Starting phenix.real_space_refine on Wed Aug 5 18:11:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ijv_35500/08_2026/8ijv_35500.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ijv_35500/08_2026/8ijv_35500.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ijv_35500/08_2026/8ijv_35500.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ijv_35500/08_2026/8ijv_35500.map" model { file = "/net/cci-nas-00/data/ceres_data/8ijv_35500/08_2026/8ijv_35500.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ijv_35500/08_2026/8ijv_35500.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8ijv_35500/08_2026/8ijv_35500.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ijv_35500/08_2026/8ijv_35500.cif" } resolution = 2.1 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= -0.002 sd= 0.094 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 9 Type Number sf(0) Gaussians P 5 5.49 5 Mg 1 5.21 5 S 65 5.16 5 Cl 4 4.86 5 Be 1 3.05 5 C 6570 2.51 5 N 1654 2.21 5 O 2229 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10532 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 7631 Classifications: {'peptide': 983} Link IDs: {'PTRANS': 47, 'TRANS': 935} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2142 Classifications: {'peptide': 268} Link IDs: {'PCIS': 4, 'PTRANS': 18, 'TRANS': 245} Chain: "A" Number of atoms: 238 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 6, 216 Unusual residues: {' MG': 1, 'PCW': 4, 'PWI': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PCW:plan-2': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 6, 216 Unusual residues: {' MG': 1, 'PCW': 4, 'PWI': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PCW:plan-2': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 189 Chain: "B" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 152 Unusual residues: {'CLR': 2, 'NAG': 3, 'PCW': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 255 Classifications: {'water': 255} Link IDs: {None: 254} Chain: "B" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 114 Classifications: {'water': 114} Link IDs: {None: 113} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C01APWI A1106 " occ=0.46 ... (42 atoms not shown) pdb="CL2 BPWI A1106 " occ=0.54 Time building chain proxies: 2.44, per 1000 atoms: 0.23 Number of scatterers: 10532 At special positions: 0 Unit cell: (81.216, 97.76, 174.464, 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) Cl 4 17.00 S 65 16.00 P 5 15.00 Mg 1 11.99 F 3 9.00 O 2229 8.00 N 1654 7.00 C 6570 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 302 " - " ASN B 99 " " NAG B 303 " - " ASN B 130 " " NAG B 304 " - " ASN B 161 " Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 462.8 milliseconds 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2340 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 10 sheets defined 50.2% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 73 through 84 Processing helix chain 'A' and resid 96 through 106 removed outlier: 3.614A pdb=" N LYS A 100 " --> pdb=" O PRO A 96 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE A 101 " --> pdb=" O GLU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 129 Processing helix chain 'A' and resid 135 through 170 removed outlier: 3.989A pdb=" N LEU A 139 " --> pdb=" O THR A 135 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE A 170 " --> pdb=" O ILE A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 270 through 273 Processing helix chain 'A' and resid 274 through 285 Processing helix chain 'A' and resid 291 through 322 Processing helix chain 'A' and resid 325 through 340 Processing helix chain 'A' and resid 344 through 362 Processing helix chain 'A' and resid 369 through 373 Processing helix chain 'A' and resid 374 through 379 removed outlier: 3.561A pdb=" N SER A 378 " --> pdb=" O GLU A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 437 Processing helix chain 'A' and resid 450 through 454 Processing helix chain 'A' and resid 459 through 473 Processing helix chain 'A' and resid 475 through 483 Processing helix chain 'A' and resid 519 through 526 removed outlier: 3.664A pdb=" N ARG A 526 " --> pdb=" O ARG A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 557 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 660 through 664 Processing helix chain 'A' and resid 665 through 669 Processing helix chain 'A' and resid 676 through 682 removed outlier: 3.580A pdb=" N ASP A 681 " --> pdb=" O MET A 677 " (cutoff:3.500A) 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: 4.072A 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 820 Processing helix chain 'A' and resid 824 through 831 removed outlier: 3.608A pdb=" N LEU A 831 " --> pdb=" O PRO A 827 " (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 839 through 843 Processing helix chain 'A' and resid 855 through 865 Processing helix chain 'A' and resid 865 through 885 Processing helix chain 'A' and resid 888 through 893 Processing helix chain 'A' and resid 895 through 901 Processing helix chain 'A' and resid 916 through 946 removed outlier: 3.622A pdb=" N ALA A 941 " --> pdb=" O MET A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 957 Processing helix chain 'A' and resid 961 through 981 Processing helix chain 'A' and resid 983 through 988 Processing helix chain 'A' and resid 994 