Starting phenix.real_space_refine on Fri Jul 3 02:26:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7w4a_32299/07_2026/7w4a_32299.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w4a_32299/07_2026/7w4a_32299.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7w4a_32299/07_2026/7w4a_32299.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w4a_32299/07_2026/7w4a_32299.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7w4a_32299/07_2026/7w4a_32299.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7w4a_32299/07_2026/7w4a_32299.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7w4a_32299/07_2026/7w4a_32299.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w4a_32299/07_2026/7w4a_32299.map" } resolution = 2.76 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1623 atoms to isotropic. 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: 9 Type Number sf(0) Gaussians P 1 5.49 5 Mg 1 5.21 5 S 64 5.16 5 Na 1 4.78 5 Be 1 3.05 5 C 6318 2.51 5 N 1638 2.21 5 O 1827 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9855 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 984, 7642 Classifications: {'peptide': 984} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 47, 'TRANS': 936} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Chain: "B" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2076 Classifications: {'peptide': 261} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 4, 'PTRANS': 17, 'TRANS': 239} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' NA': 1, '8CK': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 96 Unusual residues: {'NAG': 3, 'PCW': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Time building chain proxies: 2.01, per 1000 atoms: 0.20 Number of scatterers: 9855 At special positions: 0 Unit cell: (118.064, 91.744, 170.704, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) S 64 16.00 P 1 15.00 Mg 1 11.99 Na 1 11.00 F 4 9.00 O 1827 8.00 N 1638 7.00 C 6318 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 152 " distance=2.03 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 178 " distance=2.03 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 262 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG B 301 " - " ASN B 99 " " NAG B 302 " - " ASN B 130 " " NAG B 303 " - " ASN B 161 " Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 349.2 milliseconds 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2330 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 9 sheets defined 51.0% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 50 through 55 removed outlier: 3.536A pdb=" N GLN A 54 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 65 Processing helix chain 'A' and resid 73 through 85 Processing helix chain 'A' and resid 96 through 105 Processing helix chain 'A' and resid 107 through 130 Processing helix chain 'A' and resid 135 through 168 removed outlier: 4.006A pdb=" N LEU A 139 " --> pdb=" O THR A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 171 No H-bonds generated for 'chain 'A' and resid 169 through 171' Processing helix chain 'A' and resid 270 through 273 Processing helix chain 'A' and resid 274 through 286 Processing helix chain 'A' and resid 291 through 323 Processing helix chain 'A' and resid 325 through 340 Processing helix chain 'A' and resid 343 through 363 removed outlier: 4.440A pdb=" N ALA A 347 " --> pdb=" O GLU A 343 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 379 removed outlier: 3.540A pdb=" N ALA A 372 " --> pdb=" O ASN A 369 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU A 374 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N LEU A 376 " --> pdb=" O VAL A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 438 Processing helix chain 'A' and resid 459 through 473 Processing helix chain 'A' and resid 475 through 483 removed outlier: 3.829A pdb=" N GLU A 481 " --> pdb=" O MET A 477 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG A 482 " --> pdb=" O GLY A 478 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE A 483 " --> pdb=" O TYR A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 524 Processing helix chain 'A' and resid 540 through 556 Processing helix chain 'A' and resid 607 through 618 Processing helix chain 'A' and resid 629 through 640 Processing helix chain 'A' and resid 649 through 658 Processing helix chain 'A' and resid 665 through 669 Processing helix chain 'A' and resid 675 through 682 Processing helix chain 'A' and resid 683 through 694 Processing helix chain 'A' and resid 703 through 717 Processing helix chain 'A' and resid 727 through 729 No H-bonds generated for 'chain 'A' and resid 727 through 729' Processing helix chain 'A' and resid 730 through 737 Processing helix chain 'A' and resid 748 through 755 Processing helix chain 'A' and resid 765 through 791 removed outlier: 3.795A pdb=" N THR A 769 " --> pdb=" O ALA A 765 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LYS A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 806 Proline residue: A 798 - end of helix Processing helix chain 'A' and resid 812 through 822 Processing helix chain 'A' and resid 824 through 831 removed outlier: 3.700A pdb=" N SER A 828 " --> pdb=" O ASP A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 834 No H-bonds generated for 'chain 'A' and resid 832 through 834' Processing helix chain 'A' and resid 855 through 865 Processing helix chain 'A' and resid 865 through 886 Processing helix chain 'A' and resid 888 through 893 removed outlier: 3.532A pdb=" N VAL A 893 " --> pdb=" O PRO A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 900 Processing helix chain 'A' and resid 916 through 947 removed outlier: 3.729A pdb=" N ALA A 941 " --> pdb=" O MET A 937 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 944 " --> pdb=" O ILE A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 980 Processing helix chain 'A' and