Starting phenix.real_space_refine on Wed Mar 4 05:27:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l5j_23187/03_2026/7l5j_23187.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l5j_23187/03_2026/7l5j_23187.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7l5j_23187/03_2026/7l5j_23187.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l5j_23187/03_2026/7l5j_23187.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7l5j_23187/03_2026/7l5j_23187.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l5j_23187/03_2026/7l5j_23187.map" } resolution = 3.2 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= 0.001 sd= 0.083 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 7149 2.51 5 N 1873 2.21 5 O 2168 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11234 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2344 Classifications: {'peptide': 305} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 279} Chain: "B" Number of atoms: 2338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2338 Classifications: {'peptide': 304} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 278} Chain: "L" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1612 Classifications: {'peptide': 210} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 198} Chain: "W" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1664 Classifications: {'peptide': 220} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 204} Chain: "X" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1612 Classifications: {'peptide': 210} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 198} Chain: "Y" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1664 Classifications: {'peptide': 220} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 204} Time building chain proxies: 2.52, per 1000 atoms: 0.22 Number of scatterers: 11234 At special positions: 0 Unit cell: (112.2, 121.55, 141.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 2168 8.00 N 1873 7.00 C 7149 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " distance=2.04 Simple disulfide: pdb=" SG CYS L 133 " - pdb=" SG CYS L 193 " distance=2.03 Simple disulfide: pdb=" SG CYS W 22 " - pdb=" SG CYS W 96 " distance=2.04 Simple disulfide: pdb=" SG CYS W 146 " - pdb=" SG CYS W 201 " distance=2.03 Simple disulfide: pdb=" SG CYS X 23 " - pdb=" SG CYS X 87 " distance=2.04 Simple disulfide: pdb=" SG CYS X 133 " - pdb=" SG CYS X 193 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 96 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 146 " - pdb=" SG CYS Y 201 " 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 Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 565.6 milliseconds 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2722 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 31 sheets defined 4.9% alpha, 22.5% 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 236 through 240 removed outlier: 3.572A pdb=" N CYS A 240 " --> pdb=" O PRO A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 465 removed outlier: 3.770A pdb=" N VAL A 458 " --> pdb=" O PRO A 454 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER A 463 " --> pdb=" O SER A 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 240 removed outlier: 3.710A pdb=" N CYS B 240 " --> pdb=" O PRO B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 465 removed outlier: 3.629A pdb=" N VAL B 458 " --> pdb=" O PRO B 454 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER B 463 " --> pdb=" O SER B 459 " (cutoff:3.500A) Processing helix chain 'L' and resid 120 through 127 removed outlier: 3.749A pdb=" N GLY L 127 " --> pdb=" O GLN L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 181 through 186 removed outlier: 4.211A pdb=" N TYR L 185 " --> pdb=" O THR L 181 " (cutoff:3.500A) Processing helix chain 'W' and resid 190 through 194 removed outlier: 3.668A pdb=" N TRP W 194 " --> pdb=" O SER W 191 " (cutoff:3.500A) Processing helix chain 'X' and resid 120 through 127 removed outlier: 3.749A pdb=" N GLY X 127 " --> pdb=" O GLN X 123 " (cutoff:3.500A) Processing helix chain 'X' and resid 181 through 186 removed outlier: 4.211A pdb=" N TYR X 185 " --> pdb=" O THR X 181 " (cutoff:3.500A) Processing helix chain 'Y' and resid 190 through 194 removed outlier: 3.668A pdb=" N TRP Y 194 " --> pdb=" O SER Y 191 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 443 through 449 removed outlier: 3.835A pdb=" N ASP A 443 " --> pdb=" O ASP A 440 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU A 447 " --> pdb=" O MET A 436 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG A 431 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG A 433 " --> pdb=" O GLY A 251 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 507 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 289 through 293 removed outlier: 3.634A pdb=" N PHE A 289 " --> pdb=" O ALA A 393 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA A 291 " --> pdb=" O VAL A 391 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A 293 " --> pdb=" O GLY A 389 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY A 389 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 339 " --> pdb=" O THR A 353 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 355 through 356 Processing sheet with id=AA4, first strand: chain 'A' and resid 474 through 475 removed outlier: 3.527A pdb=" N SER A 519 " --> pdb=" O LEU A 474 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 491 through 492 removed outlier: 4.329A pdb=" N TYR A 496 " --> pdb=" O TYR A 492 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 448 through 449 removed outlier: 3.650A pdb=" N ARG B 433 " --> pdb=" O GLY B 251 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU B 507 " --> pdb=" O VAL B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 352 through 353 removed outlier: 3.792A pdb=" N VAL B 339 " --> pdb=" O THR B 353 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY B 389 " --> pdb=" O ALA B 293 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU B 356 " --> pdb=" O SER B 377 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 474 through 475 removed outlier: 3.756A pdb=" N SER B 519 " --> pdb=" O LEU B 474 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 490 through 491 Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.668A pdb=" N THR L 5 " --> pdb=" O SER L 24 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR L 70 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.704A pdb=" N GLU L 104 " --> pdb=" O MET L 11 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 52 through 53 removed outlier: 6.401A pdb=" N TRP L 34 " --> pdb=" O TRP L 46 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR L 84 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR L 96 " --> pdb=" O GLN L 89 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 131 through 132 removed outlier: 4.193A pdb=" N VAL L 131 " --> pdb=" O LEU L 178 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU L 159 " --> pdb=" O THR L 177 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 143 through 146 Processing sheet with id=AB6, first strand: chain 'L' and resid 148 through 149 Processing sheet with id=AB7, first strand: chain 'W' and resid 3 through 5 Processing sheet with id=AB8, first strand: chain 'W' and resid 11 through 12 removed outlier: 3.543A pdb=" N VAL W 12 " --> pdb=" O THR W 116 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N MET W 34 " --> pdb=" O GLN W 50 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLN W 50 " --> pdb=" O MET W 34 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TRP W 36 " --> pdb=" O ILE W 