Starting phenix.real_space_refine on Sat Aug 23 11:00:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w4a_32299/08_2025/7w4a_32299.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w4a_32299/08_2025/7w4a_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7w4a_32299/08_2025/7w4a_32299.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w4a_32299/08_2025/7w4a_32299.map" model { file = "/net/cci-nas-00/data/ceres_data/7w4a_32299/08_2025/7w4a_32299.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w4a_32299/08_2025/7w4a_32299.cif" } 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-2.0-5787/lib/python3.9/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 dihedrals: 9 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: 2.44, per 1000 atoms: 0.25 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: 1.16 Conformation dependent library (CDL) restraints added in 381.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.44 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: 1.95 Time building geometry restraints manager: 1.48 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 - 22.41: 5728 22.41 - 44.81: 315 44.81 - 67.22: 31 67.22 - 89.62: 15 89.62 - 112.03: 3 Dihedral angle restraints: 6092 sinusoidal: 2475 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=" C3 NAG B 302 " pdb=" C1 NAG B 302 " pdb=" C2 NAG B 302 " pdb=" O5 NAG B 302 " ideal model delta sinusoidal sigma weight residual -55.55 56.48 -112.03 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" N2 NAG B 302 " pdb=" C1 NAG B 302 " pdb=" C2 NAG B 302 " pdb=" O5 NAG B 302 " ideal model delta sinusoidal sigma weight residual -178.19 -67.58 -110.61 1 3.00e+01 1.11e-03 1.44e+01 ... (remaining 6089 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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.560 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 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 : 13.796 112.026 3753 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 aren 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 covalent geometry : bond 0.00571 (10068) covalent geometry : angle 0.71250 (13681) SS BOND : bond 0.00158 ( 3) SS BOND : angle 0.70251 ( 6) hydrogen bonds : bond 0.13589 ( 508) hydrogen bonds : angle 5.56355 ( 1497) link_NAG-ASN : bond 0.00419 ( 3) link_NAG-ASN : angle 3.55352 ( 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 : 0.361 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: 0.6310 time to fit residues: 93.2232 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 : 0.310 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4044 r_free = 0.4044 target = 0.180009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.129352 restraints weight = 11498.517| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.83 r_work: 0.3220 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.0990 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 : 0.557 6.373 13696 Z= 0.286 Chirality : 0.044 0.233 1549 Planarity : 0.005 0.060 1754 Dihedral : 8.095 93.693 1480 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.61 % Allowed : 6.54 % Favored : 91.85 % 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 aren not related in a simple way. whole: 1.42 (0.24), residues: 1238 helix: 1.96 (0.22), residues: 564 sheet: -0.00 (0.37), residues: 162 loop : 0.22 (0.28), residues: 512 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 covalent geometry : bond 0.00314 (10068) covalent geometry : angle 0.55392 (13681) SS BOND : bond 0.00307 ( 3) SS BOND : angle 0.85222 ( 6) hydrogen bonds : bond 0.04627 ( 508) hydrogen bonds : angle 4.61501 ( 1497) link_NAG-ASN : bond 0.00627 ( 3) link_NAG-ASN : angle 2.23625 ( 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: 17 poor density : 120 