resid 983 through 988 removed outlier: 3.682A pdb=" N ILE A 987 " --> pdb=" O GLY A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1000 Processing helix chain 'A' and resid 1001 through 1022 Processing helix chain 'A' and resid 1025 through 1032 Processing helix chain 'B' and resid 33 through 66 Processing helix chain 'B' and resid 102 through 119 removed outlier: 4.448A pdb=" N TRP B 106 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLY B 108 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LEU B 109 " --> pdb=" O THR B 105 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY B 119 " --> pdb=" O ARG B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 removed outlier: 4.109A pdb=" N GLU B 126 " --> pdb=" O ALA B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 164 removed outlier: 6.253A pdb=" N ASN B 161 " --> pdb=" O MET B 158 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLY B 164 " --> pdb=" O ASN B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 223 removed outlier: 3.809A pdb=" N THR B 223 " --> pdb=" O ALA B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 229 removed outlier: 3.556A pdb=" N PHE B 229 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 189 removed outlier: 3.546A pdb=" N ARG A 182 " --> pdb=" O ASP A 185 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N THR A 179 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LEU A 199 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N CYS A 258 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ASP A 223 " --> pdb=" O CYS A 258 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N THR A 262 " --> pdb=" O GLY A 219 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N GLY A 219 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N GLN A 264 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ALA A 217 " --> pdb=" O GLN A 264 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N LEU A 266 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU A 215 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL A 268 " --> pdb=" O ARG A 213 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ARG A 213 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N CYS A 220 " --> pdb=" O ARG A 236 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ASN A 224 " --> pdb=" O GLU A 232 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N GLU A 232 " --> pdb=" O ASN A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 189 removed outlier: 3.546A pdb=" N ARG A 182 " --> pdb=" O ASP A 185 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N THR A 179 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LEU A 199 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N CYS A 258 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ASP A 223 " --> pdb=" O CYS A 258 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N THR A 262 " --> pdb=" O GLY A 219 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N GLY A 219 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N GLN A 264 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ALA A 217 " --> pdb=" O GLN A 264 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N LEU A 266 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU A 215 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL A 268 " --> pdb=" O ARG A 213 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ARG A 213 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 365 through 367 removed outlier: 6.138A pdb=" N GLY A 740 " --> pdb=" O MET A 757 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N LEU A 759 " --> pdb=" O GLY A 740 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ALA A 742 " --> pdb=" O LEU A 759 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL A 721 " --> pdb=" O ILE A 739 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N VAL A 741 " --> pdb=" O VAL A 721 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL A 723 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N MET A 743 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N GLY A 725 " --> pdb=" O MET A 743 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL A 381 " --> pdb=" O ALA A 722 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N THR A 724 " --> pdb=" O VAL A 381 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N CYS A 383 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N VAL A 622 " --> pdb=" O MET A 697 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N PHE A 699 " --> pdb=" O VAL A 622 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N MET A 624 " --> pdb=" O PHE A 699 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N CYS A 672 " --> pdb=" O VAL A 698 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 405 through 408 removed outlier: 3.562A pdb=" N THR A 396 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N SER A 599 " --> pdb=" O SER A 398 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU A 400 " --> pdb=" O LEU A 597 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU A 597 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N PHE A 402 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 10.024A pdb=" N ALA A 595 " --> pdb=" O PHE A 402 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N PHE A 564 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LEU A 597 " --> pdb=" O LEU A 562 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU A 562 " --> pdb=" O LEU A 597 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N SER A 599 " --> pdb=" O ARG A 560 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ARG A 560 " --> pdb=" O SER A 599 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N CYS A 487 " --> pdb=" O ILE A 501 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 405 through 408 removed outlier: 3.562A pdb=" N THR A 396 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N SER A 599 " --> pdb=" O SER A 398 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU A 400 " --> pdb=" O LEU A 597 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU A 597 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N PHE A 402 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 10.024A pdb=" N ALA A 595 " --> pdb=" O PHE A 402 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N LEU A 592 " --> pdb=" O CYS A 527 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLY A 596 " --> pdb=" O LEU A 531 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 441 through 442 Processing sheet with id=AA7, first strand: chain 'A' and resid 907 through 908 Processing sheet with id=AA8, first strand: chain 'B' and resid 82 through 85 removed outlier: 3.576A pdb=" N VAL B 245 " --> pdb=" O ILE B 181 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 95 through 99 527 hydrogen bonds defined for protein. 1497 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: 1.37 Time building geometry restraints manager: 1.01 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: 3142 1.34 - 1.46: 1780 1.46 - 1.58: 5049 1.58 - 1.70: 2 1.70 - 1.82: 95 Bond restraints: 10068 Sorted by residual: bond pdb=" F3 BFD A 385 " pdb="BE BFD A 385 " ideal model delta sigma weight residual 1.529 1.763 -0.234 2.00e-02 2.50e+03 1.36e+02 bond pdb=" F2 BFD A 385 " pdb="BE BFD A 385 " ideal model delta sigma weight residual 1.535 1.754 -0.219 2.00e-02 2.50e+03 1.19e+02 bond pdb=" F1 BFD A 385 " pdb="BE BFD A 385 " ideal model delta sigma weight residual 1.542 1.753 -0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" CG BFD A 385 " pdb=" OD1 BFD A 385 " ideal model delta sigma weight residual 1.269 1.450 -0.181 2.00e-02 2.50e+03 8.15e+01 bond pdb=" C31 PCW B 304 " pdb=" O2 PCW B 304 " ideal model delta sigma weight residual 1.333 1.454 -0.121 2.00e-02 2.50e+03 3.68e+01 ... (remaining 10063 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.37: 13603 3.37 - 6.74: 62 6.74 - 10.11: 11 10.11 - 13.48: 1 13.48 - 16.86: 4 Bond angle restraints: 13681 Sorted by residual: angle pdb=" F2 BFD A 385 " pdb="BE BFD A 385 " pdb=" F3 BFD A 385 " ideal model delta sigma weight residual 112.60 95.74 16.86 3.00e+00 1.11e-01 3.16e+01 angle pdb=" OD1 BFD A 385 " pdb="BE BFD A 385 " pdb=" F1 BFD A 385 " ideal model delta sigma weight residual 102.38 118.72 -16.34 3.00e+00 1.11e-01 2.97e+01 angle pdb=" F1 BFD A 385 " pdb="BE BFD A 385 " pdb=" F3 BFD A 385 " ideal model delta sigma weight residual 111.29 95.71 15.58 3.00e+00 1.11e-01 2.70e+01 angle pdb=" C ASN A 792 " pdb=" N ILE A 793 " pdb=" CA ILE A 793 " ideal model delta sigma weight residual 120.24 123.49 -3.25 6.30e-01 2.52e+00 2.67e+01 angle pdb=" OD1 BFD A 385 " pdb="BE BFD A 385 " pdb=" F3 BFD A 385 " ideal model delta sigma weight residual 109.93 95.90 14.03 3.00e+00 1.11e-01 2.19e+01 ... (remaining 13676 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 5517 17.84 - 35.68: 416 35.68 - 53.52: 56 53.52 - 71.35: 13 71.35 - 89.19: 9 Dihedral angle restraints: 6011 sinusoidal: 2394 harmonic: 3617 Sorted by residual: dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 152 " pdb=" CB CYS B 152 " ideal model delta sinusoidal sigma weight residual 93.00 37.85 55.15 1 1.00e+01 1.00e-02 4.11e+01 dihedral pdb=" CA TYR A 863 " pdb=" C TYR A 863 " pdb=" N PHE A 864 " pdb=" CA PHE A 864 " ideal model delta harmonic sigma weight residual 180.00 -161.58 -18.42 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA ASP B 72 " pdb=" C ASP B 72 " pdb=" N TYR B 73 " pdb=" CA TYR B 73 " ideal model delta harmonic sigma weight residual -180.00 -161.84 -18.16 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 6008 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1250 0.053 - 0.106: 256 0.106 - 0.158: 39 0.158 - 0.211: 2 0.211 - 0.264: 2 Chirality restraints: 1549 Sorted by residual: chirality pdb=" C1 NAG B 302 " pdb=" ND2 ASN B 130 " pdb=" C2 NAG B 302 " pdb=" O5 NAG B 302 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CB VAL A 930 " pdb=" CA VAL A 930 " pdb=" CG1 VAL A 930 " pdb=" CG2 VAL A 930 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" C2 PCW B 304 " pdb=" C1 PCW B 304 " pdb=" C3 PCW B 304 " pdb=" O2 PCW B 304 " both_signs ideal model delta sigma weight residual False -2.32 -2.52 0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 1546 not shown) Planarity restraints: 1757 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 232 " -0.041 5.00e-02 4.00e+02 6.22e-02 6.19e+00 pdb=" N PRO A 233 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 233 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 233 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 99 " 0.001 2.00e-02 2.50e+03 1.92e-02 4.62e+00 pdb=" CG ASN B 99 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN B 99 " 0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN B 99 " -0.020 2.00e-02 2.50e+03 pdb=" C1 NAG B 301 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 237 " -0.034 5.00e-02 4.00e+02 5.27e-02 4.44e+00 pdb=" N PRO A 238 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 238 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 238 " -0.029 5.00e-02 4.00e+02 ... (remaining 1754 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 74 2.62 - 3.19: 8723 3.19 - 3.76: 15535 3.76 - 4.33: 21460 4.33 - 4.90: 35355 Nonbonded interactions: 81147 Sorted by model distance: nonbonded pdb=" F2 BFD A 385 " pdb="MG MG A1103 " model vdw 2.048 2.120 nonbonded pdb=" OD2 BFD A 385 " pdb="MG MG A1103 " model vdw 2.082 2.170 nonbonded pdb=" ND2 ASN A 792 " pdb=" O HOH A1201 " model vdw 2.146 3.120 nonbonded pdb=" OH TYR A1011 " pdb=" OH TYR B 43 " model vdw 2.174 3.040 nonbonded pdb=" O SER A 244 " pdb=" OG1 THR A 248 " model vdw 2.240 3.040 ... (remaining 81142 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.130 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 