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'W' and resid 126 through 129 removed outlier: 4.028A pdb=" N LYS W 149 " --> pdb=" O SER W 126 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LYS W 149 " --> pdb=" O LEU W 183 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU W 183 " --> pdb=" O LYS W 149 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR W 182 " --> pdb=" O VAL W 175 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL W 175 " --> pdb=" O THR W 182 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'W' and resid 142 through 144 Processing sheet with id=AC2, first strand: chain 'W' and resid 157 through 160 Processing sheet with id=AC3, first strand: chain 'X' and resid 4 through 7 removed outlier: 3.669A pdb=" N THR X 5 " --> pdb=" O SER X 24 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR X 70 " --> pdb=" O CYS X 23 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'X' and resid 10 through 13 removed outlier: 3.705A pdb=" N GLU X 104 " --> pdb=" O MET X 11 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'X' and resid 52 through 53 removed outlier: 6.401A pdb=" N TRP X 34 " --> pdb=" O TRP X 46 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR X 84 " --> pdb=" O GLN X 37 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR X 96 " --> pdb=" O GLN X 89 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'X' and resid 131 through 132 removed outlier: 4.192A pdb=" N VAL X 131 " --> pdb=" O LEU X 178 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU X 159 " --> pdb=" O THR X 177 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'X' and resid 143 through 146 Processing sheet with id=AC8, first strand: chain 'X' and resid 148 through 149 Processing sheet with id=AC9, first strand: chain 'Y' and resid 3 through 5 Processing sheet with id=AD1, first strand: chain 'Y' and resid 11 through 12 removed outlier: 3.542A pdb=" N VAL Y 12 " --> pdb=" O THR Y 116 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N MET Y 34 " --> pdb=" O GLN Y 50 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N GLN Y 50 " --> pdb=" O MET Y 34 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N TRP Y 36 " --> pdb=" O ILE Y 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Y' and resid 126 through 129 removed outlier: 4.029A pdb=" N LYS Y 149 " --> pdb=" O SER Y 126 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N LYS Y 149 " --> pdb=" O LEU Y 183 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU Y 183 " --> pdb=" O LYS Y 149 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR Y 182 " --> pdb=" O VAL Y 175 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL Y 175 " --> pdb=" O THR Y 182 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Y' and resid 142 through 144 Processing sheet with id=AD4, first strand: chain 'Y' and resid 157 through 160 232 hydrogen bonds defined for protein. 576 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: 1.35 Time building geometry restraints manager: 1.20 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: 3588 1.34 - 1.46: 2956 1.46 - 1.59: 4922 1.59 - 1.71: 0 1.71 - 1.84: 64 Bond restraints: 11530 Sorted by residual: bond pdb=" C ILE X 116 " pdb=" N PHE X 117 " ideal model delta sigma weight residual 1.332 1.355 -0.024 7.50e-03 1.78e+04 9.87e+00 bond pdb=" C ILE L 116 " pdb=" N PHE L 117 " ideal model delta sigma weight residual 1.332 1.355 -0.023 7.50e-03 1.78e+04 9.80e+00 bond pdb=" CB VAL A 271 " pdb=" CG1 VAL A 271 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.60e+00 bond pdb=" CB GLU A 427 " pdb=" CG GLU A 427 " ideal model delta sigma weight residual 1.520 1.465 0.055 3.00e-02 1.11e+03 3.31e+00 bond pdb=" CB GLN W 177 " pdb=" CG GLN W 177 " ideal model delta sigma weight residual 1.520 1.570 -0.050 3.00e-02 1.11e+03 2.75e+00 ... (remaining 11525 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.31: 15686 4.31 - 8.61: 52 8.61 - 12.92: 5 12.92 - 17.22: 0 17.22 - 21.53: 1 Bond angle restraints: 15744 Sorted by residual: angle pdb=" C PHE A 423 " pdb=" N LEU A 424 " pdb=" CA LEU A 424 " ideal model delta sigma weight residual 120.69 142.22 -21.53 2.95e+00 1.15e-01 5.33e+01 angle pdb=" C GLN A 367 " pdb=" N ALA A 368 " pdb=" CA ALA A 368 " ideal model delta sigma weight residual 122.28 118.25 4.03 8.80e-01 1.29e+00 2.10e+01 angle pdb=" CA GLN X 155 " pdb=" CB GLN X 155 " pdb=" CG GLN X 155 " ideal model delta sigma weight residual 114.10 123.08 -8.98 2.00e+00 2.50e-01 2.01e+01 angle pdb=" CA GLN L 155 " pdb=" CB GLN L 155 " pdb=" CG GLN L 155 " ideal model delta sigma weight residual 114.10 123.04 -8.94 2.00e+00 2.50e-01 2.00e+01 angle pdb=" CA GLN Y 177 " pdb=" CB GLN Y 177 " pdb=" CG GLN Y 177 " ideal model delta sigma weight residual 114.10 122.54 -8.44 2.00e+00 2.50e-01 1.78e+01 ... (remaining 15739 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 6051 17.82 - 35.65: 534 35.65 - 53.47: 167 53.47 - 71.29: 85 71.29 - 89.12: 13 Dihedral angle restraints: 6850 sinusoidal: 2597 harmonic: 4253 Sorted by residual: dihedral pdb=" CA TYR W 104 " pdb=" C TYR W 104 " pdb=" N ALA W 105 " pdb=" CA ALA W 105 " ideal model delta harmonic sigma weight residual 180.00 150.91 29.09 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA TYR Y 104 " pdb=" C TYR Y 104 " pdb=" N ALA Y 105 " pdb=" CA ALA Y 105 " ideal model delta harmonic sigma weight residual 180.00 150.95 29.05 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA GLY A 302 " pdb=" C GLY A 302 " pdb=" N GLU A 303 " pdb=" CA GLU A 303 " ideal model delta harmonic sigma weight residual 180.00 -155.49 -24.51 0 5.00e+00 4.00e-02 2.40e+01 ... (remaining 6847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1106 0.038 - 0.077: 470 0.077 - 0.115: 157 0.115 - 0.153: 35 0.153 - 0.192: 3 Chirality restraints: 1771 Sorted by residual: chirality pdb=" CA ARG W 134 " pdb=" N ARG W 134 " pdb=" C ARG W 134 " pdb=" CB ARG W 134 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.17e-01 chirality pdb=" CA ARG Y 134 " pdb=" N ARG Y 134 " pdb=" C ARG Y 134 " pdb=" CB ARG Y 134 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.81e-01 chirality pdb=" CA ASN A 364 " pdb=" N ASN A 364 " pdb=" C ASN A 364 " pdb=" CB ASN A 364 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.17e-01 ... (remaining 1768 not shown) Planarity restraints: 2019 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE X 149 " -0.010 2.00e-02 2.50e+03 2.07e-02 4.29e+00 pdb=" C ILE X 149 " 0.036 2.00e-02 2.50e+03 pdb=" O ILE X 149 " -0.014 2.00e-02 2.50e+03 pdb=" N ASP X 150 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE L 149 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.26e+00 pdb=" C ILE L 149 " 0.036 2.00e-02 2.50e+03 pdb=" O ILE L 149 " -0.014 2.00e-02 2.50e+03 pdb=" N ASP L 150 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 496 " 0.023 2.00e-02 2.50e+03 1.34e-02 3.60e+00 pdb=" CG TYR B 496 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR B 496 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR B 496 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 496 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 496 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 496 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 496 " 0.004 2.00e-02 2.50e+03 ... (remaining 2016 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 417 2.66 - 3.22: 10811 3.22 - 3.78: 15754 3.78 - 4.34: 21103 4.34 - 4.90: 35604 Nonbonded interactions: 83689 Sorted by model distance: nonbonded pdb=" O PHE X 138 " pdb=" OG1 THR X 171 " model vdw 2.099 3.040 nonbonded pdb=" O PHE L 138 " pdb=" OG1 THR L 171 " model vdw 2.100 3.040 nonbonded