Starting phenix.real_space_refine on Wed Sep 17 13:29:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dso_47148/09_2025/9dso_47148.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dso_47148/09_2025/9dso_47148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dso_47148/09_2025/9dso_47148.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dso_47148/09_2025/9dso_47148.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dso_47148/09_2025/9dso_47148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dso_47148/09_2025/9dso_47148.map" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.034 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: 5 Type Number sf(0) Gaussians Mg 1 5.21 5 S 34 5.16 5 C 5768 2.51 5 N 1514 2.21 5 O 1658 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8975 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5805 Classifications: {'peptide': 726} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 51, 'TRANS': 674} Chain breaks: 4 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 3, 'GLN:plan1': 2, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 89 Chain: "B" Number of atoms: 3046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 3046 Classifications: {'peptide': 373} Link IDs: {'PTRANS': 11, 'TRANS': 361} Chain breaks: 1 Chain: "C" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 123 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 1, 'TRANS': 14} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.30, per 1000 atoms: 0.26 Number of scatterers: 8975 At special positions: 0 Unit cell: (100.772, 89.208, 142.898, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 34 16.00 Mg 1 11.99 O 1658 8.00 N 1514 7.00 C 5768 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 376.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2110 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 8 sheets defined 47.8% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 4 through 14 Processing helix chain 'A' and resid 54 through 63 Proline residue: A 60 - end of helix Processing helix chain 'A' and resid 72 through 92 removed outlier: 3.508A pdb=" N MET A 76 " --> pdb=" O THR A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 138 removed outlier: 3.968A pdb=" N GLN A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA A 124 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU A 127 " --> pdb=" O ASP A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 Processing helix chain 'A' and resid 164 through 185 removed outlier: 3.614A pdb=" N ASP A 168 " --> pdb=" O THR A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 189 removed outlier: 3.716A pdb=" N LYS A 189 " --> pdb=" O PRO A 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 186 through 189' Processing helix chain 'A' and resid 203 through 217 Processing helix chain 'A' and resid 235 through 243 Processing helix chain 'A' and resid 254 through 262 removed outlier: 3.519A pdb=" N GLN A 258 " --> pdb=" O ASP A 254 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN A 260 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS A 262 " --> pdb=" O GLN A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 286 Processing helix chain 'A' and resid 294 through 305 removed outlier: 3.834A pdb=" N ALA A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 331 Processing helix chain 'A' and resid 347 through 359 removed outlier: 3.649A pdb=" N VAL A 357 " --> pdb=" O ASP A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'A' and resid 373 through 387 removed outlier: 3.693A pdb=" N ARG A 387 " --> pdb=" O HIS A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 410 Processing helix chain 'A' and resid 593 through 598 removed outlier: 3.526A pdb=" N VAL A 597 " --> pdb=" O THR A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 614 removed outlier: 3.936A pdb=" N ARG A 607 " --> pdb=" O GLY A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 618 No H-bonds generated for 'chain 'A' and resid 616 through 618' Processing helix chain 'A' and resid 619 through 644 Processing helix chain 'A' and resid 660 through 664 Processing helix chain 'A' and resid 681 through 688 Processing helix chain 'A' and resid 694 through 698 removed outlier: 3.519A pdb=" N ALA A 697 " --> pdb=" O SER A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 708 removed outlier: 3.856A pdb=" N SER A 707 " --> pdb=" O ARG A 703 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU A 708 " --> pdb=" O SER A 704 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 703 through 708' Processing helix chain 'A' and resid 713 through 717 Processing helix chain 'A' and resid 742 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 765 Processing helix chain 'A' and resid 780 through 789 Processing helix chain 'A' and resid 791 through 796 removed outlier: 3.510A pdb=" N ASN A 795 " --> pdb=" O GLU A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 882 Processing helix chain 'A' and resid 894 through 901 removed outlier: 3.923A pdb=" N LYS A 900 " --> pdb=" O GLY A 896 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN A 901 " --> pdb=" O ASN A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 935 Processing helix chain 'B' and resid 49 through 55 removed outlier: 3.681A pdb=" N ASP B 54 " --> pdb=" O ALA B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 73 Processing helix chain 'B' and resid 79 through 94 Processing helix chain 'B' and resid 105 through 114 Processing helix chain 'B' and resid 159 through 175 removed outlier: 3.865A pdb=" N GLY B 168 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N TYR B 169 " --> pdb=" O VAL B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 184 Processing helix chain 'B' and resid 185 through 192 removed outlier: 3.584A pdb=" N ILE B 189 " --> pdb=" O PRO B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 235 through 237 No H-bonds generated for 'chain 'B' and resid 235 through 237' Processing helix chain 'B' and resid 250 through 272 removed outlier: 4.098A pdb=" N VAL B 271 " --> pdb=" O GLN B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 306 through 311 Processing helix chain 'B' and resid 311 through 331 Processing helix chain 'B' and resid 364 through 370 Processing helix chain 'B' and resid 376 through 386 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 20 removed outlier: 6.521A pdb=" N HIS A 227 " --> pdb=" O LYS A 249 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N LEU A 251 " --> pdb=" O HIS A 227 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE A 229 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N GLU A 253 " --> pdb=" O ILE A 229 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N CYS A 228 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASN A 49 " --> pdb=" O CYS A 228 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N TYR A 230 " --> pdb=" O ASN A 49 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N TYR A 51 " --> pdb=" O TYR A 230 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ASP A 48 " --> pdb=" O ARG A 94 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 29 removed outlier: 3.574A pdb=" N VAL A 29 " --> pdb=" O VAL A 32 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 590 through 591 Processing sheet with id=AA4, first strand: chain 'A' and resid 825 through 826 Processing sheet with id=AA5, first strand: chain 'B' and resid 4 through 8 removed outlier: 3.658A pdb=" N ARG B 342 " --> pdb=" O SER B 130 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N PHE B 104 " --> pdb=" O ILE B 137 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N GLU B 139 " --> pdb=" O PHE B 104 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N TYR B 203 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY B 25 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ARG B 208 " --> pdb=" O GLU B 23 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N GLU B 23 " --> pdb=" O ARG B 208 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N GLY B 210 " --> pdb=" O PRO B 21 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 4 through 8 removed outlier: 3.658A pdb=" N ARG B 342 " --> pdb=" O SER B 130 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N PHE B 104 " --> pdb=" O ILE B 137 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N GLU B 139 " --> pdb=" O PHE B 104 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N TYR B 203 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY B 25 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ARG B 208 " --> pdb=" O GLU B 23 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N GLU B 23 " --> pdb=" O ARG B 208 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N GLY B 210 " --> pdb=" O PRO B 21 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LEU B 18 " --> pdb=" O GLU C 264 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 176 through 177 removed outlier: 3.752A pdb=" N CYS B 224 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N TYR B 239 " --> pdb=" O ARG B 275 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N ILE B 277 " --> pdb=" O TYR B 239 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLU B 241 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N GLY B 279 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LYS B 243 " --> pdb=" O GLY B 279 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LYS B 281 " --> pdb=" O LYS B 243 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N THR B 245 " --> pdb=" O LYS B 281 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 67 through 68 removed outlier: 6.643A pdb=" N LYS B 67 " --> pdb=" O HIS B 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 456 hydrogen bonds defined for protein. 