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 GLU cc_start: 0.4985 (OUTLIER) cc_final: 0.4781 (mp0) REVERT: A 140 TYR cc_start: 0.7135 (m-10) cc_final: 0.6753 (m-10) REVERT: A 193 GLN cc_start: 0.6223 (mm-40) cc_final: 0.5672 (mm-40) REVERT: A 213 ARG cc_start: 0.5838 (ttt-90) cc_final: 0.5485 (ttt180) REVERT: A 260 GLU cc_start: 0.6145 (mt-10) cc_final: 0.5818 (mt-10) REVERT: A 333 PHE cc_start: 0.7326 (t80) cc_final: 0.6984 (t80) REVERT: A 425 GLU cc_start: 0.4268 (pm20) cc_final: 0.3759 (tm-30) REVERT: A 516 MET cc_start: 0.4114 (tmt) cc_final: 0.3759 (tmt) REVERT: A 652 ASP cc_start: 0.5948 (m-30) cc_final: 0.5679 (m-30) REVERT: A 986 ASN cc_start: 0.6512 (m-40) cc_final: 0.6283 (m110) REVERT: B 114 HIS cc_start: 0.6678 (OUTLIER) cc_final: 0.6320 (t-90) REVERT: B 135 LYS cc_start: 0.7503 (ptpp) cc_final: 0.7253 (ptpp) REVERT: B 147 HIS cc_start: 0.6904 (t-90) cc_final: 0.6521 (t-170) REVERT: B 258 VAL cc_start: 0.7812 (p) cc_final: 0.7550 (m) outliers start: 17 outliers final: 5 residues processed: 128 average time/residue: 0.5720 time to fit residues: 79.0072 Evaluate side-chains 121 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 114 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 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 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: 2.9990 chunk 87 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 97 optimal weight: 0.0060 chunk 89 optimal weight: 2.9990 chunk 4 optimal weight: 0.0000 chunk 26 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4028 r_free = 0.4028 target = 0.178596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.121897 restraints weight = 11464.573| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.03 r_work: 0.3140 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10074 Z= 0.155 Angle : 0.574 8.112 13696 Z= 0.293 Chirality : 0.045 0.239 1549 Planarity : 0.005 0.060 1754 Dihedral : 7.893 87.122 1480 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.99 % Allowed : 8.82 % Favored : 89.19 % 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 aren not related in a simple way. whole: 1.34 (0.24), residues: 1238 helix: 1.91 (0.21), residues: 564 sheet: -0.05 (0.38), residues: 162 loop : 0.14 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 90 TYR 0.018 0.002 TYR A 802 PHE 0.020 0.002 PHE A 315 TRP 0.012 0.002 TRP A 998 HIS 0.005 0.001 HIS B 227 Details of bonding type rmsd covalent geometry : bond 0.00370 (10068) covalent geometry : angle 0.57171 (13681) SS BOND : bond 0.00329 ( 3) SS BOND : angle 0.92900 ( 6) hydrogen bonds : bond 0.04948 ( 508) hydrogen bonds : angle 4.61029 ( 1497) link_NAG-ASN : bond 0.00418 ( 3) link_NAG-ASN : angle 2.12066 ( 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 134 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 TYR cc_start: 0.7294 (m-10) cc_final: 0.6942 (m-10) REVERT: A 193 GLN cc_start: 0.6414 (mm-40) cc_final: 0.5662 (mm-40) REVERT: A 213 ARG cc_start: 0.5904 (ttt-90) cc_final: 0.5589 (ttt180) REVERT: A 260 GLU cc_start: 0.6383 (mt-10) cc_final: 0.6077 (mt-10) REVERT: A 320 MET cc_start: 0.6760 (OUTLIER) cc_final: 0.6400 (mmt) REVERT: A 333 PHE cc_start: 0.7437 (t80) cc_final: 0.7186 (t80) REVERT: A 425 GLU cc_start: 0.4311 (pm20) cc_final: 0.3788 (tm-30) REVERT: A 516 MET cc_start: 0.4200 (tmt) cc_final: 0.3916 (tmt) REVERT: A 652 ASP cc_start: 0.5991 (m-30) cc_final: 0.5750 (m-30) REVERT: A 686 GLU cc_start: 0.6042 (tp30) cc_final: 0.5794 (tp30) REVERT: A 986 ASN cc_start: 0.6709 (m-40) cc_final: 0.6434 (m110) REVERT: B 114 HIS cc_start: 0.6783 (OUTLIER) cc_final: 0.6421 (t-90) REVERT: B 135 LYS cc_start: 0.7620 (ptpp) cc_final: 0.7358 (ptpp) REVERT: B 147 HIS cc_start: 0.6984 (t-90) cc_final: 0.6602 (t-170) outliers start: 21 outliers final: 10 residues processed: 128 average