pdb=" OG SER W 208 " pdb=" OG1 THR W 210 " model vdw 2.122 3.040 nonbonded pdb=" OG SER Y 208 " pdb=" OG1 THR Y 210 " model vdw 2.123 3.040 nonbonded pdb=" O GLN L 123 " pdb=" OG SER L 126 " model vdw 2.145 3.040 ... (remaining 83684 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 228 through 531) selection = chain 'B' } ncs_group { reference = chain 'L' selection = chain 'X' } ncs_group { reference = chain 'W' selection = chain 'Y' } 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: 1.070 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.450 Find NCS groups from input model: 0.110 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 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 : 0.008 0.063 11538 Z= 0.337 Angle : 0.882 21.527 15760 Z= 0.467 Chirality : 0.047 0.192 1771 Planarity : 0.005 0.046 2019 Dihedral : 17.033 89.118 4104 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 16.40 % Favored : 83.53 % Rotamer: Outliers : 8.54 % Allowed : 8.30 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.15 % 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: -5.48 (0.18), residues: 1457 helix: -3.12 (0.61), residues: 34 sheet: -3.14 (0.20), residues: 510 loop : -4.20 (0.16), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Y 134 TYR 0.029 0.002 TYR B 496 PHE 0.012 0.002 PHE W 172 TRP 0.019 0.002 TRP A 460 HIS 0.003 0.001 HIS B 270 Details of bonding type rmsd covalent geometry : bond 0.00761 (11530) covalent geometry : angle 0.88080 (15744) SS BOND : bond 0.00744 ( 8) SS BOND : angle 1.50878 ( 16) hydrogen bonds : bond 0.22349 ( 232) hydrogen bonds : angle 9.92878 ( 576) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 273 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.6290 (tpt) cc_final: 0.6004 (tpt) REVERT: A 385 ASP cc_start: 0.7987 (t0) cc_final: 0.7710 (t0) REVERT: A 516 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7522 (mt-10) REVERT: A 521 VAL cc_start: 0.7806 (OUTLIER) cc_final: 0.7595 (m) REVERT: B 345 LYS cc_start: 0.8207 (ptmm) cc_final: 0.7708 (pttp) REVERT: B 366 ASP cc_start: 0.5737 (m-30) cc_final: 0.5377 (t0) REVERT: B 476 ARG cc_start: 0.7410 (mtm110) cc_final: 0.7065 (ttm-80) REVERT: L 11 MET cc_start: 0.6431 (ppp) cc_final: 0.6177 (ppp) REVERT: L 26 SER cc_start: 0.7519 (OUTLIER) cc_final: 0.7189 (m) REVERT: L 146 LYS cc_start: 0.6819 (OUTLIER) cc_final: 0.5950 (tttt) REVERT: L 159 LEU cc_start: 0.6532 (tt) cc_final: 0.6148 (tt) REVERT: W 6 GLU cc_start: 0.7425 (mp0) cc_final: 0.7219 (mt-10) REVERT: W 89 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7760 (tm-30) REVERT: W 90 ASP cc_start: 0.7478 (m-30) cc_final: 0.6986 (m-30) REVERT: W 93 LEU cc_start: 0.7669 (mm) cc_final: 0.7398 (mt) REVERT: W 103 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7584 (p90) REVERT: W 142 VAL cc_start: 0.7200 (OUTLIER) cc_final: 0.6889 (m) REVERT: X 11 MET cc_start: 0.6616 (ppp) cc_final: 0.6007 (ppp) REVERT: X 31 TYR cc_start: 0.8007 (m-80) cc_final: 0.7772 (m-80) REVERT: X 121 SER cc_start: 0.5655 (OUTLIER) cc_final: 0.5353 (m) REVERT: X 178 LEU cc_start: 0.6215 (OUTLIER) cc_final: 0.5987 (tt) REVERT: X 179 THR cc_start: 0.5934 (OUTLIER) cc_final: 0.5680 (p) REVERT: Y 142 VAL cc_start: 0.4919 (OUTLIER) cc_final: 0.4446 (m) REVERT: Y 160 TRP cc_start: 0.8027 (m100) cc_final: 0.7088 (m100) REVERT: Y 177 GLN cc_start: 0.5982 (OUTLIER) cc_final: 0.5461 (pt0) REVERT: Y 184 SER cc_start: 0.7639 (OUTLIER) cc_final: 0.7193 (t) outliers start: 105 outliers final: 23 residues processed: 361 average time/residue: 0.1023 time to fit residues: 51.9758 Evaluate side-chains 198 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 164 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 146 LYS Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain W residue 21 SER Chi-restraints excluded: chain W residue 84 THR Chi-restraints excluded: chain W residue 88 SER Chi-restraints excluded: chain W residue 103 PHE Chi-restraints excluded: chain W residue 134 ARG Chi-restraints excluded: chain W residue 141 MET Chi-restraints excluded: chain W residue 142 VAL Chi-restraints excluded: chain W residue 162 SER Chi-restraints excluded: chain W residue 182 THR Chi-restraints excluded: chain W residue 193 SER Chi-restraints excluded: chain W residue 203 VAL Chi-restraints excluded: chain W residue 208 SER Chi-restraints excluded: chain W residue 214 LYS Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain X residue 121 SER Chi-restraints excluded: chain X residue 178 LEU Chi-restraints excluded: chain X residue 179 THR Chi-restraints excluded: chain X residue 209 ASN Chi-restraints excluded: chain Y residue 142 VAL Chi-restraints excluded: chain Y residue 157 THR Chi-restraints excluded: chain Y residue 171 THR Chi-restraints excluded: chain Y residue 177 GLN Chi-restraints excluded: chain Y residue 182 THR Chi-restraints excluded: chain Y residue 184 SER Chi-restraints excluded: chain Y residue 199 VAL Chi-restraints excluded: chain Y residue 203 VAL Chi-restraints excluded: chain Y residue 208 SER Chi-restraints excluded: chain Y residue 210 THR Chi-restraints excluded: chain Y residue 214 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.0170 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 overall best weight: 1.3420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN L 188 HIS ** W 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 161 ASN ** X 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 37 GLN X 188 HIS Y 39 GLN Y 202 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.189029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.130976 restraints weight = 15876.133| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 3.66 r_work: 0.3600 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11538 Z= 0.147 Angle : 0.699 10.257 15760 Z= 0.358 Chirality : 0.047 0.296 1771 Planarity : 0.005 0.042 2019 Dihedral : 7.734 84.146 1646 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.88 % Favored : 90.12 % Rotamer: Outliers : 3.91 % Allowed : 17.17 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -4.05 (0.20), residues: 1457 helix: -1.16 (0.85), residues: 36 sheet: -2.33 (0.23), residues: 476 loop : -3.12 (0.18), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG W 65 TYR 0.014 0.001 TYR Y 151 PHE 0.018 0.002 PHE A 509 TRP 0.022 0.002 TRP X 147 HIS 0.004 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00334 (11530) covalent geometry : angle 0.69630 (15744) SS BOND : bond 0.00793 ( 8) SS BOND : angle 2.11120 ( 16) hydrogen bonds : bond 0.03323 ( 232) hydrogen bonds : angle 6.67773 ( 576) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 179 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: A 385 ASP cc_start: 0.8170 (t0) cc_final: 0.7879 (t0) REVERT: A 490 LYS cc_start: 0.7413 (mtmm) cc_final: 0.6307 (mtpp) REVERT: A 521 VAL cc_start: 0.6826 (OUTLIER) cc_final: 0.6488 (m) REVERT: B 345 LYS cc_start: 0.8282 (ptmm) cc_final: 0.7904 (tmtt) REVERT: B 348 ASP cc_start: 0.7734 (t0) cc_final: 0.6252 (m-30) REVERT: B 366 ASP cc_start: 0.6346 (m-30) cc_final: 0.5696 (t70) REVERT: B 476 ARG cc_start: 0.7310 (mtm110) cc_final: 0.6764 (ttm-80) REVERT: W 89 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7786 (tm-30) REVERT: W 93 LEU cc_start: 0.7497 (mm) cc_final: 0.7278 (mt) REVERT: W 142 VAL cc_start: 0.7038 (OUTLIER) cc_final: 0.6592 (p) REVERT: W 182 THR cc_start: 0.8694 (OUTLIER) cc_final: 0.8482 (p) REVERT: W 201 CYS cc_start: 0.7536 (OUTLIER) cc_final: 0.5850 (m) REVERT: X 11 MET cc_start: 0.7056 (ppp) cc_final: 0.6282 (ppp) REVERT: X 32 MET cc_start: 0.7384 (mtt) cc_final: 0.6900 (mtt) REVERT: X 104 GLU