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 : 0.006 0.234 10074 Z= 0.279 Angle : 0.718 16.855 13696 Z= 0.345 Chirality : 0.044 0.264 1549 Planarity : 0.004 0.062 1754 Dihedral : 13.118 89.192 3672 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.09 % Allowed : 0.00 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.29 (0.24), residues: 1238 helix: 1.76 (0.21), residues: 575 sheet: -0.01 (0.37), residues: 162 loop : 0.21 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 844 TYR 0.018 0.001 TYR A 802 PHE 0.030 0.002 PHE A 124 TRP 0.013 0.002 TRP A 427 HIS 0.009 0.001 HIS B 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.28 (10068) covalent geometry : angle 0.71250 / 0.34 (13681) SS BOND : bond 0.00158 / 0.07 ( 3) SS BOND : angle 0.70251 / 0.38 ( 6) hydrogen bonds : bond 0.13589 / 8.68 ( 508) hydrogen bonds : angle 5.56355 / 4.08 ( 1497) link_NAG-ASN : bond 0.00419 / 0.20 ( 3) link_NAG-ASN : angle 3.55352 / 1.93 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 0.309 Fit side-chains REVERT: A 140 TYR cc_start: 0.6553 (m-10) cc_final: 0.6270 (m-10) REVERT: A 213 ARG cc_start: 0.5596 (ttt-90) cc_final: 0.5284 (ttt180) REVERT: A 220 CYS cc_start: 0.6849 (t) cc_final: 0.6577 (t) REVERT: A 260 GLU cc_start: 0.5871 (mt-10) cc_final: 0.5612 (mt-10) REVERT: A 314 THR cc_start: 0.6909 (t) cc_final: 0.6619 (p) REVERT: A 320 MET cc_start: 0.6875 (mmp) cc_final: 0.6515 (mmp) REVERT: A 333 PHE cc_start: 0.7257 (t80) cc_final: 0.6890 (t80) REVERT: A 369 ASN cc_start: 0.7437 (p0) cc_final: 0.7182 (p0) REVERT: A 425 GLU cc_start: 0.4301 (pm20) cc_final: 0.3772 (tm-30) REVERT: A 585 MET cc_start: -0.1063 (mmt) cc_final: -0.1434 (mmt) REVERT: A 652 ASP cc_start: 0.5905 (m-30) cc_final: 0.5649 (m-30) REVERT: A 743 MET cc_start: 0.8061 (mmm) cc_final: 0.7789 (mpp) REVERT: A 970 PHE cc_start: 0.7261 (t80) cc_final: 0.7056 (t80) REVERT: B 147 HIS cc_start: 0.6754 (t-90) cc_final: 0.6450 (t-170) outliers start: 1 outliers final: 0 residues processed: 138 average time/residue: 0.5236 time to fit residues: 77.7192 Evaluate side-chains 108 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 0.0050 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 123 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.0470 overall best weight: 1.1496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 ASN A 706 GLN A 924 GLN A 986 ASN B 146 ASN B 289 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.179914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.130096 restraints weight = 11496.032| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.65 r_work: 0.3236 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10074 Z= 0.137 Angle : 0.553 6.606 13696 Z= 0.285 Chirality : 0.044 0.308 1549 Planarity : 0.005 0.060 1754 Dihedral : 5.556 65.345 1399 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.52 % Allowed : 6.54 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.42 (0.24), residues: 1238 helix: 1.95 (0.22), residues: 565 sheet: -0.00 (0.37), residues: 162 loop : 0.23 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 278 TYR 0.018 0.001 TYR A 802 PHE 0.016 0.002 PHE A 932 TRP 0.011 0.002 TRP A 427 HIS 0.006 0.001 HIS B 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (10068) covalent geometry : angle 0.55082 / 0.28 (13681) SS BOND : bond 0.00310 / 0.15 ( 3) SS BOND : angle 0.85720 / 0.44 ( 6) hydrogen bonds : bond 0.04664 / 3.05 ( 508) hydrogen bonds : angle 4.62475 / 3.36 ( 1497) link_NAG-ASN : bond 0.00630 / 0.31 ( 3) link_NAG-ASN : angle 1.96971 / 1.01 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 TYR cc_start: 0.7152 (m-10) cc_final: 0.6729 (m-10) REVERT: A 193 GLN cc_start: 0.6221 (mm-40) cc_final: 0.5674 (mm-40) REVERT: A 213 ARG cc_start: 0.5842 (ttt-90) cc_final: 0.5489 (ttt180) REVERT: A 260 GLU cc_start: 0.6153 (mt-10) cc_final: 0.5850 (mt-10) REVERT: A 333 PHE cc_start: 0.7333 (t80) cc_final: 0.6991 (t80) REVERT: A 425 GLU cc_start: 0.4263 (pm20) cc_final: 0.3761 (tm-30) REVERT: A 516 MET cc_start: 0.4130 (tmt) cc_final: 0.3745 (tmt) REVERT: A 652 ASP cc_start: 0.5970 (m-30) cc_final: 0.5695 (m-30) REVERT: A 986 ASN cc_start: 0.6519 (m-40) cc_final: 0.6291 (m110) REVERT: B 114 HIS cc_start: 0.6748 (OUTLIER) cc_final: 0.6408 (t-90) REVERT: B 135 LYS cc_start: 0.7526 (ptpp) cc_final: 0.7277 (ptpp) REVERT: B 147 HIS cc_start: 0.6911 (t-90) cc_final: 0.6537 (t-170) REVERT: B 258 VAL cc_start: 0.7846 (p) cc_final: 0.7576 (m) outliers start: 16 outliers final: 5 residues processed: 128 average time/residue: 0.4550 time to fit residues: 63.1075 Evaluate side-chains 122 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 116 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 114 HIS Chi-restraints excluded: chain B residue 194 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 118 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 86 optimal weight: 0.8980 chunk 64 optimal weight: 7.9990 chunk 97 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 4 optimal weight: 0.0980 chunk 26 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 234 GLN B 289 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.179302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.122235 restraints weight = 11460.909| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.12 r_work: 0.3117 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10074 Z= 0.144 Angle : 0.550 6.438 13696 Z= 0.282 Chirality : 0.044 0.329 1549 Planarity : 0.005 0.061 1754 Dihedral : 5.601 62.875 1399 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.90 % Allowed : 8.63 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.40 (0.24), residues: 1238 helix: 1.98 (0.22), residues: 564 sheet: -0.00 (0.38), residues: 162 loop : 0.16 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 278 TYR 0.017 0.002 TYR A 802 PHE 0.017 0.002 PHE A 315 TRP 0.010 0.002 TRP A 998 HIS 0.005 0.001 HIS