through 1000 removed outlier: 3.861A pdb=" N TRP A 998 " --> pdb=" O ARG A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1022 Processing helix chain 'A' and resid 1025 through 1032 Processing helix chain 'B' and resid 34 through 66 Processing helix chain 'B' and resid 102 through 119 removed outlier: 4.240A pdb=" N TRP B 106 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLY B 108 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N LEU B 109 " --> pdb=" O THR B 105 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLY B 119 " --> pdb=" O ARG B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 163 removed outlier: 6.664A pdb=" N ASN B 161 " --> pdb=" O MET B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 223 removed outlier: 4.117A pdb=" N THR B 223 " --> pdb=" O ALA B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 229 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 11.763A pdb=" N GLN A 177 " --> pdb=" O LYS A 203 " (cutoff:3.500A) removed outlier: 9.456A pdb=" N LYS A 203 " --> pdb=" O GLN A 177 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR A 179 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU A 199 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N MET A 257 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LYS A 221 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY A 261 " --> pdb=" O GLY A 219 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLY A 219 " --> pdb=" O GLY A 261 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA A 263 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ALA A 217 " --> pdb=" O ALA A 263 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLY A 265 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU A 215 " --> pdb=" O GLY A 265 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N VAL A 267 " --> pdb=" O ARG A 213 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ARG A 213 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N CYS A 220 " --> pdb=" O ARG A 236 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190 removed outlier: 11.763A pdb=" N GLN A 177 " --> pdb=" O LYS A 203 " (cutoff:3.500A) removed outlier: 9.456A pdb=" N LYS A 203 " --> pdb=" O GLN A 177 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR A 179 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU A 199 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N MET A 257 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LYS A 221 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY A 261 " --> pdb=" O GLY A 219 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLY A 219 " --> pdb=" O GLY A 261 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA A 263 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ALA A 217 " --> pdb=" O ALA A 263 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLY A 265 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU A 215 " --> pdb=" O GLY A 265 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N VAL A 267 " --> pdb=" O ARG A 213 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ARG A 213 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 365 through 367 removed outlier: 6.323A pdb=" N GLY A 740 " --> pdb=" O MET A 757 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N LEU A 759 " --> pdb=" O GLY A 740 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ALA A 742 " --> pdb=" O LEU A 759 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL A 721 " --> pdb=" O ILE A 739 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N VAL A 741 " --> pdb=" O VAL A 721 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL A 723 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N MET A 743 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N GLY A 725 " --> pdb=" O MET A 743 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N VAL A 622 " --> pdb=" O MET A 697 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N PHE A 699 " --> pdb=" O VAL A 622 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N MET A 624 " --> pdb=" O PHE A 699 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 405 through 408 removed outlier: 5.334A pdb=" N VAL A 397 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE A 601 " --> pdb=" O VAL A 397 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS A 399 " --> pdb=" O SER A 599 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N PHE A 564 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU A 597 " --> pdb=" O LEU A 562 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU A 562 " --> pdb=" O LEU A 597 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N SER A 599 " --> pdb=" O ARG A 560 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ARG A 560 " --> pdb=" O SER A 599 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N HIS A 512 " --> pdb=" O LEU A 569 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N PHE A 497 " --> pdb=" O PHE A 491 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE A 491 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N CYS A 487 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR A 503 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LYS A 485 " --> pdb=" O THR A 503 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 405 through 408 removed outlier: 5.334A pdb=" N VAL A 397 