cc_start: 0.6860 (pm20) cc_final: 0.6557 (pm20) REVERT: X 144 ASN cc_start: 0.7849 (t0) cc_final: 0.7634 (t0) REVERT: X 146 LYS cc_start: 0.7122 (ptpp) cc_final: 0.6836 (ptmt) REVERT: X 148 LYS cc_start: 0.5223 (tttt) cc_final: 0.5012 (ttpt) REVERT: X 174 MET cc_start: 0.7578 (ttt) cc_final: 0.7314 (tpp) REVERT: X 209 ASN cc_start: 0.5841 (OUTLIER) cc_final: 0.4777 (t0) REVERT: Y 22 CYS cc_start: 0.7121 (t) cc_final: 0.6386 (t) REVERT: Y 82 GLN cc_start: 0.7423 (tp40) cc_final: 0.7058 (tp40) REVERT: Y 128 TYR cc_start: 0.6296 (m-80) cc_final: 0.5878 (m-80) REVERT: Y 160 TRP cc_start: 0.8315 (m100) cc_final: 0.7753 (m100) REVERT: Y 177 GLN cc_start: 0.6224 (OUTLIER) cc_final: 0.5409 (pt0) outliers start: 48 outliers final: 20 residues processed: 217 average time/residue: 0.0938 time to fit residues: 30.1768 Evaluate side-chains 179 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain W residue 37 VAL Chi-restraints excluded: chain W residue 71 SER Chi-restraints excluded: chain W residue 84 THR Chi-restraints excluded: chain W residue 142 VAL Chi-restraints excluded: chain W residue 162 SER Chi-restraints excluded: chain W residue 182 THR Chi-restraints excluded: chain W residue 201 CYS Chi-restraints excluded: chain W residue 203 VAL Chi-restraints excluded: chain X residue 10 ILE Chi-restraints excluded: chain X residue 75 SER Chi-restraints excluded: chain X residue 116 ILE Chi-restraints excluded: chain X residue 209 ASN Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 171 THR Chi-restraints excluded: chain Y residue 177 GLN Chi-restraints excluded: chain Y residue 182 THR Chi-restraints excluded: chain Y residue 203 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 68 optimal weight: 5.9990 chunk 143 optimal weight: 10.0000 chunk 138 optimal weight: 7.9990 chunk 11 optimal weight: 0.6980 chunk 106 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 48 optimal weight: 0.0060 chunk 4 optimal weight: 8.9990 chunk 82 optimal weight: 9.9990 chunk 45 optimal weight: 8.9990 chunk 29 optimal weight: 0.0670 overall best weight: 2.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN A 402 GLN A 484 GLN B 265 GLN W 39 GLN X 37 GLN X 137 ASN ** X 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 82 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.182749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.124402 restraints weight = 15844.477| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 3.63 r_work: 0.3519 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11538 Z= 0.184 Angle : 0.677 10.215 15760 Z= 0.345 Chirality : 0.046 0.245 1771 Planarity : 0.005 0.036 2019 Dihedral : 6.413 76.630 1608 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 5.45 % Allowed : 17.66 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.15 % 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: -3.56 (0.20), residues: 1457 helix: -1.05 (0.87), residues: 37 sheet: -2.06 (0.22), residues: 529 loop : -2.71 (0.19), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 437 TYR 0.017 0.001 TYR Y 94 PHE 0.012 0.002 PHE W 152 TRP 0.019 0.002 TRP A 460 HIS 0.005 0.001 HIS L 33 Details of bonding type rmsd covalent geometry : bond 0.00432 (11530) covalent geometry : angle 0.67534 (15744) SS BOND : bond 0.00760 ( 8) SS BOND : angle 1.68416 ( 16) hydrogen bonds : bond 0.03981 ( 232) hydrogen bonds : angle 6.36130 ( 576) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 165 time to evaluate : 0.486 Fit side-chains REVERT: A 385 ASP cc_start: 0.8297 (t0) cc_final: 0.8021 (t0) REVERT: A 486 LEU cc_start: 0.6843 (OUTLIER) cc_final: 0.6390 (mp) REVERT: B 345 LYS cc_start: 0.8267 (ptmm) cc_final: 0.7842 (tmtt) REVERT: B 348 ASP cc_start: 0.7506 (t0) cc_final: 0.6173 (m-30) REVERT: B 366 ASP cc_start: 0.6295 (m-30) cc_final: 0.5678 (t70) REVERT: B 476 ARG cc_start: 0.7313 (mtm110) cc_final: 0.6788 (ttm110) REVERT: L 32 MET cc_start: 0.7564 (mmm) cc_final: 0.7284 (mtp) REVERT: L 166 ASP cc_start: 0.8078 (m-30) cc_final: 0.7336 (t0) REVERT: W 89 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7719 (tm-30) REVERT: W 93 LEU cc_start: 0.7610 (mm) cc_final: 0.7399 (mt) REVERT: W 103 PHE cc_start: 0.8035 (OUTLIER) cc_final: 0.7499 (p90) REVERT: W 142 VAL cc_start: 0.7161 (OUTLIER) cc_final: 0.6649 (p) REVERT: W 201 CYS cc_start: 0.7417 (OUTLIER) cc_final: 0.5808 (m) REVERT: X 11 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.6520 (ppp) REVERT: X 32 MET cc_start: 0.8103 (mtt) cc_final: 0.7463 (mtt) REVERT: X 78 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7323 (mt-10) REVERT: X 104 GLU cc_start: 0.7149 (pm20) cc_final: 0.6809 (pm20) REVERT: X 138 PHE cc_start: 0.7833 (p90) cc_final: 0.7228 (p90) REVERT: X 209 ASN cc_start: 0.5874 (OUTLIER) cc_final: 0.4947 (t0) REVERT: Y 6 GLU cc_start: 0.7313 (mm-30) cc_final: 0.6831 (mm-30) REVERT: Y 22 CYS cc_start: 0.6926 (t) cc_final: 0.6673 (t) REVERT: Y 82 GLN cc_start: 0.7701 (tp-100) cc_final: 0.7168 (tp-100) REVERT: Y 160 TRP cc_start: 0.8360 (m100) cc_final: 0.7791 (m100) REVERT: Y 177 GLN cc_start: 0.6581 (OUTLIER) cc_final: 0.5394 (pt0) outliers start: 67 outliers final: 38 residues processed: 215 average time/residue: 0.0818 time to fit residues: 27.0277 Evaluate side-chains 196 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 151 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain W residue 18 LEU Chi-restraints excluded: chain W residue 37 VAL Chi-restraints excluded: chain W residue 71 SER Chi-restraints excluded: chain W residue 103 PHE Chi-restraints excluded: chain W residue 141 MET Chi-restraints excluded: chain W residue 142 VAL Chi-restraints excluded: chain W residue 162 SER Chi-restraints excluded: chain W residue 201 CYS Chi-restraints excluded: chain W residue 203 VAL Chi-restraints excluded: chain W residue 210 THR Chi-restraints excluded: chain X residue 10 ILE Chi-restraints excluded: chain X residue 11 MET Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 75 SER Chi-restraints excluded: chain X residue 116 ILE Chi-restraints excluded: chain X residue 196 THR Chi-restraints excluded: chain X residue 209 ASN Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 37 VAL Chi-restraints excluded: chain Y residue 51 ILE Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 88 SER Chi-restraints excluded: chain Y residue 103 PHE Chi-restraints excluded: chain Y residue 122 THR Chi-restraints excluded: chain Y residue 177 GLN Chi-restraints excluded: chain Y residue 182 THR Chi-restraints excluded: chain Y residue 203 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 15 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 143 optimal weight: 0.4980 chunk 105 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 86 optimal weight: 0.0040 chunk 90 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 25 optimal weight: 9.