303 through 307 Processing sheet with id=AB2, first strand: chain 'B' and resid 382 through 383 removed outlier: 4.508A pdb=" N LYS B 382 " --> pdb=" O GLU B 395 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 565 through 567 removed outlier: 4.067A pdb=" N HIS B 704 " --> pdb=" O LEU B 681 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N SER B 648 " --> pdb=" O GLN B 678 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N TYR B 680 " --> pdb=" O SER B 648 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ILE B 650 " --> pdb=" O TYR B 680 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASP B 682 " --> pdb=" O ILE B 650 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL B 652 " --> pdb=" O ASP B 682 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE B 598 " --> pdb=" O SER B 648 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ILE B 650 " --> pdb=" O ILE B 598 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU B 600 " --> pdb=" O ILE B 650 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N VAL B 652 " --> pdb=" O LEU B 600 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 625 through 627 removed outlier: 3.968A pdb=" N LYS B 627 " --> pdb=" O ASN B 630 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 803 through 804 removed outlier: 4.631A pdb=" N ILE B 817 " --> pdb=" O LEU B 804 " (cutoff:3.500A) 672 hydrogen bonds defined for protein. 1848 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: 2.77 Time building geometry restraints manager: 1.88 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: 4812 1.34 - 1.46: 2326 1.46 - 1.58: 7190 1.58 - 1.69: 0 1.69 - 1.81: 150 Bond restraints: 14478 Sorted by residual: bond pdb=" C GLY A 719 " pdb=" N PRO A 720 " ideal model delta sigma weight residual 1.340 1.365 -0.025 2.76e-02 1.31e+03 8.42e-01 bond pdb=" C GLY B 719 " pdb=" N PRO B 720 " ideal model delta sigma weight residual 1.340 1.365 -0.025 2.76e-02 1.31e+03 8.37e-01 bond pdb=" N SER A 147 " pdb=" CA SER A 147 " ideal model delta sigma weight residual 1.457 1.468 -0.011 1.29e-02 6.01e+03 7.06e-01 bond pdb=" CA VAL B 47 " pdb=" CB VAL B 47 " ideal model delta sigma weight residual 1.537 1.527 0.011 1.29e-02 6.01e+03 6.77e-01 bond pdb=" C ALA B 146 " pdb=" N SER B 147 " ideal model delta sigma weight residual 1.332 1.343 -0.011 1.40e-02 5.10e+03 6.03e-01 ... (remaining 14473 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 19471 1.96 - 3.93: 177 3.93 - 5.89: 23 5.89 - 7.86: 1 7.86 - 9.82: 4 Bond angle restraints: 19676 Sorted by residual: angle pdb=" C ALA B 146 " pdb=" N SER B 147 " pdb=" CA SER B 147 " ideal model delta sigma weight residual 121.54 129.73 -8.19 1.91e+00 2.74e-01 1.84e+01 angle pdb=" C ALA A 146 " pdb=" N SER A 147 " pdb=" CA SER A 147 " ideal model delta sigma weight residual 121.54 129.72 -8.18 1.91e+00 2.74e-01 1.84e+01 angle pdb=" CA LEU A 418 " pdb=" CB LEU A 418 " pdb=" CG LEU A 418 " ideal model delta sigma weight residual 116.30 126.12 -9.82 3.50e+00 8.16e-02 7.88e+00 angle pdb=" CA LEU B 418 " pdb=" CB LEU B 418 " pdb=" CG LEU B 418 " ideal model delta sigma weight residual 116.30 126.08 -9.78 3.50e+00 8.16e-02 7.80e+00 angle pdb=" N GLY B 719 " pdb=" CA GLY B 719 " pdb=" C GLY B 719 " ideal model delta sigma weight residual 112.34 117.97 -5.63 2.04e+00 2.40e-01 7.62e+00 ... (remaining 19671 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 7662 17.98 - 35.96: 778 35.96 - 53.94: 209 53.94 - 71.91: 56 71.91 - 89.89: 21 Dihedral angle restraints: 8726 sinusoidal: 3360 harmonic: 5366 Sorted by residual: dihedral pdb=" CA ALA B 921 " pdb=" C ALA B 921 " pdb=" N VAL B 922 " pdb=" CA VAL B 922 " ideal model delta harmonic sigma weight residual -180.00 -160.83 -19.17 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ALA A 921 " pdb=" C ALA A 921 " pdb=" N VAL A 922 " pdb=" CA VAL A 922 " ideal model delta harmonic sigma weight residual 180.00 -160.91 -19.09 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA PHE B 711 " pdb=" C PHE B 711 " pdb=" N CYS B 712 " pdb=" CA CYS B 712 " ideal model delta harmonic sigma weight residual 180.00 161.07 18.93 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 8723 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1297 0.029 - 0.058: 564 0.058 - 0.087: 217 0.087 - 0.116: 148 0.116 - 0.145: 20 Chirality restraints: 2246 Sorted by residual: chirality pdb=" CG LEU A 418 " pdb=" CB LEU A 418 " pdb=" CD1 LEU A 418 " pdb=" CD2 LEU A 418 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.27e-01 chirality pdb=" CG LEU B 418 " pdb=" CB LEU B 418 " pdb=" CD1 LEU B 418 " pdb=" CD2 LEU B 418 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.09e-01 chirality pdb=" CA ILE A 266 " pdb=" N ILE A 266 " pdb=" C ILE