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE A 601 " --> pdb=" O VAL A 397 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS A 399 " --> pdb=" O SER A 599 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N SER A 529 " --> pdb=" O PHE A 594 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N GLY A 596 " --> pdb=" O SER A 529 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 441 through 442 removed outlier: 3.697A pdb=" N ALA A 441 " --> pdb=" O ILE A 457 " (cutoff:3.500A) 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 28 through 29 Processing sheet with id=AA9, first strand: chain 'B' and resid 82 through 85 Processing sheet with id=AB1, first strand: chain 'B' and resid 94 through 99 removed outlier: 4.493A pdb=" N LEU B 94 " --> pdb=" O GLU B 283 " (cutoff:3.500A) 533 hydrogen bonds defined for protein. 1509 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.11 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1623 1.29 - 1.42: 2593 1.42 - 1.55: 6056 1.55 - 1.68: 17 1.68 - 1.82: 101 Bond restraints: 10390 Sorted by residual: bond pdb=" F3 BFD A 385 " pdb="BE BFD A 385 " ideal model delta sigma weight residual 1.529 1.764 -0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" F2 BFD A 385 " pdb="BE BFD A 385 " ideal model delta sigma weight residual 1.535 1.753 -0.218 2.00e-02 2.50e+03 1.18e+02 bond pdb=" F1 BFD A 385 " pdb="BE BFD A 385 " ideal model delta sigma weight residual 1.542 1.752 -0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" CG BFD A 385 " pdb=" OD1 BFD A 385 " ideal model delta sigma weight residual 1.269 1.447 -0.178 2.00e-02 2.50e+03 7.89e+01 bond pdb=" C17APWI A1106 " pdb=" N01APWI A1106 " ideal model delta sigma weight residual 1.466 1.292 0.174 2.00e-02 2.50e+03 7.56e+01 ... (remaining 10385 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.50: 14001 5.50 - 10.99: 64 10.99 - 16.49: 9 16.49 - 21.98: 3 21.98 - 27.48: 5 Bond angle restraints: 14082 Sorted by residual: angle pdb=" C19 CLR B 306 " pdb=" C10 CLR B 306 " pdb=" C9 CLR B 306 " ideal model delta sigma weight residual 111.86 84.38 27.48 3.00e+00 1.11e-01 8.39e+01 angle pdb=" C1 CLR B 306 " pdb=" C10 CLR B 306 " pdb=" C19 CLR B 306 " ideal model delta sigma weight residual 109.60 82.90 26.70 3.00e+00 1.11e-01 7.92e+01 angle pdb=" C5 PCW A1104 " pdb=" N PCW A1104 " pdb=" C8 PCW A1104 " ideal model delta sigma weight residual 111.64 86.86 24.78 3.00e+00 1.11e-01 6.82e+01 angle pdb=" C19 CLR B 306 " pdb=" C10 CLR B 306 " pdb=" C5 CLR B 306 " ideal model delta sigma weight residual 108.37 83.64 24.73 3.00e+00 1.11e-01 6.79e+01 angle pdb=" C6 PCW A1104 " pdb=" N PCW A1104 " pdb=" C8 PCW A1104 " ideal model delta sigma weight residual 109.11 86.89 22.22 3.00e+00 1.11e-01 5.48e+01 ... (remaining 14077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 5937 35.95 - 71.90: 236 71.90 - 107.85: 16 107.85 - 143.81: 5 143.81 - 179.76: 1 Dihedral angle restraints: 6195 sinusoidal: 2562 harmonic: 3633 Sorted by residual: dihedral pdb=" C13BPWI A1106 " pdb=" C14BPWI A1106 " pdb=" O01BPWI A1106 " pdb=" C15BPWI A1106 " ideal model delta sinusoidal sigma weight residual -179.86 -0.10 -179.76 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C33 PCW A1103 " pdb=" C31 PCW A1103 " pdb=" C32 PCW A1103 " pdb=" O2 PCW A1103 " ideal model delta sinusoidal sigma weight residual 191.83 49.07 142.76 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" C33 PCW A1104 " pdb=" C31 PCW A1104 " pdb=" C32 PCW A1104 " pdb=" O2 PCW A1104 " ideal model delta sinusoidal sigma weight residual 191.83 51.54 140.29 1 3.00e+01 1.11e-03 1.89e+01 ... (remaining 6192 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.358: 1573 0.358 - 0.716: 0 0.716 - 1.074: 0 1.074 - 1.432: 0 1.432 - 1.790: 1 Chirality restraints: 1574 Sorted by residual: chirality pdb=" C10 CLR B 306 " pdb=" C1 CLR B 306 " pdb=" C5 CLR B 306 " pdb=" C9 CLR B 306 " both_signs ideal model delta sigma weight residual False -2.85 -1.06 -1.79 2.00e-01 2.50e+01 8.01e+01 chirality pdb=" C1 NAG B 303 " pdb=" ND2 ASN B 130 " pdb=" C2 NAG B 303 " pdb=" O5 NAG B 303 " both_signs ideal model delta sigma weight residual False -2.40 -2.74 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" C1 NAG B 302 " pdb=" ND2 ASN B 99 " pdb=" C2 NAG B 302 " pdb=" O5 NAG B 302 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 1571 not shown) Planarity restraints: 1780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 130 " 0.216 2.00e-02 2.50e+03 1.94e-01 4.71e+02 pdb=" CG ASN B 130 " -0.082 2.00e-02 2.50e+03 pdb=" OD1 ASN B 130 " -0.148 2.00e-02 2.50e+03 pdb=" ND2 ASN B 130 " -0.230 2.00e-02 2.50e+03 pdb=" C1 NAG B 303 " 0.244 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C01APWI A1106 " 0.006 2.00e-02 2.50e+03 5.57e-02 6.98e+01 pdb=" C07APWI A1106 " 0.000 2.00e-02 2.50e+03 pdb=" C08APWI A1106 " 0.048 2.00e-02 2.50e+03 pdb=" C09APWI A1106 " 0.101 2.00e-02 2.50e+03 pdb=" C10APWI A1106 " 0.043 2.00e-02 2.50e+03 pdb=" C11APWI A1106 " -0.014 2.00e-02 2.50e+03 pdb=" C12APWI A1106 " -0.027 2.00e-02 2.50e+03 pdb=" C13APWI A1106 " -0.089 2.00e-02 2.50e+03 pdb="CL2 APWI A1106 " -0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C01APWI A1106 " -0.028 2.00e-02 2.50e+03 4.56e-02 4.16e+01 pdb=" C02APWI A1106 " -0.045 2.00e-02 2.50e+03 pdb=" C03APWI A1106 " -0.016 2.00e-02 2.50e+03 