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN ** X 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 165 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.187667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.129608 restraints weight = 15862.827| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 3.69 r_work: 0.3545 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11538 Z= 0.102 Angle : 0.601 13.332 15760 Z= 0.300 Chirality : 0.044 0.185 1771 Planarity : 0.004 0.063 2019 Dihedral : 5.395 65.670 1604 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 3.42 % Allowed : 20.10 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.15 % 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: -3.11 (0.21), residues: 1457 helix: -0.79 (0.86), residues: 36 sheet: -1.85 (0.22), residues: 517 loop : -2.33 (0.19), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG W 65 TYR 0.012 0.001 TYR L 139 PHE 0.012 0.001 PHE X 117 TRP 0.012 0.001 TRP A 460 HIS 0.002 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00232 (11530) covalent geometry : angle 0.60083 (15744) SS BOND : bond 0.00385 ( 8) SS BOND : angle 1.04634 ( 16) hydrogen bonds : bond 0.02857 ( 232) hydrogen bonds : angle 5.80804 ( 576) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 164 time to evaluate : 0.363 Fit side-chains REVERT: B 238 ARG cc_start: 0.8164 (ttp80) cc_final: 0.7593 (ttm110) REVERT: B 345 LYS cc_start: 0.8205 (ptmm) cc_final: 0.7456 (pttp) REVERT: B 348 ASP cc_start: 0.7501 (t0) cc_final: 0.6182 (m-30) REVERT: B 366 ASP cc_start: 0.6306 (m-30) cc_final: 0.5667 (t70) REVERT: B 476 ARG cc_start: 0.7253 (mtm110) cc_final: 0.6815 (ttm110) REVERT: L 166 ASP cc_start: 0.8054 (m-30) cc_final: 0.7283 (t0) REVERT: W 89 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7642 (tm-30) REVERT: W 93 LEU cc_start: 0.7606 (mm) cc_final: 0.7399 (mt) REVERT: W 103 PHE cc_start: 0.7937 (OUTLIER) cc_final: 0.7456 (p90) REVERT: W 141 MET cc_start: 0.6540 (mtt) cc_final: 0.6280 (mtt) REVERT: W 142 VAL cc_start: 0.7271 (OUTLIER) cc_final: 0.6737 (p) REVERT: W 201 CYS cc_start: 0.7380 (OUTLIER) cc_final: 0.5730 (m) REVERT: X 32 MET cc_start: 0.8002 (mtt) cc_final: 0.7343 (mtt) REVERT: X 78 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7253 (mt-10) REVERT: X 138 PHE cc_start: 0.7861 (p90) cc_final: 0.7229 (p90) REVERT: Y 6 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7369 (mm-30) REVERT: Y 22 CYS cc_start: 0.6779 (t) cc_final: 0.6541 (t) REVERT: Y 82 GLN cc_start: 0.7737 (tp-100) cc_final: 0.7292 (tp-100) REVERT: Y 160 TRP cc_start: 0.8331 (m100) cc_final: 0.7727 (m100) REVERT: Y 177 GLN cc_start: 0.6514 (OUTLIER) cc_final: 0.5420 (pt0) REVERT: Y 200 THR cc_start: 0.6494 (p) cc_final: 0.6254 (t) outliers start: 42 outliers final: 24 residues processed: 197 average time/residue: 0.0920 time to fit residues: 27.3729 Evaluate side-chains 181 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain W residue 71 SER Chi-restraints excluded: chain W residue 76 LYS Chi-restraints excluded: chain W residue 99 LEU Chi-restraints excluded: chain W residue 103 PHE Chi-restraints excluded: chain W residue 142 VAL Chi-restraints excluded: chain W residue 201 CYS Chi-restraints excluded: chain W residue 203 VAL Chi-restraints excluded: chain W residue 210 THR Chi-restraints excluded: chain X residue 10 ILE Chi-restraints excluded: chain X residue 75 SER Chi-restraints excluded: chain X residue 116 ILE Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 57 THR Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 88 SER Chi-restraints excluded: chain Y residue 103 PHE Chi-restraints excluded: chain Y residue 177 GLN Chi-restraints excluded: chain Y residue 203 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 103 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 105 optimal weight: 3.9990 chunk 93 optimal weight: 20.0000 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN L 137 ASN ** X 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 197 HIS ** 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 = 0.4295 r_free = 0.4295 target = 0.181614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.123661 restraints weight = 15776.020| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 3.62 r_work: 0.3509 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.4797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11538 Z= 0.174 Angle : 0.654 14.039 15760 Z= 0.329 Chirality : 0.045 0.154 1771 Planarity : 0.005 0.047 2019 Dihedral : 5.340 55.282 1600 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.30 % Favored : 89.70 % Rotamer: Outliers : 4.07 % Allowed : 20.42 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.15 % 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: -2.88 (0.21), residues: 1457 helix: -0.91 (0.83), residues: 37 sheet: -1.53 (0.22), residues: 538 loop : -2.28 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Y 65 TYR 0.014 0.001 TYR W 151 PHE 0.010 0.002 PHE B 289 TRP 0.013 0.001 TRP A 460 HIS 0.003 0.001 HIS X 33 Details of bonding type rmsd covalent geometry : bond 0.00411 (11530) covalent geometry : angle 0.65262 (15744) SS BOND : bond 0.00655 ( 8) SS BOND : angle 1.52572 ( 16) hydrogen bonds : bond 0.03568 ( 232) hydrogen bonds : angle 5.99679 ( 576) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 161 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: B 345 LYS cc_start: 0.8244 (ptmm) cc_final: 0.7834 (tmtt) REVERT: B 348 ASP cc_start: 0.7337 (t0) cc_final: 0.6034 (m-30) REVERT: B 366 ASP cc_start: 0.6494 (m-30) cc_final: 0.5736 (t70) REVERT: B 476 ARG cc_start: 0.7083 (mtm110) cc_final: 0.6571 (ttm110) REVERT: B 520 TRP cc_start: 0.5406 (m100) cc_final: 0.5146 (m100) REVERT: L 166 ASP cc_start: 0.8081 (m-30) cc_final: 0.7288 (t70) REVERT: W 28 ASP cc_start: 0.7666 (t0) cc_final: 0.7115 (t0) REVERT: W 57 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8262 (p) REVERT: W 65 ARG cc_start: 0.6982 (ttp-110) cc_final: 0.6774 (ttp-110) REVERT: W 89 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7653 (tm-30) REVERT: W 93 LEU cc_start: 0.7635 (mm) cc_final: 0.7387 (mt) REVERT: W 103 PHE cc_start: 0.8078 (OUTLIER) cc_final: 0.7367 (p90) REVERT: W 142 VAL cc_start: 0.7352 (OUTLIER) cc_final: 0.6881 (p) REVERT: W 201 CYS cc_start: 0.7337 (OUTLIER) cc_final: 0.5589 (m) REVERT: X 32 MET cc_start: 0.8363 (mtt) cc_final: 0.7679 (mtt) REVERT: X 78 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7336 (mt-10) REVERT: X 138 PHE cc_start: 0.8049 (p90) cc_final: 0.7395 (p90) REVERT: X 160 ASN cc_start: 0.6519 (p0) cc_final: 0.5160 (m-40) REVERT: Y 6 GLU cc_start: 0.7425 (mm-30) cc_final: 0.6916 (mm-30) REVERT: Y 22 CYS cc_start: 0.6721 (t) cc_final: 0.6467 (t) REVERT: Y 82 GLN cc_start: 0.7729 (tp-100) cc_final: 0.7247 (tp-100) REVERT: Y 160 TRP cc_start: 0.8199 (m100) cc_final: 0.7628 (m100) REVERT: Y 177 GLN cc_start: 0.6551 (OUTLIER) cc_final: 0.5487 (pt0) REVERT: Y 200 THR cc_start: 0.6484 (p) cc_final: 0.6228 (t) outliers start: 50 outliers final: 34 residues processed: 197 average time/residue: 0.0885 time to fit residues: 25.9193 Evaluate side-chains 190 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 151 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain W residue 37 VAL Chi-restraints excluded: chain W residue 56 SER Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain W residue 71 SER Chi-restraints excluded: chain W residue 103 PHE Chi-restraints excluded: chain W residue 142 VAL Chi-restraints excluded: chain W residue 148 VAL Chi-restraints excluded: chain W residue 156 VAL Chi-restraints excluded: chain W residue 169 VAL Chi-restraints excluded: chain W residue 201 CYS Chi-restraints excluded: chain W residue 203 VAL Chi-restraints excluded: chain W residue 210 THR Chi-restraints excluded: chain X residue 10 ILE Chi-restraints excluded: chain X residue 75 SER Chi-restraints excluded: chain X residue 103 LEU Chi-restraints excluded: chain X residue 116 ILE Chi-restraints excluded: chain X residue 167 SER Chi-restraints excluded: chain X residue 196 THR Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 103 PHE Chi-restraints excluded: chain Y residue 146 CYS Chi-restraints excluded: chain Y residue 177 GLN Chi-restraints excluded: chain Y residue 182 THR Chi-restraints excluded: chain Y residue 203 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 67 optimal weight: 10.0000 chunk 130 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 