1275 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.72 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2914 1.34 - 1.45: 1306 1.45 - 1.57: 4925 1.57 - 1.69: 0 1.69 - 1.80: 52 Bond restraints: 9197 Sorted by residual: bond pdb=" N TYR A 789 " pdb=" CA TYR A 789 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 7.03e+00 bond pdb=" N THR B 176 " pdb=" CA THR B 176 " ideal model delta sigma weight residual 1.454 1.478 -0.024 1.29e-02 6.01e+03 3.49e+00 bond pdb=" C THR B 176 " pdb=" O THR B 176 " ideal model delta sigma weight residual 1.234 1.250 -0.016 1.26e-02 6.30e+03 1.65e+00 bond pdb=" CA THR B 176 " pdb=" C THR B 176 " ideal model delta sigma weight residual 1.522 1.507 0.015 1.23e-02 6.61e+03 1.54e+00 bond pdb=" C TYR A 789 " pdb=" O TYR A 789 " ideal model delta sigma weight residual 1.233 1.250 -0.017 1.49e-02 4.50e+03 1.32e+00 ... (remaining 9192 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 11917 1.14 - 2.29: 424 2.29 - 3.43: 84 3.43 - 4.57: 28 4.57 - 5.71: 8 Bond angle restraints: 12461 Sorted by residual: angle pdb=" N ILE A 911 " pdb=" CA ILE A 911 " pdb=" C ILE A 911 " ideal model delta sigma weight residual 113.53 109.33 4.20 9.80e-01 1.04e+00 1.83e+01 angle pdb=" CA THR B 176 " pdb=" CB THR B 176 " pdb=" OG1 THR B 176 " ideal model delta sigma weight residual 109.60 105.00 4.60 1.50e+00 4.44e-01 9.41e+00 angle pdb=" C GLU A 345 " pdb=" N ASN A 346 " pdb=" CA ASN A 346 " ideal model delta sigma weight residual 121.54 127.17 -5.63 1.91e+00 2.74e-01 8.70e+00 angle pdb=" N HIS B 373 " pdb=" CA HIS B 373 " pdb=" C HIS B 373 " ideal model delta sigma weight residual 112.68 108.92 3.76 1.33e+00 5.65e-01 8.00e+00 angle pdb=" C GLN A 192 " pdb=" CA GLN A 192 " pdb=" CB GLN A 192 " ideal model delta sigma weight residual 110.34 114.10 -3.76 1.40e+00 5.10e-01 7.23e+00 ... (remaining 12456 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.68: 4976 16.68 - 33.37: 442 33.37 - 50.05: 84 50.05 - 66.74: 15 66.74 - 83.42: 5 Dihedral angle restraints: 5522 sinusoidal: 2258 harmonic: 3264 Sorted by residual: dihedral pdb=" CA GLN A 803 " pdb=" C GLN A 803 " pdb=" N HIS A 804 " pdb=" CA HIS A 804 " ideal model delta harmonic sigma weight residual 180.00 -157.45 -22.55 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA GLN A 192 " pdb=" C GLN A 192 " pdb=" N VAL A 193 " pdb=" CA VAL A 193 " ideal model delta harmonic sigma weight residual -180.00 -158.57 -21.43 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA SER A 347 " pdb=" C SER A 347 " pdb=" N ILE A 348 " pdb=" CA ILE A 348 " ideal model delta harmonic sigma weight residual 180.00 158.66 21.34 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 5519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 855 0.035 - 0.070: 355 0.070 - 0.106: 100 0.106 - 0.141: 32 0.141 - 0.176: 3 Chirality restraints: 1345 Sorted by residual: chirality pdb=" CB ILE B 374 " pdb=" CA ILE B 374 " pdb=" CG1 ILE B 374 " pdb=" CG2 ILE B 374 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.76e-01 chirality pdb=" CA TYR A 754 " pdb=" N TYR A 754 " pdb=" C TYR A 754 " pdb=" CB TYR A 754 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.90e-01 chirality pdb=" CA ILE A 843 " pdb=" N ILE A 843 " pdb=" C ILE A 843 " pdb=" CB ILE A 843 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.33e-01 ... (remaining 1342 not shown) Planarity restraints: 1617 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 616 " 0.027 5.00e-02 4.00e+02 4.14e-02 2.75e+00 pdb=" N PRO A 617 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 617 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 617 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 754 " 0.014 2.00e-02 2.50e+03 1.11e-02 2.48e+00 pdb=" CG TYR A 754 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR A 754 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR A 754 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 754 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 754 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 754 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 754 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 192 " 0.007 2.00e-02 2.50e+03 1.50e-02 2.26e+00 pdb=" CD GLN A 192 " -0.026 2.00e-02 2.50e+03 pdb=" OE1 GLN A 192 " 0.010 2.00e-02 2.50e+03 pdb=" NE2 GLN A 192 " 0.009 2.00e-02 2.50e+03 ... (remaining 1614 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 971 2.75 - 3.29: 8615 3.29 - 3.82: 14994 3.82 - 4.36: 18342 4.36 - 4.90: 31459 Nonbonded interactions: 74381 Sorted by model distance: nonbonded pdb=" NH2 ARG A 922 " pdb=" OE2 GLU B 297 " model vdw 2.209 3.120 nonbonded pdb=" NH1 ARG A 922 " pdb=" O GLU B 292 " model vdw 2.259 3.120 nonbonded pdb=" O ASN A 346 " pdb=" OG SER A 347 " model vdw 2.294 3.040 nonbonded pdb=" O VAL B 9 " pdb=" NH2 ARG B 12 " model vdw 2.299 3.120 nonbonded pdb=" OE1 GLU