A 266 " pdb=" CB ILE A 266 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 2243 not shown) Planarity restraints: 2584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 764 " 0.032 5.00e-02 4.00e+02 4.83e-02 3.74e+00 pdb=" N PRO B 765 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 765 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 765 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 764 " 0.027 5.00e-02 4.00e+02 4.08e-02 2.67e+00 pdb=" N PRO A 765 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 765 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 765 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 723 " 0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO A 724 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 724 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 724 " 0.020 5.00e-02 4.00e+02 ... (remaining 2581 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2406 2.76 - 3.30: 13494 3.30 - 3.83: 25977 3.83 - 4.37: 31812 4.37 - 4.90: 51937 Nonbonded interactions: 125626 Sorted by model distance: nonbonded pdb=" NH1 ARG A 880 " pdb=" OD1 ASP A 884 " model vdw 2.231 3.120 nonbonded pdb=" NH1 ARG B 880 " pdb=" OD1 ASP B 884 " model vdw 2.232 3.120 nonbonded pdb=" OH TYR B 654 " pdb=" O GLU B 662 " model vdw 2.239 3.040 nonbonded pdb=" O PRO A 107 " pdb=" OG1 THR A 111 " model vdw 2.250 3.040 nonbonded pdb=" OH TYR A 654 " pdb=" O GLU A 662 " model vdw 2.251 3.040 ... (remaining 125621 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: 0.03 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.540 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 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 : 0.003 0.033 14478 Z= 0.126 Angle : 0.520 9.825 19676 Z= 0.273 Chirality : 0.043 0.145 2246 Planarity : 0.004 0.048 2584 Dihedral : 16.625 89.893 5274 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.89 % Favored : 98.00 % Rotamer: Outliers : 2.35 % Allowed : 16.53 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.20), residues: 1854 helix: 1.54 (0.18), residues: 808 sheet: 0.41 (0.41), residues: 188 loop : 0.18 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 296 TYR 0.016 0.002 TYR A 349 PHE 0.011 0.001 PHE A 287 TRP 0.004 0.001 TRP B 932 HIS 0.004 0.001 HIS B 730 Details of bonding type rmsd covalent geometry : bond 0.00279 (14478) covalent geometry : angle 0.51961 (19676) hydrogen bonds : bond 0.14248 ( 672) hydrogen bonds : angle 5.82248 ( 1848) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 212 time to evaluate : 0.604 Fit side-chains revert: symmetry clash outliers start: 35 outliers final: 33 residues processed: 245 average time/residue: 0.5921 time to fit residues: 157.9658 Evaluate side-chains 244 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 211 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 627 LYS Chi-restraints excluded: chain A residue 670 GLU Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 920 VAL Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 627 LYS Chi-restraints excluded: chain B residue 670 GLU Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 906 SER Chi-restraints excluded: chain B residue 922 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 0.0470 chunk 149 optimal weight: 5.9990 overall best weight: 3.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 HIS A 45 GLN A 378 GLN ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 HIS B 19 HIS B 45 GLN ** B 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.150611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.119236 restraints weight = 13193.145| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.42 r_work: 0.3217 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.0621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 14478 Z= 0.228 Angle : 0.630 8.197 19676 Z= 0.340 Chirality : 0.049 0.187 2246 Planarity : 0.005 0.053 2584 Dihedral : 7.299 58.148 2057 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.48 % Favored : 97.41 % Rotamer: Outliers : 3.83 % Allowed : 14.99 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.19), residues: 1854 helix: 1.49 (0.18), residues: 792 sheet: 0.48 (0.41), residues: 188 loop : 0.10 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 316 TYR 0.018 0.002 TYR A 349 PHE 0.016 0.002 PHE B 15 TRP 0.007 0.002 TRP B 109 HIS 0.006 0.001 HIS A 606 Details of bonding type rmsd covalent geometry : bond 0.00529 (14478) covalent geometry : angle 0.63034 (19676) hydrogen bonds : bond 0.05671 ( 672) hydrogen bonds : angle 4.88364 ( 1848) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 210 time to evaluate : 0.519 Fit side-chains revert: symmetry clash REVERT: B 541 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.6918 (mp0) outliers start: 57 outliers final: 38 residues processed: 252 average time/residue: 0.6474 time to fit residues: 178.0729 Evaluate side-chains 251 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 212 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 627 LYS Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 670 GLU Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 295 LYS Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 541 GLU Chi-restraints excluded: chain B residue 627 LYS Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 670 GLU Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 906 SER Chi-restraints excluded: chain B residue 920 VAL Chi-restraints excluded: chain B residue 922 VAL Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 939 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 94 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 149 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 179 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 378 GLN ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 HIS A 687 ASN B 45 GLN B 378 GLN ** B 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 HIS B 687 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.154629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.122764 restraints weight = 13332.732| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.44 r_work: 0.3264 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.0695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14478 Z= 0.109 Angle : 0.500 8.144 19676 Z= 0.266 Chirality : 0.042 0.137 2246 Planarity : 0.004 0.051 2584 Dihedral : 6.362 58.383 2048 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.78 % Favored : 98.11 % Rotamer: Outliers : 2.55 % Allowed : 16.40 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 1.36 (0.20), residues: 1854 helix: 1.84 (0.18), residues: 804 sheet: 0.57 (0.39), residues: 190 loop : 0.17 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 296 TYR 0.017 0.001 TYR B 110 PHE 0.011 0.001 PHE A 15 TRP 0.005 0.001 TRP B 932 HIS 0.003 0.001 HIS B 477 Details of bonding type rmsd covalent geometry : bond 0.00233 (14478) covalent geometry : angle 0.50032 (19676) hydrogen bonds : bond 0.04042 ( 672) hydrogen bonds : angle 4.43569 ( 1848) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 220 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 295 LYS cc_start: 0.7661 (tptp) cc_final: 0.7165 (pttt) REVERT: A 826 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.6620 (pp20) outliers start: 38 outliers final: 19 residues processed: 246 average time/residue: 0.5610 time to fit residues: 150.2036 Evaluate side-chains 236 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 216 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 670 GLU Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 826 GLU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 670 GLU Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 922 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 151 optimal weight: 20.0000 chunk 133 optimal weight: 0.5980 chunk 81 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 140 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 72 optimal weight: 8.9990 chunk 55 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 378 GLN ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 HIS A 687 ASN B 45 GLN B 378 GLN ** B 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 HIS B 687 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.154084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.122471 restraints weight = 13492.946| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.48 r_work: 0.3255 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.0744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14478 Z= 0.117 Angle : 0.508 8.197 19676 Z= 0.269 Chirality : 0.043 0.139 2246 Planarity : 0.004 0.052 2584 Dihedral : 5.769 57.901 2028 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.32 % Favored : 97.57 % Rotamer: Outliers : 2.69 % Allowed : 16.33 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 1.44 (0.20), residues: 1854 helix: 1.94 (0.18), residues: 804 sheet: 0.60 (0.39), residues: 190 loop : 0.17 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 296 TYR 0.015 0.001 TYR B 349 PHE 0.012 0.001 PHE A 15 TRP 0.005 0.001 TRP A 932 HIS 0.003 0.001 HIS A 446 Details of bonding type rmsd covalent geometry : bond 0.00256 (14478) covalent geometry : angle 0.50794 (19676) hydrogen bonds : bond 0.04071 ( 672) hydrogen bonds : angle 4.36323 ( 1848) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 216 time to evaluate : 0.381 Fit side-chains REVERT: A 173 ARG cc_start: 0.7956 (mtp180) cc_final: 