14 optimal weight: 0.0060 chunk 5 optimal weight: 0.0050 chunk 85 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.0014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN A 402 GLN W 50 GLN ** X 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 177 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.184907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.127304 restraints weight = 15760.163| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 3.63 r_work: 0.3556 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.5029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11538 Z= 0.108 Angle : 0.588 13.580 15760 Z= 0.294 Chirality : 0.043 0.148 1771 Planarity : 0.004 0.041 2019 Dihedral : 4.825 47.461 1599 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 3.74 % Allowed : 21.89 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.15 % 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: -2.60 (0.21), residues: 1457 helix: -0.48 (0.86), residues: 36 sheet: -1.32 (0.23), residues: 519 loop : -2.11 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Y 65 TYR 0.013 0.001 TYR W 151 PHE 0.009 0.001 PHE B 466 TRP 0.012 0.001 TRP A 460 HIS 0.002 0.000 HIS A 270 Details of bonding type rmsd covalent geometry : bond 0.00251 (11530) covalent geometry : angle 0.58717 (15744) SS BOND : bond 0.00391 ( 8) SS BOND : angle 0.92731 ( 16) hydrogen bonds : bond 0.02840 ( 232) hydrogen bonds : angle 5.54518 ( 576) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 161 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 471 GLU cc_start: 0.7134 (tp30) cc_final: 0.6887 (tp30) REVERT: B 238 ARG cc_start: 0.8149 (ttp80) cc_final: 0.7944 (ttm110) REVERT: B 345 LYS cc_start: 0.8154 (ptmm) cc_final: 0.7679 (pttp) REVERT: B 474 LEU cc_start: 0.7866 (mm) cc_final: 0.7634 (mm) REVERT: B 476 ARG cc_start: 0.7104 (mtm110) cc_final: 0.6649 (ttm110) REVERT: B 520 TRP cc_start: 0.5359 (m100) cc_final: 0.5133 (m100) REVERT: W 18 LEU cc_start: 0.7745 (mt) cc_final: 0.7430 (mt) REVERT: W 28 ASP cc_start: 0.7615 (t0) cc_final: 0.7073 (t0) REVERT: W 89 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7582 (tm-30) REVERT: W 103 PHE cc_start: 0.7854 (OUTLIER) cc_final: 0.7279 (p90) REVERT: W 142 VAL cc_start: 0.7266 (OUTLIER) cc_final: 0.6850 (p) REVERT: X 32 MET cc_start: 0.8293 (mtt) cc_final: 0.7650 (mtt) REVERT: X 78 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7317 (mt-10) REVERT: X 138 PHE cc_start: 0.7904 (p90) cc_final: 0.7151 (p90) REVERT: X 160 ASN cc_start: 0.6492 (p0) cc_final: 0.4998 (m-40) REVERT: Y 11 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8483 (mt) REVERT: Y 82 GLN cc_start: 0.7719 (tp-100) cc_final: 0.7346 (tp-100) REVERT: Y 160 TRP cc_start: 0.8157 (m100) cc_final: 0.7571 (m100) REVERT: Y 200 THR cc_start: 0.6465 (p) cc_final: 0.6192 (t) outliers start: 46 outliers final: 32 residues processed: 196 average time/residue: 0.0877 time to fit residues: 25.7235 Evaluate side-chains 184 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain W residue 37 VAL Chi-restraints excluded: chain W residue 55 SER Chi-restraints excluded: chain W residue 56 SER Chi-restraints excluded: chain W residue 103 PHE Chi-restraints excluded: chain W residue 142 VAL Chi-restraints excluded: chain W residue 148 VAL Chi-restraints excluded: chain W residue 169 VAL Chi-restraints excluded: chain W residue 201 CYS Chi-restraints excluded: chain W residue 203 VAL Chi-restraints excluded: chain W residue 210 THR Chi-restraints excluded: chain X residue 10 ILE Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 75 SER Chi-restraints excluded: chain X residue 103 LEU Chi-restraints excluded: chain X residue 116 ILE Chi-restraints excluded: chain X residue 196 THR Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 88 SER Chi-restraints excluded: chain Y residue 103 PHE Chi-restraints excluded: chain Y residue 146 CYS Chi-restraints excluded: chain Y residue 203 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 95 optimal weight: 7.9990 chunk 88 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 104 optimal weight: 8.9990 chunk 109 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN B 371 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 89 GLN X 155 GLN ** X 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.176357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.118882 restraints weight = 15952.218| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 3.59 r_work: 0.3450 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.5498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 11538 Z= 0.252 Angle : 0.737 15.291 15760 Z= 0.373 Chirality : 0.046 0.178 1771 Planarity : 0.005 0.044 2019 Dihedral : 5.527 38.096 1596 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.42 % Favored : 87.58 % Rotamer: Outliers : 4.64 % Allowed : 22.05 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.15 % 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: -2.84 (0.21), residues: 1457 helix: -0.97 (0.80), residues: 37 sheet: -1.42 (0.23), residues: 516 loop : -2.31 (0.19), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG W 65 TYR 0.020 0.002 TYR X 85 PHE 0.014 0.002 PHE X 95 TRP 0.018 0.002 TRP A 285 HIS 0.004 0.001 HIS B 242 Details of bonding type rmsd covalent geometry : bond 0.00598 (11530) covalent geometry : angle 0.73531 (15744) SS BOND : bond 0.00903 ( 8) SS BOND : angle 1.78170 ( 16) hydrogen bonds : bond 0.04290 ( 232) hydrogen bonds : angle 6.30163 ( 576) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 144 time to evaluate : 0.349 Fit side-chains REVERT: A 385 ASP cc_start: 0.8307 (t0) cc_final: 0.8059 (t0) REVERT: A 523 ARG cc_start: 0.5307 (mtp180) cc_final: 0.4532 (mpt180) REVERT: B 238 ARG cc_start: 0.8203 (ttp80) cc_final: 0.7982 (ttp80) REVERT: B 345 LYS cc_start: 0.8231 (ptmm) cc_final: 0.7823 (tmtt) REVERT: B 348 ASP cc_start: 0.7423 (t0) cc_final: 0.6067 (m-30) REVERT: B 476 ARG cc_start: 0.7162 (mtm110) cc_final: 0.6585 (ttm110) REVERT: L 166 ASP cc_start: 0.8050 (m-30) cc_final: 0.7383 (t70) REVERT: W 28 ASP cc_start: 0.7768 (t0) cc_final: 0.7156 (t0) REVERT: W 65 ARG cc_start: 0.6988 (ttp-110) cc_final: 0.6758 (ttp-110) REVERT: W 89 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7729 (tm-30) REVERT: W 103 PHE cc_start: 0.8211 (OUTLIER) cc_final: 0.7333 (p90) REVERT: W 142 VAL cc_start: 0.7631 (OUTLIER) cc_final: 0.7403 (p) REVERT: X 89 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8419 (pp30) REVERT: X 138 PHE cc_start: 0.8195 (p90) cc_final: 0.7428 (p90) REVERT: X 160 ASN cc_start: 0.6527 (p0) cc_final: 0.5364 (m-40) REVERT: Y 6 GLU cc_start: 0.7069 (mm-30) cc_final: 0.6491 (mm-30) REVERT: Y 20 LEU cc_start: 0.6777 (OUTLIER) cc_final: 0.6569 (mm) REVERT: Y 22 CYS cc_start: 0.6858 (t) cc_final: 0.6611 (t) REVERT: Y 82 GLN cc_start: 0.7768 (tp-100) cc_final: 0.7299 (tp-100) REVERT: Y 111 GLN cc_start: 0.8776 (tp40) cc_final: 0.8468 (tp-100) REVERT: Y 160 TRP cc_start: 0.8135 (m100) cc_final: 0.7619 (m100) outliers start: 57 outliers final: 45 residues processed: 190 average time/residue: 0.0915 time to fit residues: 26.0409 Evaluate side-chains 187 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 138 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain W residue 37 VAL Chi-restraints excluded: chain W residue 55 SER Chi-restraints excluded: chain W residue 56 SER Chi-restraints excluded: chain W residue 64 LEU Chi-restraints excluded: chain W residue 71 SER Chi-restraints excluded: chain W residue 103 PHE Chi-restraints excluded: chain W residue 142 VAL Chi-restraints excluded: chain W residue 148 VAL Chi-restraints