B 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (10068) covalent geometry : angle 0.54817 / 0.28 (13681) SS BOND : bond 0.00300 / 0.14 ( 3) SS BOND : angle 0.86966 / 0.44 ( 6) hydrogen bonds : bond 0.04741 / 3.10 ( 508) hydrogen bonds : angle 4.56361 / 3.31 ( 1497) link_NAG-ASN : bond 0.00416 / 0.20 ( 3) link_NAG-ASN : angle 1.74762 / 0.87 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 TYR cc_start: 0.7262 (m-10) cc_final: 0.6861 (m-10) REVERT: A 193 GLN cc_start: 0.6417 (mm-40) cc_final: 0.5674 (mm-40) REVERT: A 213 ARG cc_start: 0.5864 (ttt-90) cc_final: 0.5543 (ttt180) REVERT: A 260 GLU cc_start: 0.6289 (mt-10) cc_final: 0.5980 (mt-10) REVERT: A 320 MET cc_start: 0.6752 (OUTLIER) cc_final: 0.6435 (mmt) REVERT: A 333 PHE cc_start: 0.7421 (t80) cc_final: 0.7153 (t80) REVERT: A 425 GLU cc_start: 0.4335 (pm20) cc_final: 0.3815 (tm-30) REVERT: A 516 MET cc_start: 0.4198 (tmt) cc_final: 0.3920 (tmt) REVERT: A 652 ASP cc_start: 0.5981 (m-30) cc_final: 0.5742 (m-30) REVERT: A 686 GLU cc_start: 0.6099 (tp30) cc_final: 0.5810 (tp30) REVERT: A 986 ASN cc_start: 0.6628 (m-40) cc_final: 0.6363 (m110) REVERT: B 114 HIS cc_start: 0.6761 (OUTLIER) cc_final: 0.6383 (t-90) REVERT: B 135 LYS cc_start: 0.7629 (ptpp) cc_final: 0.7350 (ptpp) REVERT: B 147 HIS cc_start: 0.6976 (t-90) cc_final: 0.6578 (t-170) outliers start: 20 outliers final: 9 residues processed: 128 average time/residue: 0.4131 time to fit residues: 57.4594 Evaluate side-chains 119 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 906 ASP Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain B residue 114 HIS Chi-restraints excluded: chain B residue 194 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 47 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 289 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.178842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.124985 restraints weight = 11578.531| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.17 r_work: 0.3156 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10074 Z= 0.148 Angle : 0.556 7.818 13696 Z= 0.284 Chirality : 0.044 0.337 1549 Planarity : 0.005 0.059 1754 Dihedral : 5.684 61.628 1399 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.18 % Allowed : 10.24 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.35 (0.24), residues: 1238 helix: 1.94 (0.21), residues: 570 sheet: -0.07 (0.38), residues: 162 loop : 0.11 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 90 TYR 0.018 0.002 TYR A 802 PHE 0.019 0.002 PHE A 970 TRP 0.010 0.002 TRP A 998 HIS 0.005 0.001 HIS B 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (10068) covalent geometry : angle 0.55382 / 0.28 (13681) SS BOND : bond 0.00321 / 0.15 ( 3) SS BOND : angle 0.86088 / 0.43 ( 6) hydrogen bonds : bond 0.04731 / 3.10 ( 508) hydrogen bonds : angle 4.53429 / 3.30 ( 1497) link_NAG-ASN : bond 0.00466 / 0.23 ( 3) link_NAG-ASN : angle 1.71187 / 0.86 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 TYR cc_start: 0.7232 (m-10) cc_final: 0.6802 (m-10) REVERT: A 193 GLN cc_start: 0.6434 (mm-40) cc_final: 0.5690 (mm-40) REVERT: A 232 GLU cc_start: 0.5697 (tt0) cc_final: 0.5231 (tt0) REVERT: A 234 GLN cc_start: 0.7244 (mm-40) cc_final: 0.6952 (mm110) REVERT: A 260 GLU cc_start: 0.6381 (mt-10) cc_final: 0.6068 (mt-10) REVERT: A 320 MET cc_start: 0.6808 (OUTLIER) cc_final: 0.6450 (mmt) REVERT: A 333 PHE cc_start: 0.7388 (t80) cc_final: 0.7127 (t80) REVERT: A 425 GLU cc_start: 0.4483 (pm20) cc_final: 0.3903 (tm-30) REVERT: A 652 ASP cc_start: 0.5968 (m-30) cc_final: 0.5732 (m-30) REVERT: A 696 GLU cc_start: 0.7364 (mt-10) cc_final: 0.7111 (mt-10) REVERT: A 986 ASN cc_start: 0.6712 (m-40) cc_final: 0.6446 (m110) REVERT: B 114 HIS cc_start: 0.6719 (OUTLIER) cc_final: 0.6348 (t-90) REVERT: B 126 GLU cc_start: 0.6201 (mm-30) cc_final: 0.5890 (mm-30) REVERT: B 135 LYS cc_start: 0.7567 (ptpp) cc_final: 0.7271 (ptpp) REVERT: B 147 HIS cc_start: 0.6956 (t-90) cc_final: 0.6566 (t-170) REVERT: B 193 ASN cc_start: 0.6757 (m-40) cc_final: 0.6481 (t0) outliers start: 23 outliers final: 13 residues processed: 134 average time/residue: 0.4469 time to fit residues: 64.8046 Evaluate side-chains 128 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 906 ASP Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain B residue 114 HIS Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 250 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 95 optimal weight: 0.1980 chunk 45 optimal weight: 0.3980 chunk 2 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 289 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.180027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.123586 restraints weight = 11527.018| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.93 r_work: 0.3157 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10074 Z= 0.117 Angle : 0.513 9.384 13696 Z= 0.261 Chirality : 0.043 0.329 1549 Planarity : 0.004 0.056 1754 Dihedral : 5.484 56.729 1399 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.90 % Allowed : 12.61 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.24), residues: 1238 helix: 2.11 (0.22), residues: 565 sheet: 0.01 (0.38), residues: 162 loop : 0.15 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 278 TYR 0.016 0.001 TYR A 802 PHE 0.018 0.001 PHE A 970 TRP 0.009 0.001 TRP A 401 HIS 0.004 0.001 HIS B 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (10068) covalent geometry : angle 0.51106 / 0.26 (13681) SS BOND : bond 0.00242 / 0.12 ( 3) SS BOND : angle 0.68693 / 0.33 ( 6) hydrogen bonds : bond 0.04189 / 2.74 ( 508) hydrogen bonds : angle 4.36018 / 3.18 ( 1497) link_NAG-ASN : bond 0.00496 / 0.24 ( 3) link_NAG-ASN : angle 1.67105 / 0.83 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 ASP cc_start: 0.5874 (OUTLIER) cc_final: 0.5508 (m-30) REVERT: A 140 TYR cc_start: 0.7169 (m-10) cc_final: 0.6692 (m-10) REVERT: A 193 GLN