0.7609 (mtt180) REVERT: A 295 LYS cc_start: 0.7662 (tptp) cc_final: 0.7170 (pttt) REVERT: A 316 ARG cc_start: 0.8260 (ptt-90) cc_final: 0.7470 (ptm160) REVERT: A 826 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.6600 (pp20) REVERT: A 832 LEU cc_start: 0.7844 (tp) cc_final: 0.7580 (tm) REVERT: B 173 ARG cc_start: 0.7934 (mtp180) cc_final: 0.7584 (mtt180) REVERT: B 295 LYS cc_start: 0.7705 (OUTLIER) cc_final: 0.7201 (pttt) outliers start: 40 outliers final: 24 residues processed: 238 average time/residue: 0.6103 time to fit residues: 158.7696 Evaluate side-chains 240 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 214 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 670 GLU Chi-restraints excluded: chain A residue 826 GLU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 295 LYS Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 670 GLU Chi-restraints excluded: chain B residue 922 VAL Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 939 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 44 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 chunk 158 optimal weight: 5.9990 chunk 178 optimal weight: 7.9990 chunk 70 optimal weight: 8.9990 chunk 142 optimal weight: 0.9980 chunk 67 optimal weight: 10.0000 chunk 140 optimal weight: 4.9990 chunk 150 optimal weight: 0.0060 chunk 153 optimal weight: 8.9990 overall best weight: 2.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 378 GLN ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 HIS B 45 GLN B 378 GLN ** B 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.153202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.118495 restraints weight = 13388.486| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.64 r_work: 0.3232 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.0720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14478 Z= 0.165 Angle : 0.564 8.269 19676 Z= 0.301 Chirality : 0.045 0.151 2246 Planarity : 0.005 0.050 2584 Dihedral : 6.015 58.224 2026 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.59 % Favored : 97.30 % Rotamer: Outliers : 3.16 % Allowed : 15.99 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 1.32 (0.20), residues: 1854 helix: 1.81 (0.18), residues: 792 sheet: 0.60 (0.39), residues: 190 loop : 0.16 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 296 TYR 0.017 0.002 TYR B 349 PHE 0.014 0.002 PHE B 15 TRP 0.005 0.001 TRP B 109 HIS 0.005 0.001 HIS B 353 Details of bonding type rmsd covalent geometry : bond 0.00377 (14478) covalent geometry : angle 0.56379 (19676) hydrogen bonds : bond 0.04686 ( 672) hydrogen bonds : angle 4.48964 ( 1848) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 213 time to evaluate : 0.590 Fit side-chains REVERT: A 49 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7289 (mptt) REVERT: A 173 ARG cc_start: 0.8049 (mtp180) cc_final: 0.7706 (mtt180) REVERT: A 295 LYS cc_start: 0.7709 (tptp) cc_final: 0.7211 (pttt) REVERT: A 316 ARG cc_start: 0.8336 (ptt-90) cc_final: 0.7548 (ptm160) REVERT: A 541 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7103 (mp0) REVERT: A 826 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.6506 (pp20) REVERT: A 887 LYS cc_start: 0.7791 (tttt) cc_final: 0.7157 (tttt) REVERT: B 173 ARG cc_start: 0.8028 (mtp180) cc_final: 0.7682 (mtt180) REVERT: B 295 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7258 (pttt) REVERT: B 541 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7087 (mp0) REVERT: B 826 GLU cc_start: 0.6747 (OUTLIER) cc_final: 0.6503 (mp0) outliers start: 47 outliers final: 32 residues processed: 242 average time/residue: 0.6138 time to fit residues: 162.2566 Evaluate side-chains 252 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 214 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 670 GLU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 826 GLU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 295 LYS Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 541 GLU Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 670 GLU Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 826 GLU Chi-restraints excluded: chain B residue 922 VAL Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 939 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 169 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 18 optimal weight: 0.5980 chunk 121 optimal weight: 1.9990 chunk 165 optimal weight: 0.0270 chunk 161 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 chunk 174 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 overall best weight: 1.1042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 378 GLN ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 HIS A 687 ASN B 45 GLN B 378 GLN ** B 