Starting phenix.real_space_refine on Tue Jul 29 08:12:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l5j_23187/07_2025/7l5j_23187.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l5j_23187/07_2025/7l5j_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7l5j_23187/07_2025/7l5j_23187.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l5j_23187/07_2025/7l5j_23187.map" model { file = "/net/cci-nas-00/data/ceres_data/7l5j_23187/07_2025/7l5j_23187.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l5j_23187/07_2025/7l5j_23187.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.55, per 1000 atoms: 0.58 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: 2.42 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.35 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: 3.18 Time building geometry restraints manager: 2.94 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: 0.990 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: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 26.280 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.990 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.019 0.002 TRP A 460 HIS 0.003 0.001 HIS B 270 PHE 0.012 0.002 PHE W 172 TYR 0.029 0.002 TYR B 496 ARG 0.008 0.001 ARG Y 134 Details of bonding type rmsd hydrogen bonds : bond 0.22349 ( 232) hydrogen bonds : angle 9.92878 ( 576) SS BOND : bond 0.00744 ( 8) SS BOND : angle 1.50878 ( 16) covalent geometry : bond 0.00761 (11530) covalent geometry : angle 0.88080 (15744) *********************** 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 : 1.282 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: 0.6987 (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 121 LYS cc_start: 0.7577 (OUTLIER) cc_final: 0.7366 (ttmt) 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: 0.2866 time to fit residues: 144.2726 Evaluate side-chains 199 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 164 time to evaluate : 1.526 ------------------------------------------------------------------------------- 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 121 LYS 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 123 optimal weight: 9.9990 chunk 110 optimal weight: 10.0000 chunk 61 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 114 optimal weight: 30.0000 chunk 44 optimal weight: 0.8980 chunk 69 optimal weight: 0.0980 chunk 85 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** L 188 HIS ** W 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 50 GLN 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 = 0.4374 r_free = 0.4374 target = 0.190251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.132140 restraints weight = 15762.250| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 3.69 r_work: 0.3613 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.2842 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= 0.138 Angle : 0.693 10.060 15760 Z= 0.354 Chirality : 0.046 0.302 1771 Planarity : 0.005 0.041 2019 Dihedral : 7.671 83.671 1650 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer: Outliers : 3.66 % Allowed : 17.09 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.05 (0.20), residues: 1457 helix: -1.12 (0.85), residues: 36 sheet: -2.32 (0.23), residues: 476 loop : -3.12 (0.18), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP X 147 HIS 0.004 0.001 HIS A 242 PHE 0.019 0.002 PHE A 509 TYR 0.014 0.001 TYR Y 151 ARG 0.004 0.001 ARG W 65 Details of bonding type rmsd hydrogen bonds : bond 0.03363 ( 232) hydrogen bonds : angle 6.64437 ( 576) SS BOND : bond 0.00505 ( 8) SS BOND : angle 2.21812 ( 16) covalent geometry : bond 0.00316 (11530) covalent geometry : angle 0.69020 (15744) *********************** 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 225 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 180 time to evaluate : 1.315 Fit side-chains revert: symmetry clash REVERT: A 385 ASP cc_start: 0.8166 (t0) cc_final: 0.7862 (t0) REVERT: A 490 LYS cc_start: 0.7405 (mtmm) cc_final: 0.6256 (mtpp) REVERT: A 521 VAL cc_start: 0.6825 (OUTLIER) cc_final: 0.6513 (m) REVERT: B 345 LYS cc_start: 0.8263 (ptmm) cc_final: 0.7855 (tmtt) REVERT: B 348 ASP cc_start: 0.7718 (t0) cc_final: 0.6190 (m-30) REVERT: B 366 ASP cc_start: 0.6337 (m-30) cc_final: 0.5692 (t70) REVERT: B 476 ARG cc_start: 0.7281 (mtm110) cc_final: 0.6748 (ttm-80) REVERT: W 89 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7772 (tm-30) REVERT: W 93 LEU cc_start: 0.7440 (mm) cc_final: 0.7191 (mt) REVERT: W 142 VAL cc_start: 0.7024 (OUTLIER) cc_final: 0.6580 (p) REVERT: W 182 THR cc_start: 0.8713 (OUTLIER) cc_final: 0.8481 (p) REVERT: W 201 CYS cc_start: 0.7512 (OUTLIER) cc_final: 0.6234 (p) REVERT: X 11 MET cc_start: 0.7057 (ppp) cc_final: 0.6279 (ppp) REVERT: X 32 MET cc_start: 0.7294 (mtt) cc_final: 0.6816 (mtt) REVERT: X 104 GLU cc_start: 0.6813 (pm20) cc_final: 0.6497 (pm20) REVERT: X 144 ASN cc_start: 0.7842 (t0) cc_final: 0.7638 (t0) REVERT: X 146 LYS cc_start: 0.7171 (ptpp) cc_final: 0.6886 (ptmt) REVERT: X 148 LYS cc_start: 0.5265 (tttt) cc_final: 0.5063 (ttpt) REVERT: X 209 ASN cc_start: 0.5932 (OUTLIER) cc_final: 0.4858 (t0) REVERT: Y 22 CYS cc_start: 0.7064 (t) cc_final: 0.6345 (t) REVERT: Y 128 TYR cc_start: 0.6331 (m-80) cc_final: 0.5908 (m-80) REVERT: Y 160 TRP cc_start: 0.8296 (m100) cc_final: 0.7701 (m100) REVERT: Y 177 GLN cc_start: 0.6223 (OUTLIER) cc_final: 0.5405 (pt0) outliers start: 45 outliers final: 19 residues processed: 216 average time/residue: 0.3143 time to fit residues: 98.8066 Evaluate side-chains 176 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 1.581 ------------------------------------------------------------------------------- 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 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 82 optimal weight: 8.9990 chunk 16 optimal weight: 0.9990 chunk 123 optimal weight: 0.0980 chunk 107 optimal weight: 6.9990 chunk 78 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 105 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 120 optimal weight: 20.0000 chunk 104 optimal weight: 8.9990 chunk 111 optimal weight: 0.7980 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 37 GLN X 137 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.191495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.133428 restraints weight = 15824.855| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 3.70 r_work: 0.3627 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11538 Z= 0.106 Angle : 0.598 10.559 15760 Z= 0.302 Chirality : 0.044 0.233 1771 Planarity : 0.004 0.034 2019 Dihedral : 5.969 77.629 1608 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 4.07 % Allowed : 18.14 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.20), residues: 1457 helix: -0.73 (0.91), residues: 36 sheet: -2.09 (0.21), residues: 535 loop : -2.57 (0.19), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 460 HIS 0.001 0.000 HIS B 242 PHE 0.017 0.001 PHE A 509 TYR 0.009 0.001 TYR W 95 ARG 0.005 0.000 ARG W 65 Details of bonding type rmsd hydrogen bonds : bond 0.03056 ( 232) hydrogen bonds : angle 5.87063 ( 576) SS BOND : bond 0.00337 ( 8) SS BOND : angle 1.33431 ( 16) covalent geometry : bond 0.00242 (11530) covalent geometry : angle 0.59697 (15744) *********************** 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 217 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 167 time to evaluate : 1.265 Fit side-chains REVERT: A 276 LEU cc_start: 0.8040 (mt) cc_final: 0.7830 (mt) REVERT: A 402 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7815 (pt0) REVERT: B 345 LYS cc_start: 0.8157 (ptmm) cc_final: 0.7441 (pttp) REVERT: B 348 ASP cc_start: 0.7491 (t0) cc_final: 0.6151 (m-30) REVERT: B 366 ASP cc_start: 0.6178 (m-30) cc_final: 0.5643 (t70) REVERT: B 476 ARG cc_start: 0.7192 (mtm110) cc_final: 0.6738 (ttm110) REVERT: B 524 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7027 (pt) REVERT: L 166 ASP cc_start: 0.8096 (m-30) cc_final: 0.7357 (t0) REVERT: W 65 ARG cc_start: 0.7434 (ttp-110) cc_final: 0.7171 (ttp-110) REVERT: W 89 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7732 (tm-30) REVERT: W 142 VAL cc_start: 0.7228 (OUTLIER) cc_final: 