A 378 " pdb=" OG SER A 668 " model vdw 2.304 3.040 ... (remaining 74376 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.450 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 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 : 0.004 0.039 9197 Z= 0.176 Angle : 0.543 5.714 12461 Z= 0.292 Chirality : 0.043 0.176 1345 Planarity : 0.004 0.041 1617 Dihedral : 13.115 83.422 3412 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.25), residues: 1099 helix: 1.21 (0.25), residues: 431 sheet: 0.77 (0.43), residues: 132 loop : 0.99 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 117 TYR 0.026 0.002 TYR A 754 PHE 0.016 0.002 PHE B 257 TRP 0.015 0.002 TRP A 355 HIS 0.005 0.001 HIS A 227 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 9197) covalent geometry : angle 0.54332 (12461) hydrogen bonds : bond 0.15082 ( 415) hydrogen bonds : angle 6.35755 ( 1275) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.371 Fit side-chains REVERT: A 178 THR cc_start: 0.8738 (m) cc_final: 0.8501 (m) REVERT: A 640 MET cc_start: 0.8253 (tpp) cc_final: 0.8013 (tpt) REVERT: A 673 LYS cc_start: 0.7537 (mmtp) cc_final: 0.7325 (tppt) REVERT: A 786 LYS cc_start: 0.7727 (ttpt) cc_final: 0.7526 (ttpp) REVERT: B 34 GLU cc_start: 0.7405 (mt-10) cc_final: 0.7159 (mt-10) REVERT: B 95 LYS cc_start: 0.8135 (ttpp) cc_final: 0.7858 (ttpp) REVERT: B 351 ASN cc_start: 0.7789 (t0) cc_final: 0.7507 (t0) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.7130 time to fit residues: 110.1580 Evaluate side-chains 104 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.2980 chunk 106 optimal weight: 10.0000 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 HIS B 64 GLN B 250 ASN B 267 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.152186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.114302 restraints weight = 9636.960| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.64 r_work: 0.3000 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9197 Z= 0.208 Angle : 0.576 8.123 12461 Z= 0.297 Chirality : 0.046 0.157 1345 Planarity : 0.005 0.051 1617 Dihedral : 4.266 23.380 1211 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.07 % Allowed : 8.57 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.25), residues: 1099 helix: 1.37 (0.25), residues: 431 sheet: 0.77 (0.42), residues: 131 loop : 0.85 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 607 TYR 0.015 0.002 TYR A 641 PHE 0.015 0.002 PHE B 66 TRP 0.017 0.002 TRP A 355 HIS 0.005 0.001 HIS A 227 Details of bonding type rmsd covalent geometry : bond 0.00518 ( 9197) covalent geometry : angle 0.57605 (12461) hydrogen bonds : bond 0.05156 ( 415) hydrogen bonds : angle 4.82645 ( 1275) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.264 Fit side-chains REVERT: A 178 THR cc_start: 0.8521 (m) cc_final: 0.8254 (m) REVERT: A 395 ARG cc_start: 0.6612 (ttm-80) cc_final: 0.6092 (ttm170) REVERT: A 606 GLU cc_start: 0.6450 (OUTLIER) cc_final: 0.6162 (tm-30) REVERT: A 786 LYS cc_start: 0.7672 (ttpt) cc_final: 0.7420 (ttpp) REVERT: B 34 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7282 (mt-10) REVERT: B 95 LYS cc_start: 0.8081 (ttpp) cc_final: 0.7813 (ttpp) REVERT: B 351 ASN cc_start: 0.7927 (t0) cc_final: 0.7477 (t0) outliers start: 20 outliers final: 9 residues processed: 114 average time/residue: 0.6770 time to fit residues: 81.9204 Evaluate side-chains 101 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 849 ARG Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 315 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 101 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 HIS A 373 ASN B 64 GLN B 250 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.152143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.113882 restraints weight = 9566.504| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.64 r_work: 0.3000 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9197 Z= 0.185 Angle : 0.544 7.783 12461 Z= 0.280 Chirality : 0.045 0.159 1345 Planarity : 0.004 0.054 1617 Dihedral : 4.246 23.513 1211 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.48 % Allowed : 11.26 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.25), residues: 1099 helix: 1.45 (0.25), residues: 431 sheet: 0.57 (0.41), residues: 141 loop : 0.90 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 607 TYR 0.014 0.002 TYR A 921 PHE 0.013 0.002 PHE B 66 TRP 0.018 0.002 TRP A 355 HIS 0.005 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 9197) covalent geometry : angle 0.54369 (12461) hydrogen bonds : bond 0.04792 ( 415) hydrogen bonds : angle 4.63218 ( 1275) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 0.376 Fit side-chains REVERT: A 304 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7319 (tp30) REVERT: A 395 ARG cc_start: 0.6634 (ttm-80) cc_final: 0.6111 (ttm170) REVERT: A 606 GLU cc_start: 0.6411 (OUTLIER) cc_final: 0.6135 (tm-30) REVERT: A 673 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7626 (mttp) REVERT: A 786 LYS cc_start: 0.7731 (ttpt) cc_final: 0.7395 (ttpp) REVERT: B 3 VAL cc_start: 0.7041 (p) cc_final: 0.6652 (m) REVERT: B 34 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7376 (mt-10) REVERT: B 95 LYS cc_start: 0.8077 (ttpp) cc_final: 0.7808 (ttpp) REVERT: B 250 ASN cc_start: 0.8237 (OUTLIER) cc_final: 0.7896 (p0) REVERT: B 351 ASN cc_start: 0.7933 (t0) cc_final: 0.7437 (t0) outliers start: 24 outliers final: 11 residues processed: 109 average time/residue: 0.6592 time to fit residues: 76.5438 Evaluate side-chains 106 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 673 LYS Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 849 ARG Chi-restraints excluded: chain A residue 868 SER Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 243 LYS Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 315 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 16 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 96 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 HIS A 373 ASN B 250 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.150931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.113178 restraints weight = 9734.450| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.65 r_work: 0.2984 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9197 Z= 0.213 Angle : 0.568 8.320 12461 Z= 0.291 Chirality : 0.046 0.181 1345 Planarity : 0.005 0.054 1617 Dihedral : 4.313 23.910 1211 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.58 % Allowed : 12.50 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.25), residues: 1099 helix: 1.37 (0.25), residues: 431 sheet: 0.56 (0.42), residues: 138 loop : 0.85 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 117 TYR 0.015 0.002 TYR A 641 PHE 0.014 0.002 PHE B 66 TRP 0.018 0.002 TRP A 355 HIS 0.005 0.001 HIS A 227 Details of bonding type rmsd covalent geometry : bond 0.00534 ( 9197) covalent geometry : angle 0.56762 (12461) hydrogen bonds : bond 0.04894 ( 415) hydrogen bonds : angle 4.64120 ( 1275) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.363 Fit side-chains REVERT: A 88 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7397 (mp) REVERT: A 304 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7271 (tp30) REVERT: A 366 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.7639 (mtt) REVERT: A 395 ARG cc_start: 0.6626 (ttm-80) cc_final: 0.6084 (ttm170) REVERT: A 606 GLU cc_start: 0.6375 (OUTLIER) cc_final: 0.6067 (tm-30) REVERT: A 786 LYS cc_start: 0.7763 (ttpt) cc_final: 0.7395 (ttpp) REVERT: B 3 VAL cc_start: 0.7040 (OUTLIER) cc_final: 0.6640 (m) REVERT: B 8 PHE cc_start: 0.7861 (t80) cc_final: 0.7570 (t80) REVERT: B 34 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7395 (mt-10) REVERT: B 95 LYS cc_start: 0.8080 (ttpp) cc_final: 0.7795 (ttpp) REVERT: B 351 ASN cc_start: 0.7936 (t0) cc_final: 0.7426 (t0) outliers start: 25 outliers final: 16 residues processed: 108 average time/residue: 0.6263 time to fit residues: 72.3299 Evaluate side-chains 110 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 703 ARG Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 849 ARG Chi-restraints excluded: chain A residue 868 SER Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 347 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 72 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 109 optimal weight: 7.9990 chunk 43 optimal weight: 0.5980 chunk 87 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 HIS A 373 ASN B 64 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.153482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.116017 restraints weight = 9609.656| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.65 r_work: 0.3024 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9197 Z= 0.124 Angle : 0.486 7.250 12461 Z= 0.252 Chirality : 0.042 0.139 1345 Planarity : 0.004 0.052 1617 Dihedral : 4.072 22.410 1211 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.48 % Allowed : 13.12 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.25), residues: 1099 helix: 1.64 (0.25), residues: 432 sheet: 0.58 (0.42), residues: 140 loop : 0.98 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 117 TYR 0.013 0.001 TYR A 921 PHE 0.012 0.001 PHE B 257 TRP 0.016 0.002 TRP A 355 HIS 0.004 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 9197) covalent geometry : angle 0.48583 (12461) hydrogen bonds : bond 0.04133 ( 415) hydrogen bonds : angle 4.41176 ( 1275) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.365 Fit side-chains REVERT: A 366 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7594 (mtt) REVERT: A 395 ARG cc_start: 0.6677 (ttm-80) cc_final: 0.6166 (ttm170) REVERT: A 606 GLU cc_start: 0.6433 (OUTLIER) cc_final: 0.6160 (tm-30) REVERT: A 619 