cc_start: 0.6415 (mm-40) cc_final: 0.5718 (mm-40) REVERT: A 232 GLU cc_start: 0.5666 (tt0) cc_final: 0.5175 (tt0) REVERT: A 234 GLN cc_start: 0.7177 (mm-40) cc_final: 0.6889 (mm110) REVERT: A 260 GLU cc_start: 0.6387 (mt-10) cc_final: 0.6036 (mt-10) REVERT: A 320 MET cc_start: 0.6749 (OUTLIER) cc_final: 0.6373 (mmt) REVERT: A 333 PHE cc_start: 0.7363 (t80) cc_final: 0.7117 (t80) REVERT: A 425 GLU cc_start: 0.4423 (pm20) cc_final: 0.3885 (tm-30) REVERT: A 477 MET cc_start: 0.4125 (tpp) cc_final: 0.3521 (pmt) REVERT: A 516 MET cc_start: 0.4113 (tmt) cc_final: 0.3709 (tmt) REVERT: A 652 ASP cc_start: 0.5930 (m-30) cc_final: 0.5688 (m-30) REVERT: A 686 GLU cc_start: 0.5795 (mp0) cc_final: 0.5446 (tp30) REVERT: A 696 GLU cc_start: 0.7323 (mt-10) cc_final: 0.7044 (mt-10) REVERT: A 760 LEU cc_start: 0.7333 (mt) cc_final: 0.7115 (mm) REVERT: A 986 ASN cc_start: 0.6564 (m-40) cc_final: 0.6292 (m110) REVERT: B 114 HIS cc_start: 0.6686 (OUTLIER) cc_final: 0.6304 (t-90) REVERT: B 126 GLU cc_start: 0.6192 (mm-30) cc_final: 0.5884 (mm-30) REVERT: B 135 LYS cc_start: 0.7511 (ptpp) cc_final: 0.7198 (ptpp) REVERT: B 147 HIS cc_start: 0.6926 (t-90) cc_final: 0.6546 (t-170) REVERT: B 193 ASN cc_start: 0.6733 (m-40) cc_final: 0.6467 (t0) outliers start: 20 outliers final: 11 residues processed: 131 average time/residue: 0.4536 time to fit residues: 64.3651 Evaluate side-chains 129 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 114 HIS Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 250 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 10 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 65 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 15 optimal weight: 0.0670 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 104 GLN A 898 GLN B 289 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.180395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.130617 restraints weight = 11617.684| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.67 r_work: 0.3229 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10074 Z= 0.116 Angle : 0.511 8.862 13696 Z= 0.260 Chirality : 0.043 0.325 1549 Planarity : 0.004 0.055 1754 Dihedral : 5.427 55.654 1399 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.46 % Allowed : 12.51 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.55 (0.24), residues: 1238 helix: 2.16 (0.21), residues: 566 sheet: 0.03 (0.39), residues: 162 loop : 0.17 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 278 TYR 0.021 0.001 TYR B 60 PHE 0.014 0.001 PHE A 932 TRP 0.009 0.001 TRP A 915 HIS 0.004 0.001 HIS B 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (10068) covalent geometry : angle 0.50938 / 0.26 (13681) SS BOND : bond 0.00223 / 0.11 ( 3) SS BOND : angle 0.67896 / 0.33 ( 6) hydrogen bonds : bond 0.04119 / 2.70 ( 508) hydrogen bonds : angle 4.28431 / 3.13 ( 1497) link_NAG-ASN : bond 0.00487 / 0.24 ( 3) link_NAG-ASN : angle 1.62948 / 0.81 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: A 140 TYR cc_start: 0.7198 (m-10) cc_final: 0.6678 (m-10) REVERT: A 193 GLN cc_start: 0.6459 (mm-40) cc_final: 0.5778 (mm-40) REVERT: A 232 GLU cc_start: 0.5668 (tt0) cc_final: 0.5196 (tt0) REVERT: A 234 GLN cc_start: 0.7193 (mm-40) cc_final: 0.6936 (mm110) REVERT: A 260 GLU cc_start: 0.6371 (mt-10) cc_final: 0.6054 (mt-10) REVERT: A 320 MET cc_start: 0.6705 (OUTLIER) cc_final: 0.6339 (mmt) REVERT: A 333 PHE cc_start: 0.7376 (t80) cc_final: 0.7154 (t80) REVERT: A 425 GLU cc_start: 0.4362 (pm20) cc_final: 0.3875 (tm-30) REVERT: A 477 MET cc_start: 0.3958 (tpp) cc_final: 0.2758 (ppp) REVERT: A 516 MET cc_start: 0.4161 (tmt) cc_final: 0.3726 (tmt) REVERT: A 652 ASP cc_start: 0.5966 (m-30) cc_final: 0.5722 (m-30) REVERT: A 686 GLU cc_start: 0.5839 (mp0) cc_final: 0.5469 (tp30) REVERT: A 696 GLU cc_start: 0.7274 (mt-10) cc_final: 0.6996 (mt-10) REVERT: A 986 ASN cc_start: 0.6530 (m-40) cc_final: 0.6262 (m110) REVERT: B 114 HIS cc_start: 0.6716 (OUTLIER) cc_final: 0.6336 (t-90) REVERT: B 126 GLU cc_start: 0.6154 (mm-30) cc_final: 0.5852 (mm-30) REVERT: B 135 LYS cc_start: 0.7495 (ptpp) cc_final: 0.7204 (ptpp) REVERT: B 147 HIS cc_start: 0.6914 (t-90) cc_final: 0.6534 (t-170) REVERT: B 193 ASN cc_start: 0.6668 (m-40) cc_final: 0.6405 (t0) outliers start: 26 outliers final: 15 residues processed: 133 average time/residue: 0.4643 time to fit residues: 67.1266 Evaluate side-chains 128 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 906 ASP Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 114 HIS Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 250 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 101 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.180370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.126156 restraints weight = 11550.509| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.07 r_work: 0.3151 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10074 Z= 0.119 Angle : 0.540 10.687 13696 Z= 0.270 Chirality : 0.043 0.326 1549 Planarity : 0.004 0.054 1754 Dihedral : 5.475 55.564 1399 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.27 % Allowed : 13.27 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.57 (0.24), residues: 1238 helix: 2.17 (0.22), residues: 566 sheet: 0.03 (0.39), residues: 162 loop : 0.18 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 278 TYR 0.016 0.001 TYR A 802 PHE 0.021 0.001 PHE A 970 TRP 0.009 0.001 TRP A 915 HIS 0.004 0.001 HIS B 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (10068) covalent geometry : angle 0.53192 / 0.27 (13681) SS BOND : bond 0.00228 / 0.11 ( 3) SS BOND : angle 0.66861 / 0.32 ( 6) hydrogen bonds : bond 0.04133 / 2.71 ( 508) hydrogen bonds : angle 4.27265 / 3.13 ( 1497) link_NAG-ASN : bond 0.00556 / 0.28 ( 3) link_NAG-ASN : angle 3.63154 / 1.92 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 136 ASP cc_start: 0.5905 (OUTLIER) cc_final: 0.5515 (m-30) REVERT: A 140 TYR cc_start: 0.7182 (m-10) cc_final: 0.6650 (m-10) REVERT: A 193 GLN cc_start: 0.6494 (mm-40) cc_final: 0.5799 (mm-40) REVERT: A 260 GLU cc_start: 0.6416 (mt-10) cc_final: 0.6073 (mt-10) REVERT: A 320 MET cc_start: 0.6728 (OUTLIER) cc_final: 0.6361 (mmt) REVERT: A 333 PHE cc_start: 0.7429 (t80) cc_final: 0.7216 (t80) REVERT: A 425 GLU cc_start: 0.4328 (pm20) cc_final: 0.3818 (tm-30) REVERT: A 477 MET cc_start: 0.3819 (tpp) cc_final: 0.2614 (ppp) REVERT: A 516 MET cc_start: 0.4159 (tmt) cc_final: 0.3721 (tmt) REVERT: A 652 ASP cc_start: 0.5937 (m-30) cc_final: 0.5695 (m-30) REVERT: A 686 GLU cc_start: 0.5894 (mp0) cc_final: 0.5480 (tp30) REVERT: A 696 GLU cc_start: 0.7342 (mt-10) cc_final: 0.7062 (mt-10) REVERT: A 986 ASN cc_start: 0.6534 (m-40) cc_final: 0.6237 (m110) REVERT: B 109 LEU cc_start: 0.6575 (mt) cc_final: 0.6335 (mm) REVERT: B 114 HIS cc_start: 0.6695 (OUTLIER) cc_final: 0.6318 (t-90) REVERT: B 126 GLU cc_start: 0.6149 (mm-30) cc_final: 0.5852 (mm-30) REVERT: B 135 LYS cc_start: 0.7474 (ptpp) cc_final: 0.7158 (ptpp) REVERT: B 147 HIS cc_start: 0.6915 (t-90) cc_final: 0.6514 (t-170) REVERT: B 193 ASN cc_start: 0.6630 (m-40) cc_final: 0.6388 (t0) outliers start: 24 outliers final: 15 residues processed: 132 average time/residue: 0.4667 time to fit residues: 66.9973 Evaluate side-chains 131 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 906 ASP Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 114 HIS Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 250 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 87 optimal weight: 3.9990 chunk 34 optimal weight: 0.2980 chunk 123 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 115 optimal weight: 4.9990 chunk 113 optimal weight: 0.5980 chunk 3 optimal weight: 5.9990 chunk 71 optimal weight: 0.1980 chunk 93 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 234 GLN A 971 GLN B 289 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.180152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.126234 restraints weight = 11512.388| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.14 r_work: 0.3157 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10074 Z= 0.123 Angle : 0.534 10.045 13696 Z= 0.270 Chirality : 0.043 0.327 1549 Planarity : 0.004 0.057 1754 Dihedral : 5.544 56.377 1399 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.09 % Allowed : 13.93 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.56 (0.24), residues: 1238 helix: 2.16 (0.21), residues: 566 sheet: 0.02 (0.39), residues: 162 loop : 0.19 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 278 TYR 0.016 0.001 TYR A 802 PHE 0.021 0.001 PHE A 970 TRP 0.009 0.001 TRP A 915 HIS 0.004 0.001 HIS B 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (10068) covalent geometry : angle 0.53278 / 0.27 (13681) SS BOND : bond 0.00235 / 0.11 ( 3) SS BOND : angle 0.68825 / 0.34 ( 6) hydrogen bonds : bond 0.04211 / 2.76 ( 508) hydrogen bonds : angle 4.27846 / 3.13 ( 1497) link_NAG-ASN : bond 0.00495 / 0.25 ( 3) link_NAG-ASN : angle 1.29365 / 0.74 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 136 ASP cc_start: 0.5927 (OUTLIER) cc_final: 0.5519 (m-30) REVERT: A 140 TYR cc_start: 0.7224 (m-10) cc_final: 0.6686 (m-10) REVERT: A 193 GLN cc_start: 0.6462 (mm-40) cc_final: 0.5785 (mm-40) REVERT: A 260 GLU cc_start: 0.6386 (mt-10) cc_final: 0.6067 (mt-10) REVERT: A 320 MET cc_start: 0.6731 (OUTLIER) cc_final: 0.6362 (mmt) REVERT: A 333 PHE cc_start: 0.7379 (t80) cc_final: 0.7175 (t80) REVERT: A 425 GLU cc_start: 0.4357 (pm20) cc_final: 0.3841 (tm-30) REVERT: A 477 MET cc_start: 0.3877 (tpp) cc_final: 0.2661 (ppp) REVERT: A 516 MET cc_start: 0.4181 (tmt) cc_final: 0.3961 (tmt) REVERT: A 652 ASP cc_start: 0.5971 (m-30) cc_final: 0.5738 (m-30) REVERT: A 686 GLU cc_start: 0.5842 (mp0) cc_final: 0.5474 (tp30) REVERT: A 696 GLU cc_start: 0.7373 (mt-10) cc_final: 0.7090 (mt-10) REVERT: A 986 ASN cc_start: 0.6550 (m-40) cc_final: 0.6253 (m110) REVERT: B 109 LEU cc_start: 0.6571 (mt) cc_final: 0.6349 (mm) REVERT: B 114 HIS cc_start: 0.6681 (OUTLIER) cc_final: 0.6328 (t-90) REVERT: B 126 GLU cc_start: 0.6154 (mm-30) cc_final: 0.5859 (mm-30) REVERT: B 135 LYS cc_start: 0.7416 (ptpp) cc_final: 0.6891 (mtmm) REVERT: B 147 HIS cc_start: 0.6940 (t-90) cc_final: 0.6515 (t-170) REVERT: B 193 ASN cc_start: 0.6646 (m-40) cc_final: 0.6382 (t0) outliers start: 22 outliers final: 15 residues processed: 125 average time/residue: 0.4258 time to fit residues: 58.0135 Evaluate side-chains 129 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 906 ASP Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 114 HIS Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 250 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 63 optimal weight: 0.5980 chunk 111 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 38 optimal weight: 0.3980 chunk 56 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 971 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.181097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.122787 restraints weight = 11535.952| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.96 r_work: 0.3200 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10074 Z= 0.106 Angle : 0.519 13.184 13696 Z= 0.258 Chirality : 0.043 0.317 1549 Planarity : 0.004 0.058 1754 Dihedral : 5.338 51.324 1399 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.52 % Allowed : 14.50 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.71 (0.24), residues: 1238 helix: 2.29 (0.22), residues: 565 sheet: 0.14 (0.39), residues: 162 loop : 0.24 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 278 TYR 0.014 0.001 TYR A 802 PHE 0.013 0.001 PHE A 161 TRP 0.009 0.001 TRP A 915 HIS 0.003 0.001 HIS B 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (10068) covalent geometry : angle 0.51788 / 0.26 (13681) SS BOND : bond 0.00182 / 0.09 ( 3) SS BOND : angle 