0.6702 (p) REVERT: W 176 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.7099 (tt) REVERT: W 201 CYS cc_start: 0.7335 (OUTLIER) cc_final: 0.6082 (p) REVERT: X 11 MET cc_start: 0.7266 (ppp) cc_final: 0.6862 (ppp) REVERT: X 32 MET cc_start: 0.7420 (mtt) cc_final: 0.6841 (mtt) REVERT: X 78 GLU cc_start: 0.7455 (mm-30) cc_final: 0.6784 (mt-10) REVERT: X 104 GLU cc_start: 0.6903 (pm20) cc_final: 0.6694 (pm20) REVERT: X 138 PHE cc_start: 0.7486 (p90) cc_final: 0.7257 (p90) REVERT: X 148 LYS cc_start: 0.5168 (tttt) cc_final: 0.4872 (ttpt) REVERT: X 172 TYR cc_start: 0.7472 (m-10) cc_final: 0.7151 (m-10) REVERT: X 209 ASN cc_start: 0.5913 (OUTLIER) cc_final: 0.4947 (t0) REVERT: Y 82 GLN cc_start: 0.7484 (tp40) cc_final: 0.7025 (tp-100) REVERT: Y 160 TRP cc_start: 0.8285 (m100) cc_final: 0.7697 (m100) REVERT: Y 177 GLN cc_start: 0.6407 (OUTLIER) cc_final: 0.5424 (pt0) REVERT: Y 200 THR cc_start: 0.6505 (p) cc_final: 0.6244 (t) outliers start: 50 outliers final: 21 residues processed: 204 average time/residue: 0.2124 time to fit residues: 64.8887 Evaluate side-chains 178 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 304 VAL 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 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 75 SER Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain W residue 18 LEU 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 176 LEU 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 X residue 209 ASN Chi-restraints excluded: chain Y residue 11 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 57 optimal weight: 0.0020 chunk 105 optimal weight: 0.9990 chunk 137 optimal weight: 0.5980 chunk 25 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 106 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 142 optimal weight: 7.9990 chunk 118 optimal weight: 10.0000 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN A 266 ASN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.190065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.132114 restraints weight = 15621.091| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 3.65 r_work: 0.3612 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11538 Z= 0.109 Angle : 0.598 13.460 15760 Z= 0.297 Chirality : 0.043 0.176 1771 Planarity : 0.004 0.036 2019 Dihedral : 5.283 70.291 1603 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 4.15 % Allowed : 18.80 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.21), residues: 1457 helix: -0.68 (0.89), residues: 36 sheet: -1.71 (0.23), residues: 487 loop : -2.33 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 460 HIS 0.002 0.000 HIS Y 170 PHE 0.012 0.001 PHE X 117 TYR 0.014 0.001 TYR B 496 ARG 0.006 0.000 ARG Y 65 Details of bonding type rmsd hydrogen bonds : bond 0.02888 ( 232) hydrogen bonds : angle 5.59533 ( 576) SS BOND : bond 0.00527 ( 8) SS BOND : angle 1.48123 ( 16) covalent geometry : bond 0.00253 (11530) covalent geometry : angle 0.59637 (15744) *********************** 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 216 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 165 time to evaluate : 1.339 Fit side-chains REVERT: A 471 GLU cc_start: 0.6916 (tp30) cc_final: 0.6610 (tp30) REVERT: B 238 ARG cc_start: 0.7925 (ttp80) cc_final: 0.7425 (ttm110) REVERT: B 345 LYS cc_start: 0.8181 (ptmm) cc_final: 0.7796 (tmtt) REVERT: B 348 ASP cc_start: 0.7450 (t0) cc_final: 0.6159 (m-30) REVERT: B 366 ASP cc_start: 0.6295 (m-30) cc_final: 0.5778 (t70) REVERT: B 476 ARG cc_start: 0.7138 (mtm110) cc_final: 0.6717 (ttm110) REVERT: B 524 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7117 (pt) REVERT: L 166 ASP cc_start: 0.8088 (m-30) cc_final: 0.7303 (t0) REVERT: W 65 ARG cc_start: 0.7440 (ttp-110) cc_final: 0.7103 (ttp-110) REVERT: W 89 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7699 (tm-30) REVERT: W 142 VAL cc_start: 0.7094 (OUTLIER) cc_final: 0.6610 (p) REVERT: W 201 CYS cc_start: 0.7295 (OUTLIER) cc_final: 0.6034 (p) REVERT: X 11 MET cc_start: 0.7462 (OUTLIER) cc_final: 0.7094 (ppp) REVERT: X 32 MET cc_start: 0.7626 (mtt) cc_final: 0.7042 (mtt) REVERT: X 78 GLU cc_start: 0.7495 (mm-30) cc_final: 0.6740 (mt-10) REVERT: X 104 GLU cc_start: 0.7052 (pm20) cc_final: 0.6775 (pm20) REVERT: X 138 PHE cc_start: 0.7591 (p90) cc_final: 0.7367 (p90) REVERT: X 172 TYR cc_start: 0.7592 (m-10) cc_final: 0.7292 (m-10) REVERT: Y 34 MET cc_start: 0.8503 (mtt) cc_final: 0.8296 (mtt) REVERT: Y 82 GLN cc_start: 0.7703 (tp40) cc_final: 0.7191 (tp-100) REVERT: Y 96 CYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7659 (p) REVERT: Y 160 TRP cc_start: 0.8278 (m100) cc_final: 0.7633 (m100) REVERT: Y 177 GLN cc_start: 0.6265 (OUTLIER) cc_final: 0.5271 (pt0) REVERT: Y 200 THR cc_start: 0.6390 (p) cc_final: 0.6136 (t) outliers start: 51 outliers final: 29 residues processed: 202 average time/residue: 0.2031 time to fit residues: 61.5078 Evaluate side-chains 189 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 467 THR 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 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 56 SER Chi-restraints excluded: chain W residue 71 SER Chi-restraints excluded: chain W residue 99 LEU 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 11 MET Chi-restraints excluded: chain X residue 75 SER Chi-restraints excluded: chain X residue 116 ILE Chi-restraints excluded: chain X residue 159 LEU Chi-restraints excluded: chain X residue 196 THR Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 96 CYS Chi-restraints excluded: chain Y residue 103 PHE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 38 optimal weight: 5.9990 chunk 114 optimal weight: 20.0000 chunk 83 optimal weight: 4.9990 chunk 133 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 14 optimal weight: 0.0030 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 7.9990 overall best weight: 3.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 402 GLN A 484 GLN B 261 ASN B 265 GLN L 137 ASN W 39 GLN W 50 GLN X 36 GLN X 89 GLN X 155 GLN ** X 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 82 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.180014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.120631 restraints weight = 15824.794| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 3.74 r_work: 0.3460 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.4959 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 : 0.745 13.971 15760 Z= 0.380 Chirality : 0.047 0.179 1771 Planarity : 0.005 0.035 2019 Dihedral : 5.945 60.556 1600 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.46 % Favored : 88.54 % Rotamer: Outliers : 4.48 % Allowed : 20.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.21), residues: 1457 helix: -1.43 (0.77), residues: 37 sheet: -1.55 (0.23), residues: 500 loop : -2.42 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 285 HIS 0.004 0.001 HIS L 33 PHE 0.013 0.002 PHE X 95 TYR 0.023 0.002 TYR X 85 ARG 0.005 0.001 ARG B 437 Details of bonding type rmsd hydrogen bonds : bond 0.04221 ( 232) hydrogen bonds : angle 6.40536 ( 576) SS BOND : bond 0.01042 ( 8) SS BOND : angle 2.27039 ( 16) covalent geometry : bond 0.00595 (11530) covalent geometry : angle 0.74136 (15744) *********************** 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: 55 poor density : 156 time to evaluate : 1.115 Fit side-chains REVERT: A 385 ASP cc_start: 0.8350 (t0) cc_final: 0.8104 (t0) REVERT: A 486 LEU cc_start: 0.6757 (OUTLIER) cc_final: 0.6181 (mp) REVERT: B 326 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8255 (mp) REVERT: B 345 LYS cc_start: 0.8234 (ptmm) cc_final: 0.7939 (tmtt) REVERT: B 476 ARG cc_start: 0.7149 (mtm110) cc_final: 0.6646 (ttm110) REVERT: L 166 ASP cc_start: 0.7992 (m-30) cc_final: 0.7356 (t70) REVERT: W 28 ASP cc_start: 0.7731 (t0) cc_final: 0.7202 (t0) REVERT: W 89 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7728 (tm-30) REVERT: W 103 PHE cc_start: 0.8124 (OUTLIER) cc_final: 0.7259 (p90) REVERT: W 142 VAL cc_start: 0.7351 (OUTLIER) cc_final: 0.6959 (p) REVERT: W 201 CYS cc_start: 0.7501 (OUTLIER) cc_final: 0.5834 (m) REVERT: X 11 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.7347 (ppp) REVERT: X 32 MET