pdb=" C04APWI A1106 " -0.001 2.00e-02 2.50e+03 pdb=" C05APWI A1106 " -0.026 2.00e-02 2.50e+03 pdb=" C06APWI A1106 " -0.036 2.00e-02 2.50e+03 pdb=" C07APWI A1106 " 0.089 2.00e-02 2.50e+03 pdb="CL1 APWI A1106 " 0.062 2.00e-02 2.50e+03 ... (remaining 1777 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 129 2.56 - 3.14: 8347 3.14 - 3.73: 17964 3.73 - 4.31: 25929 4.31 - 4.90: 39940 Nonbonded interactions: 92309 Sorted by model distance: nonbonded pdb=" O THR A 387 " pdb="MG MG A1102 " model vdw 1.973 2.170 nonbonded pdb="MG MG A1102 " pdb=" O HOH A1204 " model vdw 2.021 2.170 nonbonded pdb=" F2 BFD A 385 " pdb="MG MG A1102 " model vdw 2.104 2.120 nonbonded pdb=" CE LYS B 135 " pdb=" O HOH B 463 " model vdw 2.141 3.440 nonbonded pdb=" F1 BFD A 385 " pdb=" OG1 THR A 626 " model vdw 2.152 2.990 ... (remaining 92304 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=0.46 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.230 Find NCS groups from input model: 0.060 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:6.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 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 : 0.009 0.423 10396 Z= 0.450 Angle : 1.142 29.579 14097 Z= 0.484 Chirality : 0.066 1.790 1574 Planarity : 0.006 0.125 1777 Dihedral : 18.473 179.758 3846 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.73 % Allowed : 17.78 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.24), residues: 1244 helix: 1.65 (0.22), residues: 579 sheet: 0.43 (0.41), residues: 155 loop : -0.04 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1020 TYR 0.017 0.001 TYR A 802 PHE 0.022 0.002 PHE A 333 TRP 0.017 0.002 TRP A 997 HIS 0.003 0.001 HIS B 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00786 / 0.40 (10390) covalent geometry : angle 1.09833 / 0.47 (14082) SS BOND : bond 0.00315 / 0.16 ( 3) SS BOND : angle 0.62786 / 0.54 ( 6) hydrogen bonds : bond 0.12070 / 8.09 ( 510) hydrogen bonds : angle 5.55949 / 3.96 ( 1509) link_NAG-ASN : bond 0.24432 / 11.63 ( 3) link_NAG-ASN : angle 12.39495 / 5.89 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 29 residues processed: 145 average time/residue: 0.6862 time to fit residues: 106.1927 Evaluate side-chains 145 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 495 ASN Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 508 ARG Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 946 ARG Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 261 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 665 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.168848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.121659 restraints weight = 8731.123| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.41 r_work: 0.3158 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3043 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.0542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10396 Z= 0.137 Angle : 0.708 30.392 14097 Z= 0.328 Chirality : 0.066 1.900 1574 Planarity : 0.005 0.057 1777 Dihedral : 13.472 154.298 1606 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.76 % Allowed : 15.71 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.24), residues: 1244 helix: 1.73 (0.22), residues: 588 sheet: 0.45 (0.41), residues: 154 loop : 0.00 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 328 TYR 0.020 0.001 TYR A 802 PHE 0.014 0.002 PHE A 315 TRP 0.013 0.001 TRP A 997 HIS 0.004 0.001 HIS B 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (10390) covalent geometry : angle 0.70513 / 0.33 (14082) SS BOND : bond 0.00368 / 0.18 ( 3) SS BOND : angle 0.74495 / 0.67 ( 6) hydrogen bonds : bond 0.04908 / 3.33 ( 510) hydrogen bonds : angle 4.48293 / 3.22 ( 1509) link_NAG-ASN : bond 0.00776 / 0.38 ( 3) link_NAG-ASN : angle 2.67265 / 1.98 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 113 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 GLN cc_start: 0.7869 (mp10) cc_final: 0.7645 (mm-40) REVERT: A 247 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7396 (mm-30) REVERT: A 505 GLU cc_start: 0.5784 (OUTLIER) cc_final: 0.5479 (tp30) REVERT: A 835 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.7784 (mttp) REVERT: A 844 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7882 (mtt-85) REVERT: B 78 LYS cc_start: 0.8720 (mmtp) cc_final: 0.8128 (mmmt) REVERT: B 135 LYS cc_start: 0.7675 (tptm) cc_final: 0.7149 (mmpt) outliers start: 40 outliers final: 22 residues processed: 144 average time/residue: 0.6502 time to fit residues: 100.0247 Evaluate side-chains 136 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 844 ARG Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 946 ARG Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 261 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 61 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 72 optimal weight: 7.9990 chunk 56 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 665 ASN A 792 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.168833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.122225 restraints weight = 11567.994| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.89 r_work: 0.3125 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.0598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10396 Z= 0.135 Angle : 0.702 30.297 14097 Z= 