time/residue: 0.5493 time to fit residues: 76.2264 Evaluate side-chains 118 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 47 optimal weight: 0.4980 chunk 51 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 36 optimal weight: 0.0030 chunk 85 optimal weight: 0.3980 chunk 48 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 0.0060 overall best weight: 0.3606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.181360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.122552 restraints weight = 11617.699| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.93 r_work: 0.3196 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10074 Z= 0.103 Angle : 0.495 9.316 13696 Z= 0.249 Chirality : 0.041 0.171 1549 Planarity : 0.004 0.054 1754 Dihedral : 7.306 83.026 1480 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.42 % Allowed : 11.09 % Favored : 87.49 % 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 aren not related in a simple way. whole: 1.62 (0.24), residues: 1238 helix: 2.19 (0.22), residues: 573 sheet: 0.07 (0.38), residues: 162 loop : 0.19 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 278 TYR 0.013 0.001 TYR A 802 PHE 0.014 0.001 PHE A 161 TRP 0.009 0.001 TRP A 401 HIS 0.004 0.001 HIS B 227 Details of bonding type rmsd covalent geometry : bond 0.00218 (10068) covalent geometry : angle 0.49151 (13681) SS BOND : bond 0.00192 ( 3) SS BOND : angle 0.57115 ( 6) hydrogen bonds : bond 0.03774 ( 508) hydrogen bonds : angle 4.30868 ( 1497) link_NAG-ASN : bond 0.00432 ( 3) link_NAG-ASN : angle 2.21099 ( 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 135 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: A 140 TYR cc_start: 0.7149 (m-10) cc_final: 0.6685 (m-10) REVERT: A 193 GLN cc_start: 0.6355 (mm-40) cc_final: 0.5638 (mm-40) REVERT: A 260 GLU cc_start: 0.6380 (mt-10) cc_final: 0.6066 (mt-10) REVERT: A 320 MET cc_start: 0.6606 (mmp) cc_final: 0.6218 (mmt) REVERT: A 333 PHE cc_start: 0.7356 (t80) cc_final: 0.7108 (t80) REVERT: A 425 GLU cc_start: 0.4389 (pm20) cc_final: 0.3800 (tm-30) REVERT: A 516 MET cc_start: 0.4235 (tmt) cc_final: 0.3936 (tmt) REVERT: A 652 ASP cc_start: 0.5956 (m-30) cc_final: 0.5697 (m-30) REVERT: A 760 LEU cc_start: 0.7373 (mt) cc_final: 0.7172 (mm) REVERT: A 986 ASN cc_start: 0.6401 (m-40) cc_final: 0.6140 (m110) REVERT: B 114 HIS cc_start: 0.6724 (OUTLIER) cc_final: 0.6349 (t-90) REVERT: B 135 LYS cc_start: 0.7490 (ptpp) cc_final: 0.7213 (ptpp) REVERT: B 147 HIS cc_start: 0.6976 (t-90) cc_final: 0.6611 (t-170) outliers start: 15 outliers final: 8 residues processed: 131 average time/residue: 0.5404 time to fit residues: 76.7948 Evaluate side-chains 118 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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 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 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: 0.0010 chunk 45 optimal weight: 0.5980 chunk 2 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 8 optimal weight: 6.9990 chunk 19 optimal weight: 0.0060 chunk 56 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 overall best weight: 0.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 289 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.181722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.132230 restraints weight = 11557.565| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.68 r_work: 0.3261 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10074 Z= 0.098 Angle : 0.485 8.179 13696 Z= 0.244 Chirality : 0.041 0.173 1549 Planarity : 0.004 0.054 1754 Dihedral : 7.031 80.580 1480 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.90 % Allowed : 12.23 % Favored : 85.88 % 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 aren not related in a simple way. whole: 1.75 (0.24), residues: 1238 helix: 2.32 (0.22), residues: 565 sheet: 0.20 (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 0.013 0.001 TYR A 802 PHE 0.013 0.001 PHE A 161 TRP 0.008 0.001 TRP A 401 HIS 0.004 0.001 HIS B 227 Details of bonding type rmsd covalent geometry : bond 0.00212 (10068) covalent geometry : angle 0.48218 (13681) SS BOND : bond 0.00178 ( 3) SS BOND : angle 0.69843 ( 6) hydrogen bonds : bond 0.03614 ( 508) hydrogen bonds : angle 4.16017 ( 1497) link_NAG-ASN : bond 0.00396 ( 3) link_NAG-ASN : angle 2.21058 ( 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 : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 TYR cc_start: 0.7126 (m-10) cc_final: 0.6654 (m-10) REVERT: A 193 GLN cc_start: 0.6264 (mm-40) cc_final: 0.5653 (mm-40) REVERT: A 260 GLU cc_start: 0.6408 (mt-10) cc_final: 0.6117 (mt-10) REVERT: A 320 MET cc_start: 0.6589 (OUTLIER) cc_final: 0.6271 (mmt) REVERT: A 333 PHE cc_start: 0.7307 (t80) cc_final: 0.7089 (t80) REVERT: A 425 GLU cc_start: 0.4407 (pm20) cc_final: 0.3853 (tm-30) REVERT: A 477 MET cc_start: 0.4140 (tpp) cc_final: 0.2796 (ppp) REVERT: A 516 MET cc_start: 0.4218 (tmt) cc_final: 0.3961 (tmt) REVERT: A 531 LEU cc_start: 0.4513 (OUTLIER) cc_final: 0.4196 (mp) REVERT: A 652 ASP cc_start: 0.5943 (m-30) cc_final: 0.5680 (m-30) REVERT: A 986 ASN cc_start: 0.6246 (m-40) cc_final: 0.5970 (m110) REVERT: B 114 HIS cc_start: 0.6705 (OUTLIER) cc_final: 0.6342 (t-90) REVERT: B 147 HIS cc_start: 0.6930 (t-90) cc_final: 0.6577 (t-170) outliers start: 20 outliers final: 8 residues processed: 130 average time/residue: 0.5295 time to fit residues: 75.0028 Evaluate side-chains 124 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 302 ASP Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 585 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 10 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 15 optimal weight: 9.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4041 r_free = 0.4041 target = 0.179816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.128095 restraints weight = 11623.813| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.06 r_work: 0.3218 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10074 Z= 0.126 Angle : 0.536 9.773 13696 Z= 0.269 Chirality : 0.043 0.182 1549 Planarity : 0.004 0.056 1754 Dihedral : 7.261 78.743 1480 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.37 % Allowed : 12.99 % Favored : 84.64 % 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 aren not related in a simple way. whole: 1.63 (0.24), residues: 1238 helix: 2.20 (0.21), residues: 565 sheet: 0.18 (0.39), residues: 162 loop : 0.19 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 692 TYR 0.020 0.001 TYR B 60 PHE 0.015 0.001 PHE A 932 TRP 0.008 0.001 TRP A 915 HIS 0.005 0.001 HIS B 227 Details of bonding type rmsd covalent geometry : bond 0.00294 (10068) covalent geometry : angle 0.53233 (13681) SS BOND : bond 0.00257 ( 3) SS BOND : angle 0.99030 ( 6) hydrogen bonds : bond 0.04243 ( 508) hydrogen bonds : angle 4.28914 ( 1497) link_NAG-ASN : bond 0.00403 ( 3) link_NAG-ASN : angle 2.26357 ( 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 140 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 TYR cc_start: 0.7142 (m-10) cc_final: 0.6697 (m-10) REVERT: A 193 GLN cc_start: 0.6407 (mm-40) cc_final: 0.5759 (mm-40) REVERT: A 232 GLU cc_start: 0.5765 (tt0) cc_final: 0.5204 (tm-30) REVERT: A 260 GLU cc_start: 0.6312 (mt-10) cc_final: 0.5995 (mt-10) REVERT: A 320 MET cc_start: 0.6626 (OUTLIER) cc_final: 0.6240 (mmt) REVERT: A 333 PHE cc_start: 0.7332 (t80) cc_final: 0.7130 (t80) REVERT: A 425 GLU cc_start: 0.4431 (pm20) cc_final: 0.3931 (tm-30) REVERT: A 516 MET cc_start: 0.4271 (tmt) cc_final: 0.3961 (tmt) REVERT: A 531 LEU cc_start: 0.4471 (OUTLIER) cc_final: 0.4131 (mp) REVERT: A 