cc_start: 0.8499 (mtt) cc_final: 0.7800 (mtt) REVERT: X 89 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8546 (pp30) REVERT: X 138 PHE cc_start: 0.8071 (p90) cc_final: 0.7350 (p90) REVERT: X 160 ASN cc_start: 0.6853 (p0) cc_final: 0.5581 (m-40) REVERT: X 166 ASP cc_start: 0.6686 (OUTLIER) cc_final: 0.6479 (m-30) REVERT: Y 160 TRP cc_start: 0.8180 (m100) cc_final: 0.7635 (m100) outliers start: 55 outliers final: 34 residues processed: 195 average time/residue: 0.1868 time to fit residues: 54.9163 Evaluate side-chains 181 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 139 time to evaluate : 1.115 ------------------------------------------------------------------------------- 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 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 B residue 234 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 357 MET 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 18 LEU Chi-restraints excluded: chain W residue 37 VAL 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 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 89 GLN Chi-restraints excluded: chain X residue 116 ILE Chi-restraints excluded: chain X residue 166 ASP Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 70 ILE 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 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 111 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 144 optimal weight: 10.0000 chunk 48 optimal weight: 0.6980 chunk 104 optimal weight: 8.9990 chunk 51 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN W 50 GLN X 165 GLN X 188 HIS ** X 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 209 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.183496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.125748 restraints weight = 15747.889| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 3.71 r_work: 0.3532 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.5167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11538 Z= 0.116 Angle : 0.617 12.725 15760 Z= 0.310 Chirality : 0.044 0.154 1771 Planarity : 0.005 0.068 2019 Dihedral : 5.076 48.614 1599 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 4.23 % Allowed : 21.07 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.21), residues: 1457 helix: -0.82 (0.83), residues: 37 sheet: -1.42 (0.24), residues: 489 loop : -2.13 (0.19), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Y 47 HIS 0.006 0.001 HIS X 188 PHE 0.010 0.001 PHE B 466 TYR 0.013 0.001 TYR W 151 ARG 0.004 0.000 ARG X 90 Details of bonding type rmsd hydrogen bonds : bond 0.03051 ( 232) hydrogen bonds : angle 5.70239 ( 576) SS BOND : bond 0.00351 ( 8) SS BOND : angle 1.12213 ( 16) covalent geometry : bond 0.00268 (11530) covalent geometry : angle 0.61635 (15744) *********************** 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 210 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 158 time to evaluate : 1.224 Fit side-chains REVERT: A 402 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7751 (pt0) REVERT: A 523 ARG cc_start: 0.5325 (mtp180) cc_final: 0.4730 (mpt180) REVERT: B 345 LYS cc_start: 0.8108 (ptmm) cc_final: 0.7636 (pttp) REVERT: B 476 ARG cc_start: 0.7086 (mtm110) cc_final: 0.6555 (ttm110) REVERT: B 520 TRP cc_start: 0.5171 (m100) cc_final: 0.4929 (m100) REVERT: L 166 ASP cc_start: 0.7972 (m-30) cc_final: 0.7197 (t70) REVERT: W 65 ARG cc_start: 0.7307 (ttm110) cc_final: 0.6883 (ttp-110) REVERT: W 89 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7690 (tm-30) REVERT: W 103 PHE cc_start: 0.7878 (OUTLIER) cc_final: 0.7190 (p90) REVERT: W 141 MET cc_start: 0.6082 (tpp) cc_final: 0.5878 (tpp) REVERT: W 142 VAL cc_start: 0.7418 (OUTLIER) cc_final: 0.7077 (p) REVERT: X 32 MET cc_start: 0.8406 (mtt) cc_final: 0.7728 (mtt) REVERT: X 138 PHE cc_start: 0.8026 (p90) cc_final: 0.7303 (p90) REVERT: X 160 ASN cc_start: 0.6535 (p0) cc_final: 0.5043 (m-40) REVERT: X 209 ASN cc_start: 0.5823 (OUTLIER) cc_final: 0.5556 (m-40) REVERT: Y 82 GLN cc_start: 0.7779 (tp-100) cc_final: 0.7222 (tp-100) REVERT: Y 160 TRP cc_start: 