0.324 Chirality : 0.066 1.919 1574 Planarity : 0.005 0.055 1777 Dihedral : 13.158 153.777 1584 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.48 % Allowed : 15.33 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.24), residues: 1244 helix: 1.77 (0.22), residues: 588 sheet: 0.73 (0.42), residues: 144 loop : -0.06 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 278 TYR 0.021 0.001 TYR A 802 PHE 0.022 0.002 PHE A 970 TRP 0.014 0.001 TRP A 997 HIS 0.004 0.001 HIS B 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (10390) covalent geometry : angle 0.69887 / 0.32 (14082) SS BOND : bond 0.00372 / 0.18 ( 3) SS BOND : angle 0.64545 / 0.56 ( 6) hydrogen bonds : bond 0.04809 / 3.25 ( 510) hydrogen bonds : angle 4.44164 / 3.20 ( 1509) link_NAG-ASN : bond 0.00662 / 0.33 ( 3) link_NAG-ASN : angle 2.83282 / 1.92 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 113 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 GLN cc_start: 0.7896 (mp10) cc_final: 0.7659 (mm-40) REVERT: A 247 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7450 (mm-30) REVERT: A 505 GLU cc_start: 0.5794 (OUTLIER) cc_final: 0.5491 (tp30) REVERT: A 689 GLU cc_start: 0.7884 (tp30) cc_final: 0.7647 (tp30) REVERT: A 835 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.7802 (mttp) REVERT: A 844 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7925 (mtt-85) REVERT: B 78 LYS cc_start: 0.8728 (mmtp) cc_final: 0.8117 (mmmt) REVERT: B 135 LYS cc_start: 0.7662 (tptm) cc_final: 0.7131 (mmpt) outliers start: 37 outliers final: 28 residues processed: 142 average time/residue: 0.6267 time to fit residues: 94.9383 Evaluate side-chains 144 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 844 ARG Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 946 ARG Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 261 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 43 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 97 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 6 optimal weight: 0.5980 chunk 51 optimal weight: 6.9990 chunk 104 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 35 optimal weight: 0.3980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 665 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.168781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.121077 restraints weight = 9327.188| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.53 r_work: 0.3152 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.0599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 10396 Z= 0.147 Angle : 0.728 30.297 14097 Z= 0.331 Chirality : 0.066 1.919 1574 Planarity : 0.005 0.055 1777 Dihedral : 13.158 153.777 1584 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.01 % Allowed : 15.99 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.24), residues: 1244 helix: 1.77 (0.22), residues: 588 sheet: 0.73 (0.42), residues: 144 loop : -0.06 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 278 TYR 0.021 0.001 TYR A 802 PHE 0.022 0.002 PHE A 970 TRP 0.014 0.001 TRP A 997 HIS 0.004 0.001 HIS B 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (10390) covalent geometry : angle 0.69887 / 0.32 (14082) SS BOND : bond 0.00372 / 0.18 ( 3) SS BOND : angle 0.64544 / 0.56 ( 6) hydrogen bonds : bond 0.04809 / 3.25 ( 510) hydrogen bonds : angle 4.44164 / 3.20 ( 1509) link_NAG-ASN : bond 0.06962 / 3.50 ( 3) link_NAG-ASN : angle 8.07988 / 6.43 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 GLN cc_start: 0.7875 (mp10) cc_final: 0.7639 (mm-40) REVERT: A 247 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7403 (mm-30) REVERT: A 505 GLU cc_start: 0.5785 (OUTLIER) cc_final: 0.5480 (tp30) REVERT: A 689 GLU cc_start: 0.7865 (tp30) cc_final: 0.7621 (tp30) REVERT: A 835 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.7794 (mttp) REVERT: A 844 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7885 (mtt-85) REVERT: B 78 LYS cc_start: 0.8716 (mmtp) cc_final: 0.8110 (mmmt) REVERT: B 135 LYS cc_start: 0.7648 (tptm) cc_final: 0.7137 (mmpt) outliers start: 32 outliers final: 28 residues processed: 137 average time/residue: 0.6641 time to fit residues: 96.9940 Evaluate side-chains 144 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 844 ARG Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 946 ARG Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 261 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 39 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 50 optimal weight: 0.0970 chunk 44 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 79 optimal weight: 0.0870 chunk 116 optimal weight: 0.0070 chunk 100 optimal weight: 0.