ASP cc_start: 0.6263 (OUTLIER) cc_final: 0.5488 (t0) REVERT: A 673 LYS cc_start: 0.7767 (mttp) cc_final: 0.7300 (ptmm) REVERT: A 786 LYS cc_start: 0.7721 (ttpt) cc_final: 0.7407 (ttpp) REVERT: A 798 VAL cc_start: 0.8143 (OUTLIER) cc_final: 0.7936 (p) REVERT: B 3 VAL cc_start: 0.7027 (p) cc_final: 0.6655 (m) REVERT: B 34 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7313 (mt-10) REVERT: B 95 LYS cc_start: 0.7989 (ttpp) cc_final: 0.7727 (ttpp) REVERT: B 254 THR cc_start: 0.7778 (OUTLIER) cc_final: 0.7456 (p) REVERT: B 351 ASN cc_start: 0.7853 (t0) cc_final: 0.7359 (t0) REVERT: B 354 ARG cc_start: 0.7622 (mmt90) cc_final: 0.7411 (mmt90) outliers start: 24 outliers final: 13 residues processed: 119 average time/residue: 0.6524 time to fit residues: 82.7967 Evaluate side-chains 117 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 703 ARG Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 849 ARG Chi-restraints excluded: chain A residue 868 SER Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 315 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 16 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 89 optimal weight: 0.0050 chunk 70 optimal weight: 0.0020 chunk 99 optimal weight: 0.0370 overall best weight: 0.3280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 HIS A 373 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.156909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.119903 restraints weight = 9606.409| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.66 r_work: 0.3072 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9197 Z= 0.090 Angle : 0.448 7.171 12461 Z= 0.232 Chirality : 0.041 0.133 1345 Planarity : 0.004 0.049 1617 Dihedral : 3.788 19.817 1211 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.17 % Allowed : 13.84 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.94 (0.25), residues: 1099 helix: 1.89 (0.25), residues: 435 sheet: 0.73 (0.42), residues: 140 loop : 1.12 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 8 TYR 0.011 0.001 TYR A 921 PHE 0.011 0.001 PHE B 257 TRP 0.016 0.001 TRP A 291 HIS 0.004 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00193 ( 9197) covalent geometry : angle 0.44844 (12461) hydrogen bonds : bond 0.03592 ( 415) hydrogen bonds : angle 4.20981 ( 1275) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.396 Fit side-chains REVERT: A 88 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7388 (mp) REVERT: A 366 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7585 (mtt) REVERT: A 395 ARG cc_start: 0.6650 (ttm-80) cc_final: 0.6074 (ttm170) REVERT: A 606 GLU cc_start: 0.6491 (OUTLIER) cc_final: 0.6133 (tm-30) REVERT: A 673 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7202 (pptt) REVERT: B 3 VAL cc_start: 0.6922 (p) cc_final: 0.6555 (m) REVERT: B 34 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7234 (mt-10) REVERT: B 95 LYS cc_start: 0.7920 (ttpp) cc_final: 0.7699 (ptmm) REVERT: B 372 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7442 (mt-10) outliers start: 21 outliers final: 10 residues processed: 115 average time/residue: 0.6543 time to fit residues: 80.1878 Evaluate side-chains 110 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 673 LYS Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 703 ARG Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain A residue 868 SER Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 372 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 21 optimal weight: 3.9990 chunk 63 optimal weight: 0.3980 chunk 5 optimal weight: 3.9990 chunk 14 optimal weight: 0.2980 chunk 71 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 75 optimal weight: 0.0170 chunk 93 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 45 optimal weight: 0.2980 overall best weight: 0.4020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 HIS A 373 ASN B 64 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.157382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.120148 restraints weight = 9657.592| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.67 r_work: 0.3077 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9197 Z= 0.090 Angle : 0.451 7.715 12461 Z= 0.231 Chirality : 0.041 0.133 1345 Planarity : 0.004 0.049 1617 Dihedral : 3.699 19.117 1211 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.86 % Allowed : 14.77 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.09 (0.26), residues: 1099 helix: 2.04 (0.25), residues: 439 sheet: 0.71 (0.42), residues: 140 loop : 1.22 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 8 TYR 0.010 0.001 TYR A 921 PHE 0.010 0.001 PHE B 257 TRP 0.014 0.001 TRP A 291 HIS 0.004 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00200 ( 9197) covalent geometry : angle 0.45077 (12461) hydrogen bonds : bond 0.03541 ( 415) hydrogen bonds : angle 4.13220 ( 