0.58724 / 0.28 ( 6) hydrogen bonds : bond 0.03841 / 2.52 ( 508) hydrogen bonds : angle 4.18905 / 3.07 ( 1497) link_NAG-ASN : bond 0.01129 / 0.59 ( 3) link_NAG-ASN : angle 1.28229 / 0.65 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.237 Fit side-chains REVERT: A 136 ASP cc_start: 0.5970 (OUTLIER) cc_final: 0.5550 (m-30) REVERT: A 140 TYR cc_start: 0.7229 (m-10) cc_final: 0.6659 (m-10) REVERT: A 193 GLN cc_start: 0.6395 (mm-40) cc_final: 0.5768 (mm-40) REVERT: A 260 GLU cc_start: 0.6407 (mt-10) cc_final: 0.6082 (mt-10) REVERT: A 320 MET cc_start: 0.6671 (OUTLIER) cc_final: 0.6303 (mmt) REVERT: A 333 PHE cc_start: 0.7396 (t80) cc_final: 0.7188 (t80) REVERT: A 425 GLU cc_start: 0.4310 (pm20) cc_final: 0.3812 (tm-30) REVERT: A 477 MET cc_start: 0.3771 (tpp) cc_final: 0.2658 (ppp) REVERT: A 516 MET cc_start: 0.4116 (tmt) cc_final: 0.3730 (tmt) REVERT: A 652 ASP cc_start: 0.5925 (m-30) cc_final: 0.5691 (m-30) REVERT: A 686 GLU cc_start: 0.5822 (mp0) cc_final: 0.5463 (tp30) REVERT: A 696 GLU cc_start: 0.7366 (mt-10) cc_final: 0.7097 (mt-10) REVERT: A 738 ASP cc_start: 0.8033 (m-30) cc_final: 0.7760 (m-30) REVERT: A 986 ASN cc_start: 0.6399 (m-40) cc_final: 0.6091 (m110) REVERT: B 109 LEU cc_start: 0.6604 (mt) cc_final: 0.6381 (mm) REVERT: B 114 HIS cc_start: 0.6687 (OUTLIER) cc_final: 0.6312 (t-90) REVERT: B 135 LYS cc_start: 0.7422 (ptpp) cc_final: 0.6910 (mtmm) REVERT: B 147 HIS cc_start: 0.6958 (t-90) cc_final: 0.6559 (t-170) REVERT: B 267 GLU cc_start: 0.7265 (pt0) cc_final: 0.6863 (tm-30) outliers start: 16 outliers final: 13 residues processed: 126 average time/residue: 0.4096 time to fit residues: 56.3705 Evaluate side-chains 128 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 114 HIS Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 250 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 78 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 4 optimal weight: 0.0010 chunk 7 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 369 ASN B 289 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.181056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.126675 restraints weight = 11470.136| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.83 r_work: 0.3169 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10074 Z= 0.107 Angle : 0.525 13.119 13696 Z= 0.260 Chirality : 0.043 0.320 1549 Planarity : 0.004 0.059 1754 Dihedral : 5.245 50.634 1399 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.61 % Allowed : 14.31 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.69 (0.24), residues: 1238 helix: 2.27 (0.22), residues: 566 sheet: 0.14 (0.39), residues: 162 loop : 0.22 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 278 TYR 0.023 0.001 TYR B 60 PHE 0.013 0.001 PHE A 932 TRP 0.009 0.001 TRP B 106 HIS 0.004 0.001 HIS B 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (10068) covalent geometry : angle 0.52356 / 0.26 (13681) SS BOND : bond 0.00187 / 0.09 ( 3) SS BOND : angle 0.80343 / 0.43 ( 6) hydrogen bonds : bond 0.03841 / 2.52 ( 508) hydrogen bonds : angle 4.17359 / 3.06 ( 1497) link_NAG-ASN : bond 0.00895 / 0.46 ( 3) link_NAG-ASN : angle 1.74984 / 0.88 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: A 140 TYR cc_start: 0.7248 (m-10) cc_final: 0.6668 (m-10) REVERT: A 193 GLN cc_start: 0.6377 (mm-40) cc_final: 0.5749 (mm-40) REVERT: A 260 GLU cc_start: 0.6368 (mt-10) cc_final: 0.6045 (mt-10) REVERT: A 320 MET cc_start: 0.6681 (mmp) cc_final: 0.6300 (mmt) REVERT: A 333 PHE cc_start: 0.7380 (t80) cc_final: 0.7173 (t80) REVERT: A 425 GLU cc_start: 0.4315 (pm20) cc_final: 0.3812 (tm-30) REVERT: A 477 MET cc_start: 0.3784 (tpp) cc_final: 0.2644 (ppp) REVERT: A 516 MET cc_start: 0.4102 (tmt) cc_final: 0.3711 (tmt) REVERT: A 652 ASP cc_start: 0.5904 (m-30) cc_final: 0.5696 (m-30) REVERT: A 686 GLU cc_start: 0.5809 (mp0) cc_final: 0.5418 (mp0) REVERT: A 696 GLU cc_start: 0.7379 (mt-10) cc_final: 0.7126 (mt-10) REVERT: A 986 ASN cc_start: 0.6445 (m-40) cc_final: 0.6149 (m110) REVERT: B 114 HIS cc_start: 0.6672 (OUTLIER) cc_final: 0.6294 (t-90) REVERT: B 135 LYS cc_start: 0.7385 (ptpp) cc_final: 0.7037 (mtmm) REVERT: B 147 HIS cc_start: 0.6954 (t-90) cc_final: 0.6538 (t-170) REVERT: B 267 GLU cc_start: 0.7250 (pt0) cc_final: 0.6872 (tm-30) outliers start: 17 outliers final: 12 residues processed: 125 average time/residue: 0.4241 time to fit residues: 57.7644 Evaluate side-chains 123 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 114 HIS Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 250 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 369 ASN A 415 GLN B 289 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.179104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.129523 restraints weight = 11542.771| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.65 r_work: 0.3209 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10074 Z= 0.161 Angle : 0.588 9.988 13696 Z= 0.298 Chirality : 0.046 0.344 1549 Planarity : 0.005 0.060 1754 Dihedral : 5.850 63.817 1399 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.61 % Allowed : 14.41 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.40 (0.24), residues: 1238 helix: 1.99 (0.21), residues: 565 sheet: -0.02 (0.37), residues: 177 loop : 0.15 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 256 TYR 0.018 0.002 TYR A 802 PHE 0.017 0.002 PHE A 932 TRP 0.010 0.002 TRP A 915 HIS 0.004 0.001 HIS B 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 (10068) covalent geometry : angle 0.58564 / 0.30 (13681) SS BOND : bond 0.00290 / 0.14 ( 3) SS BOND : angle 1.10172 / 0.60 ( 6) hydrogen bonds : bond 0.04816 / 3.16 ( 508) hydrogen bonds : angle 4.43783 / 3.25 ( 1497) link_NAG-ASN : bond 0.00636 / 0.32 ( 3) link_NAG-ASN : angle 2.06945 / 1.03 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3943.51 seconds wall clock time: 67 minutes 34.05 seconds (4054.05 seconds total)