0.8205 (m100) cc_final: 0.7508 (m100) REVERT: Y 177 GLN cc_start: 0.6421 (OUTLIER) cc_final: 0.5587 (pt0) outliers start: 52 outliers final: 33 residues processed: 197 average time/residue: 0.2205 time to fit residues: 63.9573 Evaluate side-chains 185 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 147 time to evaluate : 1.153 ------------------------------------------------------------------------------- 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 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 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 W residue 37 VAL Chi-restraints excluded: chain W residue 55 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 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 19 VAL 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 11 LEU Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 51 ILE 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 177 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 73 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 122 optimal weight: 0.2980 chunk 79 optimal weight: 7.9990 chunk 145 optimal weight: 9.9990 chunk 121 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 chunk 60 optimal weight: 9.9990 chunk 110 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- 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 = 0.4267 r_free = 0.4267 target = 0.178528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.121181 restraints weight = 15959.847| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 3.62 r_work: 0.3477 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.5448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 11538 Z= 0.197 Angle : 0.687 15.766 15760 Z= 0.345 Chirality : 0.045 0.163 1771 Planarity : 0.005 0.057 2019 Dihedral : 5.289 41.582 1599 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.12 % Favored : 88.88 % Rotamer: Outliers : 4.31 % Allowed : 21.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.21), residues: 1457 helix: -1.03 (0.80), residues: 37 sheet: -1.32 (0.23), residues: 505 loop : -2.24 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP Y 47 HIS 0.005 0.001 HIS X 188 PHE 0.011 0.002 PHE B 289 TYR 0.016 0.001 TYR X 85 ARG 0.003 0.001 ARG B 437 Details of bonding type rmsd hydrogen bonds : bond 0.03888 ( 232) hydrogen bonds : angle 5.98706 ( 576) SS BOND : bond 0.00744 ( 8) SS BOND : angle 2.18582 ( 16) covalent geometry : bond 0.00469 (11530) covalent geometry : angle 0.68355 (15744) *********************** 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 200 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 147 time to evaluate : 1.219 Fit side-chains REVERT: A 471 GLU cc_start: 0.7018 (tp30) cc_final: 0.6676 (tp30) REVERT: A 523 ARG cc_start: 0.5336 (mtp180) cc_final: 0.4679 (mpt180) REVERT: B 238 ARG cc_start: 0.7981 (ttm110) cc_final: 0.7737 (ttm110) REVERT: B 345 LYS cc_start: 0.8216 (ptmm) cc_final: 0.7842 (tmtt) REVERT: B 348 ASP cc_start: 0.7394 (t0) cc_final: 0.6087 (m-30) REVERT: B 447 GLU cc_start: 0.7484 (tm-30) cc_final: 0.7269 (tm-30) REVERT: B 476 ARG cc_start: 0.7183 (mtm110) cc_final: 0.6708 (ttm110) REVERT: L 141 LYS cc_start: 0.7394 (tttm) cc_final: 0.7192 (mttt) REVERT: L 166 ASP cc_start: 0.7996 (m-30) cc_final: 0.7342 (t70) REVERT: W 28 ASP cc_start: 0.7765 (t0) cc_final: 0.7193 (t0) REVERT: W 89 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7671 (tm-30) REVERT: W 103 PHE cc_start: 0.8083 (OUTLIER) cc_final: 0.7291 (p90) REVERT: W 142 VAL cc_start: 0.7655 (OUTLIER) cc_final: 0.7371 (p) REVERT: X 104 GLU cc_start: 0.7856 (pm20) cc_final: 0.7530 (pm20) REVERT: X 138 PHE cc_start: 0.8119 (p90) cc_final: 0.7313 (p90) REVERT: X 160 ASN cc_start: 0.6455 (p0) cc_final: 0.5302 (m-40) REVERT: X 209 ASN cc_start: 0.5972 (OUTLIER) cc_final: 0.5594 (m-40) REVERT: Y 82 GLN cc_start: 0.7777 (tp-100) cc_final: 0.7250 (tp-100) REVERT: Y 83 MET cc_start: 0.7243 (OUTLIER) cc_final: 0.6951 (mtp) REVERT: Y 160 TRP cc_start: 0.8194 (m100) cc_final: 0.7613 (m100) REVERT: Y 177 GLN cc_start: 0.6341 (OUTLIER) cc_final: 0.5235 (mt0) outliers start: 53 