1275) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.457 Fit side-chains REVERT: A 88 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7339 (mp) REVERT: A 395 ARG cc_start: 0.6661 (ttm-80) cc_final: 0.6093 (ttm170) REVERT: A 606 GLU cc_start: 0.6532 (OUTLIER) cc_final: 0.6151 (tm-30) REVERT: A 619 ASP cc_start: 0.5916 (OUTLIER) cc_final: 0.5307 (t0) REVERT: A 673 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.7225 (pptt) REVERT: B 3 VAL cc_start: 0.6858 (p) cc_final: 0.6507 (m) REVERT: B 34 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7215 (mt-10) REVERT: B 95 LYS cc_start: 0.7842 (ttpp) cc_final: 0.7572 (ptmm) REVERT: B 323 LEU cc_start: 0.7144 (tt) cc_final: 0.6845 (pp) outliers start: 18 outliers final: 9 residues processed: 110 average time/residue: 0.6922 time to fit residues: 80.9626 Evaluate side-chains 108 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 673 LYS Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 703 ARG Chi-restraints excluded: chain A residue 868 SER Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 315 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 67 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 107 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 HIS A 373 ASN ** A 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.155598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.118223 restraints weight = 9561.592| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.65 r_work: 0.3050 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9197 Z= 0.116 Angle : 0.474 7.653 12461 Z= 0.242 Chirality : 0.042 0.138 1345 Planarity : 0.004 0.049 1617 Dihedral : 3.791 20.254 1211 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.86 % Allowed : 14.88 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.05 (0.25), residues: 1099 helix: 2.01 (0.25), residues: 435 sheet: 0.68 (0.42), residues: 140 loop : 1.18 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 8 TYR 0.011 0.001 TYR A 641 PHE 0.010 0.001 PHE B 257 TRP 0.013 0.001 TRP A 355 HIS 0.005 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 9197) covalent geometry : angle 0.47448 (12461) hydrogen bonds : bond 0.03859 ( 415) hydrogen bonds : angle 4.18446 ( 1275) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.304 Fit side-chains REVERT: A 88 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7349 (mp) REVERT: A 304 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7213 (tp30) REVERT: A 395 ARG cc_start: 0.6658 (ttm-80) cc_final: 0.6072 (ttm170) REVERT: A 606 GLU cc_start: 0.6502 (OUTLIER) cc_final: 0.6185 (tm-30) REVERT: A 619 ASP cc_start: 0.5939 (OUTLIER) cc_final: 0.5329 (t0) REVERT: A 673 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7245 (pptt) REVERT: B 3 VAL cc_start: 0.6860 (p) cc_final: 0.6513 (m) REVERT: B 34 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7259 (mt-10) REVERT: B 95 LYS cc_start: 0.7870 (ttpp) cc_final: 0.7626 (ptmm) REVERT: B 323 LEU cc_start: 0.7106 (tt) cc_final: 0.6812 (pp) REVERT: B 372 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7526 (mt-10) outliers start: 18 outliers final: 9 residues processed: 109 average time/residue: 0.6877 time to fit residues: 79.4478 Evaluate side-chains 108 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 673 LYS Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 703 ARG Chi-restraints excluded: chain A residue 868 SER Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 372 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 68 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 HIS ** A 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.154228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.116658 restraints weight = 9625.794| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.67 r_work: 0.3028 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9197 Z= 0.130 Angle : 0.495 8.609 12461 Z= 0.252 Chirality : 0.042 0.137 1345 Planarity : 0.004 0.050 1617 Dihedral : 3.877 21.251 1211 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.48 % Allowed : 14.46 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.02 (0.25), residues: 1099 helix: 1.98 (0.25), residues: 433 sheet: 0.63 (0.42), residues: 140 loop : 1.20 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 8 TYR 0.011 0.001 TYR A 921 PHE 0.011 0.001 PHE A 7 TRP 0.013 0.002 TRP A 355 HIS 0.005 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 9197) covalent geometry : angle 0.49490 (12461) hydrogen bonds : bond 0.03983 ( 415) hydrogen bonds : angle 4.23342 ( 1275) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.388 Fit side-chains REVERT: A 88 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7339 (mp) REVERT: A 304 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7285 (tp30) REVERT: A 395 ARG cc_start: 0.6697 (ttm-80) cc_final: 0.6089 (ttm170) REVERT: A 606 GLU cc_start: 