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 665 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.168782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.121561 restraints weight = 8990.625| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.48 r_work: 0.3153 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.0599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 10396 Z= 0.147 Angle : 0.728 30.297 14097 Z= 0.331 Chirality : 0.066 1.919 1574 Planarity : 0.005 0.055 1777 Dihedral : 13.160 153.777 1584 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.01 % Allowed : 15.99 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.24), residues: 1244 helix: 1.77 (0.22), residues: 588 sheet: 0.73 (0.42), residues: 144 loop : -0.06 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 278 TYR 0.021 0.001 TYR A 802 PHE 0.022 0.002 PHE A 970 TRP 0.014 0.001 TRP A 997 HIS 0.004 0.001 HIS B 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (10390) covalent geometry : angle 0.69887 / 0.32 (14082) SS BOND : bond 0.00372 / 0.18 ( 3) SS BOND : angle 0.64541 / 0.56 ( 6) hydrogen bonds : bond 0.04809 / 3.25 ( 510) hydrogen bonds : angle 4.44164 / 3.20 ( 1509) link_NAG-ASN : bond 0.06945 / 3.49 ( 3) link_NAG-ASN : angle 8.07047 / 6.42 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 GLN cc_start: 0.7897 (mp10) cc_final: 0.7660 (mm-40) REVERT: A 247 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7404 (mm-30) REVERT: A 505 GLU cc_start: 0.5790 (OUTLIER) cc_final: 0.5486 (tp30) REVERT: A 689 GLU cc_start: 0.7865 (tp30) cc_final: 0.7621 (tp30) REVERT: A 835 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.7814 (mttp) REVERT: A 844 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7889 (mtt-85) REVERT: B 78 LYS cc_start: 0.8718 (mmtp) cc_final: 0.8122 (mmmt) REVERT: B 135 LYS cc_start: 0.7660 (tptm) cc_final: 0.7158 (mmpt) outliers start: 32 outliers final: 28 residues processed: 137 average time/residue: 0.6906 time to fit residues: 100.8612 Evaluate side-chains 144 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 844 ARG Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 946 ARG Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 261 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 95 optimal weight: 0.0060 chunk 88 optimal weight: 0.9980 chunk 59 optimal weight: 8.9990 chunk 106 optimal weight: 0.6980 chunk 2 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 89 optimal weight: 0.4980 chunk 7 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 665 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.168785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.121383 restraints weight = 9535.597| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.59 r_work: 0.3147 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.0599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 10396 Z= 0.145 Angle : 0.725 30.297 14097 Z= 0.330 Chirality : 0.066 1.919 1574 Planarity : 0.005 0.055 1777 Dihedral : 13.180 153.770 1584 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.10 % Allowed : 15.80 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.24), residues: 1244 helix: 1.77 (0.22), residues: 588 sheet: 0.73 (0.42), residues: 144 loop : -0.06 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 278 TYR 0.021 0.001 TYR A 802 PHE 0.021 0.002 PHE A 970 TRP 0.014 0.001 TRP A 997 HIS 0.004 0.001 HIS B 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (10390) covalent geometry : angle 0.69870 / 0.32 (14082) SS BOND : bond 0.00370 / 0.18 ( 3) SS BOND : angle 0.64392 / 0.56 ( 6) hydrogen bonds : bond 0.04805 / 3.25 ( 510) hydrogen bonds : angle 4.44171 / 3.20 ( 1509) link_NAG-ASN : bond 0.06291 / 3.16 ( 3) link_NAG-ASN : angle 7.71827 / 6.16 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 GLN cc_start: 0.7866 (mp10) cc_final: 0.7631 (mm-40) REVERT: A 247 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7404 (mm-30) REVERT: A 505 GLU cc_start: 0.5779 (OUTLIER) cc_final: 0.5475 (tp30) REVERT: A 689 GLU cc_start: 0.7873 (tp30) cc_final: 0.7630 (tp30) REVERT: A 835 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.7801 (mttp) REVERT: A 844 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.7893 (mtt-85) REVERT: B 78 LYS cc_start: 0.8718 (mmtp) cc_final: 0.8115 (mmmt) REVERT: B 135 LYS cc_start: 0.7658 (tptm) cc_final: 0.7143 (mmpt) outliers start: 33 outliers final: 28 residues processed: 138 average time/residue: 0.6842 time to fit residues: 100.9312 Evaluate side-chains 144 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 844 ARG Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 946 ARG Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 261 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 105 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 chunk 62 optimal weight: 0.1980 chunk 15 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 665 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.167483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.121630 restraints weight = 9456.001| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.48 r_work: 0.3126 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3015 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3015 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.0615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10396 Z= 0.168 Angle : 0.746 30.374 14097 Z= 0.347 Chirality : 0.068 1.934 1574 Planarity : 0.005 0.055 1777 Dihedral : 13.154 152.334 1584 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.67 % Allowed : 14.96 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.23), residues: 1244 helix: 1.71 (0.21), residues: 588 sheet: 0.69 (0.42), residues: 144 loop : -0.07 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 328 TYR 0.021 0.002 TYR A 802 PHE 0.017 0.002 PHE A 315 TRP 0.014 0.002 TRP A 997 HIS 0.004 0.001 HIS B 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (10390) covalent geometry : angle 0.74348 / 0.35 (14082) SS