excluded: chain W residue 156 VAL Chi-restraints excluded: chain W residue 169 VAL Chi-restraints excluded: chain W residue 203 VAL Chi-restraints excluded: chain W residue 210 THR Chi-restraints excluded: chain X residue 10 ILE Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 75 SER Chi-restraints excluded: chain X residue 89 GLN Chi-restraints excluded: chain X residue 103 LEU Chi-restraints excluded: chain X residue 183 ASP Chi-restraints excluded: chain X residue 196 THR Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 20 LEU Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 37 VAL Chi-restraints excluded: chain Y residue 55 SER Chi-restraints excluded: chain Y residue 70 ILE Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 88 SER Chi-restraints excluded: chain Y residue 103 PHE Chi-restraints excluded: chain Y residue 122 THR Chi-restraints excluded: chain Y residue 146 CYS Chi-restraints excluded: chain Y residue 182 THR Chi-restraints excluded: chain Y residue 203 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 76 optimal weight: 9.9990 chunk 38 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 chunk 137 optimal weight: 30.0000 chunk 132 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 122 optimal weight: 20.0000 chunk 29 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN A 402 GLN ** X 197 HIS ** 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 = 0.4273 r_free = 0.4273 target = 0.179421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.122091 restraints weight = 15881.738| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 3.62 r_work: 0.3492 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.5604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11538 Z= 0.161 Angle : 0.654 14.044 15760 Z= 0.328 Chirality : 0.044 0.163 1771 Planarity : 0.005 0.041 2019 Dihedral : 5.048 28.846 1596 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 4.15 % Allowed : 22.62 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.15 % 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: -2.67 (0.21), residues: 1457 helix: -0.68 (0.84), residues: 37 sheet: -1.35 (0.23), residues: 517 loop : -2.16 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG W 65 TYR 0.019 0.001 TYR L 48 PHE 0.011 0.001 PHE B 289 TRP 0.013 0.001 TRP Y 47 HIS 0.003 0.001 HIS X 33 Details of bonding type rmsd covalent geometry : bond 0.00383 (11530) covalent geometry : angle 0.65347 (15744) SS BOND : bond 0.00527 ( 8) SS BOND : angle 1.08449 ( 16) hydrogen bonds : bond 0.03477 ( 232) hydrogen bonds : angle 5.90136 ( 576) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 149 time to evaluate : 0.280 Fit side-chains REVERT: A 523 ARG cc_start: 0.5440 (mtp180) cc_final: 0.4705 (mpt-90) REVERT: B 345 LYS cc_start: 0.8167 (ptmm) cc_final: 0.7338 (pttp) REVERT: B 348 ASP cc_start: 0.7382 (t0) cc_final: 0.6063 (m-30) REVERT: B 476 ARG cc_start: 0.7158 (mtm110) cc_final: 0.6727 (ttm110) REVERT: L 166 ASP cc_start: 0.8034 (m-30) cc_final: 0.7315 (t70) REVERT: W 28 ASP cc_start: 0.7763 (t0) cc_final: 0.7221 (t0) REVERT: W 65 ARG cc_start: 0.7046 (ttp-110) cc_final: 0.6788 (ttp-110) REVERT: W 82 GLN cc_start: 0.7999 (tp40) cc_final: 0.7720 (tp40) REVERT: W 89 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7717 (tm-30) REVERT: W 90 ASP cc_start: 0.7903 (m-30) cc_final: 0.7411 (m-30) REVERT: W 103 PHE cc_start: 0.7965 (OUTLIER) cc_final: 0.7263 (p90) REVERT: W 142 VAL cc_start: 0.7446 (OUTLIER) cc_final: 0.7196 (p) REVERT: X 138 PHE cc_start: 0.8152 (p90) cc_final: 0.7301 (p90) REVERT: X 160 ASN cc_start: 0.6376 (p0) cc_final: 0.5191 (m-40) REVERT: X 167 SER cc_start: 0.5060 (OUTLIER) cc_final: 0.4550 (p) REVERT: Y 6 GLU cc_start: 0.7365 (mm-30) cc_final: 0.6856 (mm-30) REVERT: Y 11 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8416 (mt) REVERT: Y 22 CYS cc_start: 0.6855 (t) cc_final: 0.6567 (t) REVERT: Y 82 GLN cc_start: 0.7757 (tp-100) cc_final: 0.7403 (tp40) REVERT: Y 83 MET cc_start: 0.7290 (mtp) cc_final: 0.6847 (mtp) REVERT: Y 160 TRP cc_start: 0.8215 (m100) cc_final: 0.7717 (m100) outliers start: 51 outliers final: 39 residues processed: 185 average time/residue: 0.0873 time to fit residues: 24.2079 Evaluate side-chains 188 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 145 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain W residue 37 VAL Chi-restraints excluded: chain W residue 55 SER Chi-restraints excluded: chain W residue 56 SER Chi-restraints excluded: chain W residue 71 SER Chi-restraints excluded: chain W residue 103 PHE Chi-restraints excluded: chain W residue 142 VAL Chi-restraints excluded: chain W residue 148 VAL Chi-restraints excluded: chain W residue 156 VAL Chi-restraints excluded: chain W residue 169 VAL Chi-restraints excluded: chain W residue 201 CYS Chi-restraints excluded: chain W residue 203 VAL Chi-restraints excluded: chain W residue 210 THR Chi-restraints excluded: chain X residue 10 ILE Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 75 SER Chi-restraints excluded: chain X residue 103 LEU Chi-restraints excluded: chain X residue 167 SER Chi-restraints excluded: chain X residue 183 ASP Chi-restraints excluded: chain X residue 196 THR Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 37 VAL Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 88 SER Chi-restraints excluded: chain Y residue 103 PHE Chi-restraints excluded: chain Y residue 146 CYS Chi-restraints excluded: chain Y residue 182 THR Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Y residue 203 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 99 optimal weight: 6.9990 chunk 8 optimal weight: 0.0060 chunk 70 optimal weight: 9.9990 chunk 131 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 145 optimal weight: 0.5980 chunk 110 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 overall best weight: 1.0398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN A 402 GLN ** X 197 HIS ** 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 = 0.4306 r_free = 0.4306 target = 0.182898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.125870 restraints weight = 15544.172| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 3.67 r_work: 0.3539 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.5760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11538 Z= 0.111 Angle : 0.611 13.430 15760 Z= 0.304 Chirality : 0.043 0.157 1771 Planarity : 0.004 0.041 2019 Dihedral : 4.607 30.315 1596 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 3.74 % Allowed : 23.27 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.15 % 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: -2.36 (0.21), residues: 1457 helix: -0.29 (0.90), residues: 37 sheet: -1.11 (0.23), residues: 505 loop : -1.97 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG W 65 TYR 0.023 0.001 TYR L 48 PHE 0.023 0.001 PHE A 401 TRP 0.012 0.001 TRP L 46 HIS 0.003 0.001 HIS B 242 Details of bonding type rmsd covalent geometry : bond 0.00260 (11530) covalent geometry : angle 0.61099 (15744) SS BOND : bond 0.00391 ( 8) SS BOND : angle 0.76299 ( 16) hydrogen bonds : bond 0.02918 ( 232) hydrogen bonds : angle 5.48610 ( 576) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 150 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 ARG cc_start: 0.8038 (ptm160) cc_final: 0.7761 (ptm-80) REVERT: B 345 LYS cc_start: 0.8119 (ptmm) cc_final: 0.7291 (pttp) REVERT: B 348 ASP cc_start: 0.7355 (t0) cc_final: 0.5997 (m-30) REVERT: B 476 ARG cc_start: 0.7213 (mtm110) cc_final: 0.6837 (ttm110) REVERT: W 18 LEU cc_start: 0.7356 (mt) cc_final: 0.7122 (mp) REVERT: W 28 ASP cc_start: 0.7740 (t0) cc_final: 