0.6482 (OUTLIER) cc_final: 0.6188 (tm-30) REVERT: A 619 ASP cc_start: 0.5939 (OUTLIER) cc_final: 0.5293 (t0) REVERT: A 673 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7303 (pptt) REVERT: B 3 VAL cc_start: 0.6907 (p) cc_final: 0.6531 (m) REVERT: B 34 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7355 (mt-10) REVERT: B 93 LYS cc_start: 0.7743 (ttmm) cc_final: 0.7542 (mptt) REVERT: B 95 LYS cc_start: 0.7905 (ttpp) cc_final: 0.7557 (ttpp) REVERT: B 323 LEU cc_start: 0.7161 (tt) cc_final: 0.6838 (pp) outliers start: 24 outliers final: 14 residues processed: 112 average time/residue: 0.6809 time to fit residues: 81.1456 Evaluate side-chains 111 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 673 LYS Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 703 ARG Chi-restraints excluded: chain A residue 868 SER Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 347 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 86 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 6 optimal weight: 0.0040 chunk 28 optimal weight: 0.0010 chunk 45 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 94 optimal weight: 0.5980 chunk 12 optimal weight: 10.0000 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 HIS A 373 ASN ** A 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.156892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.119737 restraints weight = 9618.820| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.66 r_work: 0.3073 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9197 Z= 0.091 Angle : 0.455 8.229 12461 Z= 0.233 Chirality : 0.041 0.133 1345 Planarity : 0.004 0.060 1617 Dihedral : 3.703 19.675 1211 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.65 % Allowed : 15.50 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.12 (0.26), residues: 1099 helix: 2.09 (0.25), residues: 435 sheet: 0.70 (0.42), residues: 140 loop : 1.21 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 8 TYR 0.011 0.001 TYR A 921 PHE 0.010 0.001 PHE B 257 TRP 0.015 0.001 TRP A 291 HIS 0.005 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00203 ( 9197) covalent geometry : angle 0.45530 (12461) hydrogen bonds : bond 0.03567 ( 415) hydrogen bonds : angle 4.12924 ( 1275) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.283 Fit side-chains REVERT: A 88 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7393 (mp) REVERT: A 395 ARG cc_start: 0.6676 (ttm-80) cc_final: 0.6092 (ttm170) REVERT: A 606 GLU cc_start: 0.6538 (OUTLIER) cc_final: 0.6209 (tm-30) REVERT: A 673 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.7233 (pptt) REVERT: B 3 VAL cc_start: 0.6889 (p) cc_final: 0.6520 (m) REVERT: B 34 GLU cc_start: 0.7451 (mt-10) cc_final: 0.7203 (mt-10) REVERT: B 39 ASP cc_start: 0.8530 (t0) cc_final: 0.8162 (t70) REVERT: B 95 LYS cc_start: 0.7834 (ttpp) cc_final: 0.7625 (ptmm) REVERT: B 202 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6275 (mm-30) REVERT: B 323 LEU cc_start: 0.7144 (tt) cc_final: 0.6832 (pp) outliers start: 16 outliers final: 10 residues processed: 105 average time/residue: 0.6921 time to fit residues: 77.0195 Evaluate side-chains 107 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 673 LYS Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 703 ARG Chi-restraints excluded: chain A residue 868 SER Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 315 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 7 optimal weight: 0.0870 chunk 85 optimal weight: 3.9990 chunk 6 optimal weight: 0.0270 chunk 36 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 40 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 25 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.8220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 HIS ** A 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.155657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.118372 restraints weight = 9416.787| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.63 r_work: 0.3058 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9197 Z= 0.111 Angle : 0.471 8.240 12461 Z= 0.240 Chirality : 0.041 0.135 1345 Planarity : 0.004 0.059 1617 Dihedral : 3.745 20.217 1211 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.86 % Allowed : 15.50 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.11 (0.25), residues: 1099 helix: 2.09 (0.25), residues: 435 sheet: 0.68 (0.42), residues: 140 loop : 1.21 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 8 TYR 0.010 0.001 TYR A 921 PHE 0.010 0.001 PHE B 257 TRP 0.013 0.001 TRP A 355 HIS 0.006 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 9197) covalent geometry : angle 0.47051 (12461) hydrogen bonds : bond 0.03733 ( 415) hydrogen bonds : angle 4.15038 ( 1275) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3659.20 seconds wall clock time: 63 minutes 11.57 seconds (3791.57 seconds total)