BOND : bond 0.00437 / 0.21 ( 3) SS BOND : angle 0.73861 / 0.63 ( 6) hydrogen bonds : bond 0.05315 / 3.59 ( 510) hydrogen bonds : angle 4.46940 / 3.22 ( 1509) link_NAG-ASN : bond 0.00594 / 0.29 ( 3) link_NAG-ASN : angle 2.34665 / 1.62 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 113 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 GLN cc_start: 0.7905 (mp10) cc_final: 0.7655 (mm-40) REVERT: A 247 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7426 (mm-30) REVERT: A 453 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7830 (mttp) REVERT: A 505 GLU cc_start: 0.5801 (OUTLIER) cc_final: 0.5527 (tp30) REVERT: A 645 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6449 (mp0) REVERT: A 835 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.7876 (mttp) REVERT: A 844 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.7898 (mtt-85) REVERT: B 78 LYS cc_start: 0.8711 (mmtp) cc_final: 0.8111 (mmmt) REVERT: B 135 LYS cc_start: 0.7751 (tptm) cc_final: 0.7201 (mmpt) outliers start: 39 outliers final: 28 residues processed: 143 average time/residue: 0.7250 time to fit residues: 110.4055 Evaluate side-chains 146 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 112 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 844 ARG Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 946 ARG Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 261 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 33 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 76 optimal weight: 0.4980 chunk 120 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 665 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.167508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.120059 restraints weight = 8636.714| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.35 r_work: 0.3144 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.0620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 10396 Z= 0.182 Angle : 0.762 30.374 14097 Z= 0.351 Chirality : 0.068 1.934 1574 Planarity : 0.005 0.055 1777 Dihedral : 13.154 152.334 1584 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.20 % Allowed : 15.52 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.23), residues: 1244 helix: 1.71 (0.21), residues: 588 sheet: 0.69 (0.42), residues: 144 loop : -0.07 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 328 TYR 0.021 0.002 TYR A 802 PHE 0.017 0.002 PHE A 315 TRP 0.014 0.002 TRP A 997 HIS 0.004 0.001 HIS B 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (10390) covalent geometry : angle 0.74347 / 0.35 (14082) SS BOND : bond 0.00437 / 0.21 ( 3) SS BOND : angle 0.73860 / 0.63 ( 6) hydrogen bonds : bond 0.05315 / 3.59 ( 510) hydrogen bonds : angle 4.46940 / 3.22 ( 1509) link_NAG-ASN : bond 0.08046 / 4.00 ( 3) link_NAG-ASN : angle 6.62481 / 4.72 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 112 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 GLN cc_start: 0.7892 (mp10) cc_final: 0.7640 (mm-40) REVERT: A 247 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7406 (mm-30) REVERT: A 453 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7823 (mttp) REVERT: A 505 GLU cc_start: 0.5787 (OUTLIER) cc_final: 0.5513 (tp30) REVERT: A 645 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.6423 (mp0) REVERT: A 835 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.7864 (mttp) REVERT: A 844 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7867 (mtt-85) REVERT: B 78 LYS cc_start: 0.8693 (mmtp) cc_final: 0.8094 (mmmt) REVERT: B 135 LYS cc_start: 0.7730 (tptm) cc_final: 0.7185 (mmpt) outliers start: 34 outliers final: 28 residues processed: 137 average time/residue: 0.7177 time to fit residues: 104.8559 Evaluate side-chains 146 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 112 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 844 ARG Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 946 ARG Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 261 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 84 optimal weight: 0.3980 chunk 29 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 665 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.167544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.120710 restraints weight = 11629.708| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.93 r_work: 0.3099 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.0620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 10396 Z= 0.180 Angle : 0.761 30.375 14097 Z= 0.351 Chirality : 0.068 1.934 1574 Planarity : 0.005 0.055 1777 Dihedral : 13.159 152.331 1584 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.20 % Allowed : 15.52 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.23), residues: 1244 helix: 1.71 (0.21), residues: 588 sheet: 0.69 (0.42), residues: 144 loop : -0.07 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 328 TYR 0.021 0.002 TYR A 802 PHE 0.017 0.002 PHE A 315 TRP 0.014 0.002 TRP A 997 HIS 0.004 0.001 HIS B 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (10390) covalent geometry : angle 0.74319 / 0.35 (14082) SS BOND : bond 0.00434 / 0.21 ( 3) SS BOND : angle 0.73811 / 0.63 ( 6) hydrogen bonds : bond 0.05312 / 3.59 ( 510) hydrogen bonds : angle 4.46941 / 3.22 ( 1509) link_NAG-ASN : bond 0.07743 / 3.85 ( 3) link_NAG-ASN : angle 6.50313 / 4.64 