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 HIS B 687 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.157287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.123125 restraints weight = 13230.546| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.58 r_work: 0.3317 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.0778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14478 Z= 0.116 Angle : 0.511 8.463 19676 Z= 0.271 Chirality : 0.043 0.139 2246 Planarity : 0.004 0.051 2584 Dihedral : 5.746 58.724 2026 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.00 % Favored : 97.90 % Rotamer: Outliers : 2.76 % Allowed : 16.40 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 1.44 (0.20), residues: 1854 helix: 1.93 (0.18), residues: 804 sheet: 0.63 (0.39), residues: 190 loop : 0.18 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 296 TYR 0.015 0.001 TYR A 110 PHE 0.012 0.001 PHE B 15 TRP 0.005 0.001 TRP A 932 HIS 0.003 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00254 (14478) covalent geometry : angle 0.51092 (19676) hydrogen bonds : bond 0.04007 ( 672) hydrogen bonds : angle 4.33244 ( 1848) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 215 time to evaluate : 0.351 Fit side-chains REVERT: A 49 LYS cc_start: 0.7686 (OUTLIER) cc_final: 0.7279 (mptt) REVERT: A 173 ARG cc_start: 0.8066 (mtp180) cc_final: 0.7733 (mtt180) REVERT: A 295 LYS cc_start: 0.7755 (tptp) cc_final: 0.7279 (pttt) REVERT: A 316 ARG cc_start: 0.8318 (ptt-90) cc_final: 0.7642 (ptm160) REVERT: B 173 ARG cc_start: 0.8057 (mtp180) cc_final: 0.7722 (mtt180) REVERT: B 295 LYS cc_start: 0.7799 (OUTLIER) cc_final: 0.7283 (pttt) REVERT: B 826 GLU cc_start: 0.6810 (OUTLIER) cc_final: 0.6591 (mp0) outliers start: 41 outliers final: 26 residues processed: 237 average time/residue: 0.6184 time to fit residues: 159.3622 Evaluate side-chains 241 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 212 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 670 GLU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 295 LYS Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 670 GLU Chi-restraints excluded: chain B residue 817 ILE Chi-restraints excluded: chain B residue 826 GLU Chi-restraints excluded: chain B residue 922 VAL Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 939 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 116 optimal weight: 0.1980 chunk 56 optimal weight: 9.9990 chunk 96 optimal weight: 0.9990 chunk 78 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 184 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 378 GLN ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 GLN B 378 GLN ** B 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.155291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.120976 restraints weight = 13119.194| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.58 r_work: 0.3287 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.0747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14478 Z= 0.167 Angle : 0.568 8.269 19676 Z= 0.302 Chirality : 0.046 0.155 2246 Planarity : 0.005 0.051 2584 Dihedral : 6.004 58.021 2026 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.59 % Favored : 97.30 % Rotamer: Outliers : 2.76 % Allowed : 16.53 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 1.32 (0.19), residues: 1854 helix: 1.81 (0.18), residues: 792 sheet: 0.64 (0.40), residues: 190 loop : 0.14 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 296 TYR 0.017 0.002 TYR A 349 PHE 0.014 0.002 PHE B 15 TRP 0.005 0.001 TRP B 932 HIS 0.005 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00383 (14478) covalent geometry : angle 0.56767 (19676) hydrogen bonds : bond 0.04640 ( 672) hydrogen bonds : angle 4.45824 ( 1848) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 210 time to evaluate : 0.467 Fit side-chains REVERT: A 173 ARG cc_start: 0.8079 (mtp180) cc_final: 0.7748 (mtt180) REVERT: A 295 LYS cc_start: 0.7771 (tptp) cc_final: 0.7294 (pttt) REVERT: A 316 ARG cc_start: 0.8342 (ptt-90) cc_final: 0.7658 (ptm160) REVERT: A 541 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7129 (mp0) REVERT: B 173 ARG cc_start: 0.8063 (mtp180) cc_final: 0.7729 (mtt180) REVERT: B 295 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7329 (pttt) REVERT: B 541 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7142 (mp0) REVERT: B 826 GLU cc_start: 0.6835 (OUTLIER) cc_final: 0.6606 (mp0) outliers start: 41 outliers final: 29 residues processed: 236 average time/residue: 0.6067 time to fit residues: 155.5715 Evaluate side-chains 241 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 208 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 670 GLU Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 