652 ASP cc_start: 0.5959 (m-30) cc_final: 0.5729 (m-30) REVERT: A 686 GLU cc_start: 0.5731 (mp0) cc_final: 0.5513 (mp0) REVERT: A 986 ASN cc_start: 0.6425 (m-40) cc_final: 0.6152 (m110) REVERT: B 114 HIS cc_start: 0.6674 (OUTLIER) cc_final: 0.6300 (t-90) REVERT: B 135 LYS cc_start: 0.7403 (ptpp) cc_final: 0.6926 (mtmm) REVERT: B 147 HIS cc_start: 0.6900 (t-90) cc_final: 0.6527 (t-170) outliers start: 25 outliers final: 13 residues processed: 131 average time/residue: 0.5585 time to fit residues: 79.0654 Evaluate side-chains 125 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 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 531 LEU Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 728 VAL 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 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: 0.7980 chunk 32 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 369 ASN A 415 GLN B 289 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.179246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.129899 restraints weight = 11507.099| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.60 r_work: 0.3225 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10074 Z= 0.151 Angle : 0.571 9.995 13696 Z= 0.289 Chirality : 0.044 0.205 1549 Planarity : 0.005 0.057 1754 Dihedral : 7.568 77.412 1480 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.27 % Allowed : 13.55 % Favored : 84.17 % 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 aren not related in a simple way. whole: 1.43 (0.24), residues: 1238 helix: 2.02 (0.21), residues: 565 sheet: -0.03 (0.37), residues: 177 loop : 0.16 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 692 TYR 0.018 0.002 TYR A 802 PHE 0.017 0.002 PHE A 315 TRP 0.009 0.002 TRP A 915 HIS 0.004 0.001 HIS B 227 Details of bonding type rmsd covalent geometry : bond 0.00359 (10068) covalent geometry : angle 0.56724 (13681) SS BOND : bond 0.00305 ( 3) SS BOND : angle 0.99897 ( 6) hydrogen bonds : bond 0.04724 ( 508) hydrogen bonds : angle 4.43864 ( 1497) link_NAG-ASN : bond 0.00398 ( 3) link_NAG-ASN : angle 2.36176 ( 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 133 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: A 140 TYR cc_start: 0.7181 (m-10) cc_final: 0.6696 (m-10) REVERT: A 193 GLN cc_start: 0.6416 (mm-40) cc_final: 0.5742 (mm-40) REVERT: A 260 GLU cc_start: 0.6384 (mt-10) cc_final: 0.6082 (mt-10) REVERT: A 317 ILE cc_start: 0.6685 (mm) cc_final: 0.6410 (mt) REVERT: A 320 MET cc_start: 0.6779 (OUTLIER) cc_final: 0.6423 (mmt) REVERT: A 333 PHE cc_start: 0.7402 (t80) cc_final: 0.7194 (t80) REVERT: A 425 GLU cc_start: 0.4398 (pm20) cc_final: 0.3927 (tm-30) REVERT: A 516 MET cc_start: 0.4327 (tmt) cc_final: 0.3995 (tmt) REVERT: A 531 LEU cc_start: 0.4520 (OUTLIER) cc_final: 0.4122 (mp) REVERT: A 652 ASP cc_start: 0.5962 (m-30) cc_final: 0.5718 (m-30) REVERT: A 686 GLU cc_start: 0.5798 (mp0) cc_final: 0.5439 (tp30) REVERT: A 986 ASN cc_start: 0.6653 (m-40) cc_final: 0.6368 (m110) REVERT: B 114 HIS cc_start: 0.6704 (OUTLIER) cc_final: 0.6350 (t-90) REVERT: B 126 GLU cc_start: 0.6194 (mm-30) cc_final: 0.5882 (mm-30) REVERT: B 147 HIS cc_start: 0.6917 (t-90) cc_final: 0.6539 (t-170) outliers start: 24 outliers final: 14 residues processed: 127 average time/residue: 0.5376 time to fit residues: 74.0962 Evaluate side-chains 125 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 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 531 LEU Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 840 ILE 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: 0.8980 chunk 123 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 115 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 71 optimal weight: 0.0970 chunk 93 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4034 