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 112 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 GLN cc_start: 0.7899 (mp10) cc_final: 0.7653 (mm-40) REVERT: A 247 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7450 (mm-30) REVERT: A 453 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7821 (mttp) REVERT: A 505 GLU cc_start: 0.5799 (OUTLIER) cc_final: 0.5528 (tp30) REVERT: A 645 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.6486 (mp0) REVERT: A 835 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.7882 (mttp) REVERT: A 844 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.7940 (mtt-85) REVERT: B 78 LYS cc_start: 0.8724 (mmtp) cc_final: 0.8108 (mmmt) REVERT: B 135 LYS cc_start: 0.7770 (tptm) cc_final: 0.7193 (mmpt) outliers start: 34 outliers final: 28 residues processed: 137 average time/residue: 0.7266 time to fit residues: 106.0517 Evaluate side-chains 146 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 112 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 844 ARG Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 946 ARG Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 261 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 112 optimal weight: 0.6980 chunk 113 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 106 optimal weight: 0.8980 chunk 34 optimal weight: 0.0980 chunk 109 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 115 optimal weight: 6.9990 chunk 119 optimal weight: 0.7980 chunk 123 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 665 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.168919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.121806 restraints weight = 8632.992| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.25 r_work: 0.3166 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.0653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10396 Z= 0.125 Angle : 0.699 30.320 14097 Z= 0.322 Chirality : 0.066 1.916 1574 Planarity : 0.004 0.054 1777 Dihedral : 12.949 148.153 1584 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.73 % Allowed : 15.99 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.24), residues: 1244 helix: 1.86 (0.22), residues: 581 sheet: 0.64 (0.41), residues: 150 loop : -0.11 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 328 TYR 0.023 0.001 TYR A 802 PHE 0.039 0.002 PHE A 970 TRP 0.015 0.001 TRP A 997 HIS 0.003 0.001 HIS B 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 (10390) covalent geometry : angle 0.69652 / 0.32 (14082) SS BOND : bond 0.00276 / 0.14 ( 3) SS BOND : angle 0.61114 / 0.57 ( 6) hydrogen bonds : bond 0.04677 / 3.17 ( 510) hydrogen bonds : angle 4.36973 / 3.14 ( 1509) link_NAG-ASN : bond 0.00476 / 0.24 ( 3) link_NAG-ASN : angle 2.64742 / 1.69 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: A 193 GLN cc_start: 0.7921 (mp10) cc_final: 0.7652 (mm-40) REVERT: A 247 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7415 (mm-30) REVERT: A 689 GLU cc_start: 0.7895 (tp30) cc_final: 0.7579 (tp30) REVERT: A 835 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.7895 (mttp) REVERT: A 844 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7861 (mtt-85) REVERT: B 78 LYS cc_start: 0.8705 (mmtp) cc_final: 0.8118 (mmmt) REVERT: B 135 LYS cc_start: 0.7687 (tptm) cc_final: 0.7172 (mmpt) outliers start: 29 outliers final: 24 residues processed: 135 average time/residue: 0.6945 time to fit residues: 100.4300 Evaluate side-chains 139 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 844 ARG Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 946 ARG Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 261 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 57 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 8 optimal weight: 0.0010 chunk 16 optimal weight: 0.7980 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 665 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.168877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.121769 restraints weight = 8891.646| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.49 r_work: 0.3152 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3038 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3038 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.0647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.137 10396 Z= 0.147 Angle : 0.717 30.320 14097 Z= 0.326 Chirality : 0.066 1.916 1574 Planarity : 0.004 0.054 1777 Dihedral : 12.920 148.153 1579 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.54 % Allowed : 16.27 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.24), residues: 1244 helix: 1.86 (0.22), residues: 581 sheet: 0.64 (0.41), residues: 150 loop : -0.11 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 328 TYR 0.023 0.001 TYR A 802 PHE 0.039 0.002 PHE A 970 TRP 0.015 0.001 TRP A 997 HIS 0.003 0.001 HIS B 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 (10390) covalent geometry : angle 0.69652 / 0.32 (14082) SS BOND : bond 0.00276 / 0.14 ( 3) SS BOND : angle 0.61114 / 0.57 ( 6) hydrogen bonds : bond 0.04677 / 3.17 ( 510) hydrogen bonds : angle 4.36973 / 3.14 ( 1509) link_NAG-ASN : bond 0.09105 / 4.68 ( 3) link_NAG-ASN : angle 6.83619 / 4.97 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6431.95 seconds wall clock time: 109 minutes 40.08 seconds (6580.08 seconds total)