295 LYS Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 541 GLU Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 670 GLU Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 826 GLU Chi-restraints excluded: chain B residue 922 VAL Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 939 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 105 optimal weight: 6.9990 chunk 135 optimal weight: 0.6980 chunk 118 optimal weight: 7.9990 chunk 102 optimal weight: 0.8980 chunk 113 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 139 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 378 GLN ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 GLN B 378 GLN ** B 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.158092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.123959 restraints weight = 13250.182| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.59 r_work: 0.3327 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.0843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14478 Z= 0.108 Angle : 0.503 9.427 19676 Z= 0.265 Chirality : 0.042 0.138 2246 Planarity : 0.004 0.052 2584 Dihedral : 5.641 57.509 2026 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.89 % Favored : 98.00 % Rotamer: Outliers : 2.02 % Allowed : 17.41 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 1.48 (0.20), residues: 1854 helix: 2.00 (0.18), residues: 804 sheet: 0.56 (0.39), residues: 194 loop : 0.19 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 296 TYR 0.016 0.001 TYR A 110 PHE 0.013 0.001 PHE A 15 TRP 0.006 0.001 TRP B 932 HIS 0.004 0.001 HIS B 477 Details of bonding type rmsd covalent geometry : bond 0.00235 (14478) covalent geometry : angle 0.50347 (19676) hydrogen bonds : bond 0.03812 ( 672) hydrogen bonds : angle 4.27325 ( 1848) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 213 time to evaluate : 0.551 Fit side-chains REVERT: A 169 LYS cc_start: 0.7456 (OUTLIER) cc_final: 0.6879 (pttt) REVERT: A 295 LYS cc_start: 0.7736 (tptp) cc_final: 0.7253 (pttt) REVERT: A 316 ARG cc_start: 0.8329 (ptt-90) cc_final: 0.7648 (ptm160) REVERT: B 169 LYS cc_start: 0.7460 (OUTLIER) cc_final: 0.6880 (pttt) REVERT: B 295 LYS cc_start: 0.7778 (OUTLIER) cc_final: 0.7262 (pttt) REVERT: B 667 GLU cc_start: 0.7721 (pt0) cc_final: 0.7450 (pt0) REVERT: B 826 GLU cc_start: 0.6911 (OUTLIER) cc_final: 0.6595 (mp0) outliers start: 30 outliers final: 18 residues processed: 231 average time/residue: 0.6508 time to fit residues: 163.3545 Evaluate side-chains 233 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 211 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 670 GLU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 295 LYS Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 670 GLU Chi-restraints excluded: chain B residue 826 GLU Chi-restraints excluded: chain B residue 922 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 183 optimal weight: 1.9990 chunk 177 optimal weight: 7.9990 chunk 129 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 140 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 164 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 58 GLN A 378 GLN ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 GLN B 58 GLN ** B 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.157024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.122851 restraints weight = 13182.337| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.58 r_work: 0.3314 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.0815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14478 Z= 0.127 Angle : 0.526 8.723 19676 Z= 0.277 Chirality : 0.043 0.142 2246 Planarity : 0.004 0.051 2584 Dihedral : 5.650 58.583 2018 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.37 % Favored : 97.52 % Rotamer: Outliers : 2.35 % Allowed : 17.27 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 1.45 (0.20), residues: 1854 helix: 1.93 (0.18), residues: 804 sheet: 0.68 (0.40), residues: 190 loop : 0.19 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 296 TYR 0.016 0.002 TYR A 349 PHE 0.013 0.001 PHE A 15 TRP 0.004 0.001 TRP A 932 HIS 0.006 0.001 HIS B 477 Details of bonding type rmsd covalent geometry : bond 0.00283 (14478) covalent geometry : angle 0.52558 (19676) hydrogen bonds : bond 0.04093 ( 672) hydrogen bonds : angle 4.31663 ( 1848) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 207 time to evaluate : 0.426 Fit side-chains REVERT: A 169 LYS cc_start: 0.7485 (OUTLIER) cc_final: 0.6903 (pttt) REVERT: A 295 LYS cc_start: 0.7741 (tptp) cc_final: 0.7270 (pttt) REVERT: A 316 ARG cc_start: 0.8323 (ptt-90) cc_final: 0.7631 (ptm160) REVERT: B 169 LYS cc_start: 0.7482 (OUTLIER) cc_final: 0.6899 (pttt) REVERT: B 295 