r_free = 0.4034 target = 0.179213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.124498 restraints weight = 11481.328| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.03 r_work: 0.3183 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10074 Z= 0.154 Angle : 0.592 11.290 13696 Z= 0.297 Chirality : 0.045 0.208 1549 Planarity : 0.005 0.057 1754 Dihedral : 7.765 76.509 1480 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.09 % Allowed : 14.60 % Favored : 83.32 % 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 aren not related in a simple way. whole: 1.36 (0.24), residues: 1238 helix: 1.96 (0.21), residues: 565 sheet: -0.10 (0.37), residues: 177 loop : 0.15 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 692 TYR 0.017 0.002 TYR A 802 PHE 0.017 0.002 PHE A 932 TRP 0.009 0.002 TRP A 915 HIS 0.004 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00366 (10068) covalent geometry : angle 0.58757 (13681) SS BOND : bond 0.00290 ( 3) SS BOND : angle 0.98741 ( 6) hydrogen bonds : bond 0.04736 ( 508) hydrogen bonds : angle 4.43356 ( 1497) link_NAG-ASN : bond 0.01139 ( 3) link_NAG-ASN : angle 2.89313 ( 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 136 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.388 Fit side-chains REVERT: A 136 ASP cc_start: 0.5965 (OUTLIER) cc_final: 0.5552 (m-30) REVERT: A 140 TYR cc_start: 0.7189 (m-10) cc_final: 0.6699 (m-10) REVERT: A 193 GLN cc_start: 0.6458 (mm-40) cc_final: 0.5778 (mm-40) REVERT: A 260 GLU cc_start: 0.6415 (mt-10) cc_final: 0.6108 (mt-10) REVERT: A 317 ILE cc_start: 0.6666 (mm) cc_final: 0.6402 (mt) REVERT: A 320 MET cc_start: 0.6792 (OUTLIER) cc_final: 0.6445 (mmt) REVERT: A 333 PHE cc_start: 0.7398 (t80) cc_final: 0.7181 (t80) REVERT: A 425 GLU cc_start: 0.4316 (pm20) cc_final: 0.3830 (tm-30) REVERT: A 516 MET cc_start: 0.4196 (tmt) cc_final: 0.3895 (tmt) REVERT: A 531 LEU cc_start: 0.4441 (OUTLIER) cc_final: 0.4090 (mp) REVERT: A 652 ASP cc_start: 0.5910 (m-30) cc_final: 0.5698 (m-30) REVERT: A 686 GLU cc_start: 0.5843 (mp0) cc_final: 0.5413 (tp30) REVERT: A 694 HIS cc_start: 0.5425 (m90) cc_final: 0.5081 (m90) REVERT: A 986 ASN cc_start: 0.6676 (m-40) cc_final: 0.6392 (m110) REVERT: B 109 LEU cc_start: 0.6510 (mt) cc_final: 0.6283 (mm) REVERT: B 114 HIS cc_start: 0.6655 (OUTLIER) cc_final: 0.6297 (t-90) REVERT: B 126 GLU cc_start: 0.6250 (mm-30) cc_final: 0.5944 (mm-30) REVERT: B 135 LYS cc_start: 0.7362 (ptpp) cc_final: 0.6847 (mtmm) REVERT: B 147 HIS cc_start: 0.6924 (t-90) cc_final: 0.6527 (t-170) outliers start: 22 outliers final: 15 residues processed: 130 average time/residue: 0.5279 time to fit residues: 74.5223 Evaluate side-chains 132 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 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 531 LEU Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 728 VAL 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 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: 4.9990 chunk 111 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 14 optimal weight: 0.0370 chunk 34 optimal weight: 5.9990 chunk 48 optimal weight: 0.0970 chunk 36 optimal weight: 4.9990 overall best weight: 0.7658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4046 r_free = 0.4046 target = 0.180384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.124430 restraints weight = 11529.092| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.04 r_work: 0.3151 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10074 Z= 0.114 Angle : 0.541 10.563 13696 Z= 0.271 Chirality : 0.043 0.171 1549 Planarity : 0.004 0.058 1754 Dihedral : 7.338 74.919 1480 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.52 % Allowed : 15.45 % Favored : 83.03 % 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 aren not related in a simple