0.7195 (t0) REVERT: W 82 GLN cc_start: 0.8024 (tp40) cc_final: 0.7771 (tp40) REVERT: W 89 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7657 (tm-30) REVERT: W 90 ASP cc_start: 0.7920 (m-30) cc_final: 0.7408 (m-30) REVERT: W 103 PHE cc_start: 0.7816 (OUTLIER) cc_final: 0.7114 (p90) REVERT: X 76 ARG cc_start: 0.7389 (ttp-110) cc_final: 0.7189 (ttp-110) REVERT: X 138 PHE cc_start: 0.8028 (p90) cc_final: 0.7328 (p90) REVERT: X 167 SER cc_start: 0.5143 (OUTLIER) cc_final: 0.4666 (p) REVERT: Y 11 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8381 (mt) REVERT: Y 82 GLN cc_start: 0.7650 (tp-100) cc_final: 0.7327 (tp-100) REVERT: Y 83 MET cc_start: 0.7111 (mtp) cc_final: 0.6769 (mtp) REVERT: Y 160 TRP cc_start: 0.8121 (m100) cc_final: 0.7571 (m100) outliers start: 46 outliers final: 35 residues processed: 183 average time/residue: 0.0848 time to fit residues: 23.3483 Evaluate side-chains 186 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 148 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain W residue 37 VAL Chi-restraints excluded: chain W residue 55 SER Chi-restraints excluded: chain W residue 56 SER Chi-restraints excluded: chain W residue 71 SER Chi-restraints excluded: chain W residue 103 PHE Chi-restraints excluded: chain W residue 169 VAL Chi-restraints excluded: chain W residue 201 CYS Chi-restraints excluded: chain W residue 203 VAL Chi-restraints excluded: chain W residue 210 THR Chi-restraints excluded: chain X residue 10 ILE Chi-restraints excluded: chain X residue 75 SER Chi-restraints excluded: chain X residue 103 LEU Chi-restraints excluded: chain X residue 116 ILE Chi-restraints excluded: chain X residue 167 SER Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 88 SER Chi-restraints excluded: chain Y residue 103 PHE Chi-restraints excluded: chain Y residue 146 CYS Chi-restraints excluded: chain Y residue 182 THR Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Y residue 203 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 110 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 96 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 132 optimal weight: 8.9990 chunk 131 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 78 optimal weight: 20.0000 chunk 14 optimal weight: 7.9990 chunk 88 optimal weight: 0.9980 overall best weight: 2.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN A 402 GLN ** X 197 HIS ** 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 = 0.4311 r_free = 0.4311 target = 0.182230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.127347 restraints weight = 15588.759| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 3.42 r_work: 0.3549 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.5838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11538 Z= 0.158 Angle : 0.650 14.904 15760 Z= 0.325 Chirality : 0.044 0.163 1771 Planarity : 0.005 0.043 2019 Dihedral : 4.808 35.242 1595 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer: Outliers : 3.50 % Allowed : 23.76 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.15 % 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: -2.35 (0.21), residues: 1457 helix: -0.44 (0.86), residues: 37 sheet: -1.11 (0.23), residues: 514 loop : -1.95 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG W 65 TYR 0.019 0.001 TYR L 48 PHE 0.013 0.001 PHE A 401 TRP 0.012 0.001 TRP Y 47 HIS 0.002 0.001 HIS Y 170 Details of bonding type rmsd covalent geometry : bond 0.00377 (11530) covalent geometry : angle 0.64898 (15744) SS BOND : bond 0.00606 ( 8) SS BOND : angle 1.09248 ( 16) hydrogen bonds : bond 0.03411 ( 232) hydrogen bonds : angle 5.65296 ( 576) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 146 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 345 LYS cc_start: 0.8311 (ptmm) cc_final: 0.7860 (pttp) REVERT: B 476 ARG cc_start: 0.7515 (mtm110) cc_final: 0.7115 (ttm110) REVERT: L 166 ASP cc_start: 0.8003 (m-30) cc_final: 0.7280 (t70) REVERT: W 28 ASP cc_start: 0.7846 (t0) cc_final: 0.7398 (t0) REVERT: W 82 GLN cc_start: 0.8256 (tp40) cc_final: 0.8041 (tp40) REVERT: W 89 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7723 (tm-30) REVERT: W 90 ASP cc_start: 0.8008 (m-30) cc_final: 0.7503 (m-30) REVERT: W 103 PHE cc_start: 0.8337 (OUTLIER) cc_final: 0.7604 (p90) REVERT: X 76 ARG cc_start: 0.7565 (ttp-110) cc_final: 0.7335 (ttp-110) REVERT: X 138 PHE cc_start: 0.8339 (p90) cc_final: 0.7644 (p90) REVERT: X 167 SER cc_start: 0.5145 (OUTLIER) cc_final: 0.4636 (p) REVERT: Y 11 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8329 (mt) REVERT: Y 20 LEU cc_start: 0.6870 (OUTLIER) cc_final: 0.6658 (mm) REVERT: Y 82 GLN cc_start: 0.7742 (tp-100) cc_final: 0.7413 (tp40) REVERT: Y 160 TRP cc_start: 0.8199 (m100) cc_final: 0.7688 (m100) outliers start: 43 outliers final: 37 residues processed: 179 average time/residue: 0.0850 time to fit residues: 22.9468 Evaluate side-chains 188 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 147 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain W residue 37 VAL Chi-restraints excluded: chain W residue 55 SER Chi-restraints excluded: chain W residue 56 SER Chi-restraints excluded: chain W residue 71 SER Chi-restraints excluded: chain W residue 103 PHE Chi-restraints excluded: chain W residue 169 VAL Chi-restraints excluded: chain W residue 201 CYS Chi-restraints excluded: chain W residue 203 VAL Chi-restraints excluded: chain W residue 210 THR Chi-restraints excluded: chain X residue 10 ILE Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 75 SER Chi-restraints excluded: chain X residue 84 THR Chi-restraints excluded: chain X residue 103 LEU Chi-restraints excluded: chain X residue 116 ILE Chi-restraints excluded: chain X residue 167 SER Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 20 LEU Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 88 SER Chi-restraints excluded: chain Y residue 103 PHE Chi-restraints excluded: chain Y residue 146 CYS Chi-restraints excluded: chain Y residue 182 THR Chi-restraints excluded: chain Y residue 203 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 102 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 80 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 115 optimal weight: 10.0000 chunk 85 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN A 402 GLN W 170 HIS ** X 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.183069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.126021 restraints weight = 15740.310| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 3.68 r_work: 0.3539 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.5952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11538 Z= 0.114 Angle : 0.619 14.438 15760 Z= 0.307 Chirality : 0.043 0.157 1771 Planarity : 0.004 0.041 2019 Dihedral : 4.574 35.997 1595 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 3.50 % Allowed : 23.60 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.15 % 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: -2.20 (0.22), residues: 1457 helix: -0.40 (0.86), residues: 37 sheet: -1.02 (0.23), residues: 515 loop : -1.84 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG W 65 TYR 0.022 0.001 TYR L 48 PHE 0.013 0.001 PHE A 401 TRP 0.012 0.001 TRP L 46 HIS 0.003 0.001 HIS B 242 Details of bonding type rmsd covalent geometry : bond 0.00272 (11530) covalent geometry : angle 0.61868 (15744) SS BOND : bond 0.00407 ( 8) SS BOND : angle 0.79667 ( 16) hydrogen bonds : bond 0.02907 ( 232) hydrogen bonds : angle 5.43397 ( 576) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3095.92 seconds wall clock time: 53 minutes 35.47 seconds (3215.47 seconds total)