LYS cc_start: 0.7815 (OUTLIER) cc_final: 0.7312 (pttt) REVERT: B 826 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.6532 (mp0) outliers start: 35 outliers final: 20 residues processed: 232 average time/residue: 0.6525 time to fit residues: 164.5826 Evaluate side-chains 233 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 209 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 670 GLU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 295 LYS Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 670 GLU Chi-restraints excluded: chain B residue 826 GLU Chi-restraints excluded: chain B residue 922 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 54 optimal weight: 0.9990 chunk 154 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 40 optimal weight: 0.9980 chunk 136 optimal weight: 0.1980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 378 GLN ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 GLN ** B 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.157960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.123846 restraints weight = 13243.490| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.59 r_work: 0.3326 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.0889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14478 Z= 0.112 Angle : 0.513 8.814 19676 Z= 0.269 Chirality : 0.043 0.139 2246 Planarity : 0.004 0.052 2584 Dihedral : 5.550 56.949 2018 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.89 % Favored : 98.06 % Rotamer: Outliers : 1.61 % Allowed : 17.88 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 1.53 (0.20), residues: 1854 helix: 2.02 (0.18), residues: 804 sheet: 0.68 (0.39), residues: 190 loop : 0.20 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 296 TYR 0.015 0.001 TYR A 110 PHE 0.012 0.001 PHE A 15 TRP 0.004 0.001 TRP A 932 HIS 0.008 0.001 HIS B 477 Details of bonding type rmsd covalent geometry : bond 0.00247 (14478) covalent geometry : angle 0.51268 (19676) hydrogen bonds : bond 0.03863 ( 672) hydrogen bonds : angle 4.26791 ( 1848) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 213 time to evaluate : 0.489 Fit side-chains REVERT: A 169 LYS cc_start: 0.7474 (OUTLIER) cc_final: 0.6916 (pttt) REVERT: A 295 LYS cc_start: 0.7726 (tptp) cc_final: 0.7277 (pttt) REVERT: A 316 ARG cc_start: 0.8320 (ptt-90) cc_final: 0.7626 (ptm160) REVERT: B 169 LYS cc_start: 0.7469 (OUTLIER) cc_final: 0.6910 (pttt) REVERT: B 295 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7294 (pttt) REVERT: B 826 GLU cc_start: 0.6920 (OUTLIER) cc_final: 0.6607 (mp0) outliers start: 24 outliers final: 18 residues processed: 227 average time/residue: 0.6494 time to fit residues: 160.4130 Evaluate side-chains 232 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 210 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 670 GLU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 295 LYS Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 670 GLU Chi-restraints excluded: chain B residue 826 GLU Chi-restraints excluded: chain B residue 922 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 62 optimal weight: 10.0000 chunk 156 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 157 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 124 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 72 optimal weight: 0.0030 overall best weight: 1.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 58 GLN ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 GLN B 58 GLN ** B 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.156782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.122653 restraints weight = 13203.696| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.58 r_work: 0.3311 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.0843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14478 Z= 0.133 Angle : 0.534 8.455 19676 Z= 0.281 Chirality : 0.044 0.141 2246 Planarity : 0.004 0.051 2584 Dihedral : 5.694 58.507 2018 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.48 % Favored : 97.46 % Rotamer: Outliers : 1.55 % Allowed : 17.94 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 1.44 (0.20), residues: 1854 helix: 1.91 (0.18), residues: 804 sheet: 0.67 (0.39), residues: 190 loop : 0.19 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 296 TYR 0.016 0.002 TYR B 349 PHE 0.013 0.001 PHE A 15 TRP 0.004 0.001 TRP B 932 HIS 0.009 0.001 HIS B 477 Details of bonding type rmsd covalent geometry : bond 0.00298 (14478) covalent geometry : angle 0.53357 (19676) hydrogen bonds : bond 0.04165 ( 672) hydrogen bonds : angle 4.33050 ( 1848) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5503.29 seconds wall clock time: 94 minutes 21.32 seconds (5661.32 seconds total)