way. whole: 1.55 (0.24), residues: 1238 helix: 2.17 (0.22), residues: 564 sheet: 0.01 (0.39), residues: 162 loop : 0.17 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 278 TYR 0.015 0.001 TYR A 802 PHE 0.024 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 covalent geometry : bond 0.00258 (10068) covalent geometry : angle 0.53832 (13681) SS BOND : bond 0.00200 ( 3) SS BOND : angle 0.79108 ( 6) hydrogen bonds : bond 0.04118 ( 508) hydrogen bonds : angle 4.28695 ( 1497) link_NAG-ASN : bond 0.00647 ( 3) link_NAG-ASN : angle 2.22966 ( 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 : 0.408 Fit side-chains revert: symmetry clash REVERT: A 140 TYR cc_start: 0.7253 (m-10) cc_final: 0.6698 (m-10) REVERT: A 193 GLN cc_start: 0.6479 (mm-40) cc_final: 0.5771 (mm-40) REVERT: A 260 GLU cc_start: 0.6411 (mt-10) cc_final: 0.6062 (mt-10) REVERT: A 320 MET cc_start: 0.6719 (OUTLIER) cc_final: 0.6360 (mmt) REVERT: A 333 PHE cc_start: 0.7427 (t80) cc_final: 0.7213 (t80) REVERT: A 425 GLU cc_start: 0.4341 (pm20) cc_final: 0.3845 (tm-30) REVERT: A 516 MET cc_start: 0.4200 (tmt) cc_final: 0.3907 (tmt) REVERT: A 531 LEU cc_start: 0.4486 (OUTLIER) cc_final: 0.4159 (mp) REVERT: A 652 ASP cc_start: 0.5935 (m-30) cc_final: 0.5720 (m-30) REVERT: A 686 GLU cc_start: 0.5809 (mp0) cc_final: 0.5371 (mp0) REVERT: A 694 HIS cc_start: 0.5395 (m90) cc_final: 0.5125 (m90) REVERT: A 986 ASN cc_start: 0.6525 (m-40) cc_final: 0.6225 (m110) REVERT: B 109 LEU cc_start: 0.6610 (mt) cc_final: 0.6384 (mm) REVERT: B 114 HIS cc_start: 0.6739 (OUTLIER) cc_final: 0.6366 (t-90) REVERT: B 126 GLU cc_start: 0.6207 (mm-30) cc_final: 0.5916 (mm-30) REVERT: B 135 LYS cc_start: 0.7464 (ptpp) cc_final: 0.6997 (mtmm) REVERT: B 147 HIS cc_start: 0.6975 (t-90) cc_final: 0.6585 (t-170) outliers start: 16 outliers final: 9 residues processed: 126 average time/residue: 0.5364 time to fit residues: 73.2377 Evaluate side-chains 127 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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 302 ASP Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 728 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 78 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 4 optimal weight: 0.0040 chunk 7 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 12 optimal weight: 0.0870 chunk 37 optimal weight: 9.9990 chunk 110 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.5372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 898 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 = 0.4059 r_free = 0.4059 target = 0.181518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.126141 restraints weight = 11491.837| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.98 r_work: 0.3171 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10074 Z= 0.103 Angle : 0.517 10.469 13696 Z= 0.257 Chirality : 0.042 0.159 1549 Planarity : 0.004 0.058 1754 Dihedral : 7.012 73.232 1480 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.23 % Allowed : 15.55 % Favored : 83.22 % 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 aren not related in a simple way. whole: 1.70 (0.24), residues: 1238 helix: 2.29 (0.22), residues: 564 sheet: 0.09 (0.39), residues: 162 loop : 0.24 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 278 TYR 0.014 0.001 TYR A 157 PHE 0.024 0.001 PHE A 970 TRP 0.010 0.001 TRP B 106 HIS 0.004 0.001 HIS B 227 Details of bonding type rmsd covalent geometry : bond 0.00228 (10068) covalent geometry : angle 0.51274 (13681) SS BOND : bond 0.00160 ( 3) SS BOND : angle 0.74532 ( 6) hydrogen bonds : bond 0.03737 ( 508) hydrogen bonds : angle 4.17278 ( 1497) link_NAG-ASN : bond 0.00301 ( 3) link_NAG-ASN : angle 2.64233 ( 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: 13 poor density : 117 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: A 140 TYR cc_start: 0.7257 (m-10) cc_final: 0.6667 (m-10) REVERT: A 193 GLN cc_start: 0.6305 (mm-40) cc_final: 0.5713 (mm-40) REVERT: A 260 GLU cc_start: 0.6444 (mt-10) cc_final: 0.6094 (mt-10) REVERT: A 320 MET cc_start: 0.6653 (OUTLIER) cc_final: 0.6287 (mmt) REVERT: A 369 ASN cc_start: 0.7748 (p0) cc_final: 0.7504 (p0) REVERT: A 425 GLU cc_start: 0.4332 (pm20) cc_final: 0.3818 (tm-30) REVERT: A 516 MET cc_start: 0.4248 (tmt) cc_final: 0.3942 (tmt) REVERT: A 531 LEU cc_start: 0.4482 (OUTLIER) cc_final: 0.4176 (mp) REVERT: A 652 ASP cc_start: 0.5944 (m-30) cc_final: 0.5729 (m-30) REVERT: A 686 GLU cc_start: 0.5764 (mp0) cc_final: 0.5335 (mp0) REVERT: A 838 SER cc_start: 0.6884 (p) cc_final: 0.6573 (m) REVERT: A 986 ASN cc_start: 0.6408 (m-40) cc_final: 0.6099 (m110) REVERT: B 109 LEU cc_start: 0.6669 (mt) cc_final: 0.6421 (mm) REVERT: B 114 HIS cc_start: 0.6710 (OUTLIER) cc_final: 0.6333 (t-90) REVERT: B 147 HIS cc_start: 0.6969 (t-90) cc_final: 0.6598 (t-170) REVERT: B 267 GLU cc_start: 0.7163 (pt0) cc_final: 0.6562 (tm-30) outliers start: 13 outliers final: 10 residues processed: 125 average time/residue: 0.5326 time to fit residues: 72.4552 Evaluate side-chains 124 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 302 ASP Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 728 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.444 > 50: distance: 116 - 120: 6.805 distance: 120 - 121: 12.782 distance: 120 - 126: 18.752 distance: 121 - 122: 22.813 distance: 121 - 124: 28.572 distance: 122 - 123: 32.908 distance: 122 - 127: 18.341 distance: 123 - 140: 22.731 distance: 124 - 125: 27.808 distance: 125 - 126: 17.806 distance: 127 - 128: 18.465 distance: 128 - 129: 34.213 distance: 128 - 131: 20.023 distance: 129 - 130: 36.808 distance: 129 - 132: 26.485 distance: 132 - 133: 16.731 distance: 133 - 134: 16.030 distance: 133 - 136: 21.015 distance: 134 - 135: 18.835 distance: 134 - 140: 21.221 distance: 136 - 137: 6.846 distance: 137 - 138: 14.652 distance: 137 - 139: 24.319 distance: 140 - 141: 10.360 distance: 141 - 142: 32.618 distance: 142 - 143: 11.550 distance: 142 - 144: 23.150 distance: 144 - 145: 12.291 distance: 145 - 146: 21.576 distance: 145 - 148: 11.150 distance: 146 - 147: 9.426 distance: 146 - 151: 21.872 distance: 148 - 149: 29.666 distance: 148 - 150: 31.334 distance: 151 - 152: 8.715 distance: 152 - 153: 26.067 distance: 152 - 155: 14.596 distance: 153 - 154: 11.032 distance: 153 - 163: 11.745 distance: 155 - 156: 12.007 distance: 156 - 157: 21.245 distance: 156 - 158: 20.471 distance: 157 - 159: 18.378 distance: 158 - 160: 11.016 distance: 159 - 161: 16.018 distance: 160 - 161: 12.010 distance: 161 - 162: 8.198 distance: 163 - 164: 9.424 distance: 164 - 165: 35.144 distance: 164 - 167: 16.689 distance: 165 - 166: 14.351 distance: 165 - 169: 29.264 distance: 166 - 187: 41.384 distance: 167 - 168: 33.012 distance: 169 - 170: 16.236 distance: 170 - 171: 9.669 distance: 170 - 173: 16.228 distance: 171 - 172: 18.748 distance: 171 - 177: 16.936 distance: 173 - 174: 18.697 distance: 174 - 175: 15.721 distance: 174 - 176: 21.554 distance: 177 - 178: 21.533 distance: 178 - 179: 22.733 distance: 178 - 181: 27.137 distance: 179 - 180: 18.410 distance: 179 - 187: 14.925 distance: 181 - 182: 28.504 distance: 182 - 183: 22.543 distance: 182 - 184: 22.366 distance: 183 - 185: 33.240 distance: 184 - 186: 30.720 distance: 185 - 186: 6.800 distance: 187 - 188: 20.286 distance: 188 - 189: 17.302 distance: 188 - 191: 10.956 distance: 189 - 190: 16.496 distance: 189 - 199: 10.596 distance: 191 - 192: 13.551 distance: 192 - 193: 14.567 distance: 192 - 194: 14.789 distance: 193 - 195: 24.631 distance: 194 - 196: 10.915 distance: 195 - 197: 27.750 distance: 196 - 197: 13.383 distance: 197 - 198: 8.681