outliers final: 41 residues processed: 186 average time/residue: 0.2034 time to fit residues: 56.5038 Evaluate side-chains 188 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 142 time to evaluate : 1.240 ------------------------------------------------------------------------------- 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 402 GLN Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 357 MET 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 57 THR 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 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 116 ILE 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 X residue 209 ASN Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 83 MET 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 177 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 71 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 2 optimal weight: 0.4980 chunk 112 optimal weight: 5.9990 chunk 5 optimal weight: 0.1980 chunk 78 optimal weight: 20.0000 chunk 103 optimal weight: 0.0000 chunk 111 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 402 GLN ** X 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 177 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.185412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.128074 restraints weight = 15670.409| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 3.72 r_work: 0.3563 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.5555 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= 0.101 Angle : 0.604 12.498 15760 Z= 0.300 Chirality : 0.043 0.153 1771 Planarity : 0.004 0.049 2019 Dihedral : 4.665 30.356 1599 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 3.17 % Allowed : 23.19 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.22), residues: 1457 helix: -0.52 (0.87), residues: 37 sheet: -1.17 (0.24), residues: 493 loop : -1.93 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Y 47 HIS 0.003 0.001 HIS B 242 PHE 0.011 0.001 PHE B 466 TYR 0.013 0.001 TYR W 151 ARG 0.003 0.000 ARG Y 101 Details of bonding type rmsd hydrogen bonds : bond 0.02836 ( 232) hydrogen bonds : angle 5.38542 ( 576) SS BOND : bond 0.00276 ( 8) SS BOND : angle 1.30419 ( 16) covalent geometry : bond 0.00231 (11530) covalent geometry : angle 0.60298 (15744) *********************** 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 194 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 155 time to evaluate : 1.171 Fit side-chains REVERT: A 471 GLU cc_start: 0.7012 (tp30) cc_final: 0.6794 (tp30) REVERT: B 238 ARG cc_start: 0.7906 (ttm110) cc_final: 0.7309 (ttp-110) REVERT: B 345 LYS cc_start: 0.8099 (ptmm) cc_final: 0.7311 (pttp) REVERT: B 348 ASP cc_start: 0.7316 (t0) cc_final: 0.5965 (m-30) REVERT: B 476 ARG cc_start: 0.7102 (mtm110) cc_final: 0.6634 (ttm110) REVERT: L 166 ASP cc_start: 0.7898 (m-30) cc_final: 0.7213 (t70) REVERT: W 28 ASP cc_start: 0.7722 (t0) cc_final: 0.7135 (t0) REVERT: W 89 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7604 (tm-30) REVERT: W 103 PHE cc_start: 0.7751 (OUTLIER) cc_final: 0.7163 (p90) REVERT: X 138 PHE cc_start: 0.7980 (p90) cc_final: 0.7271 (p90) REVERT: Y 11 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8453 (mt) REVERT: Y 82 GLN cc_start: 0.7712 (tp-100) cc_final: 0.7244 (tp-100) REVERT: Y 160 TRP cc_start: 0.8126 (m100) cc_final: 0.7537 (m100) outliers start: 39 outliers final: 31 residues processed: 183 average time/residue: 0.1954 time to fit residues: 53.9473 Evaluate side-chains 185 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 1.145 ------------------------------------------------------------------------------- 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 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 103 PHE 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 116 ILE Chi-restraints excluded: chain X residue 183 ASP Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 22 CYS 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 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 58 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 142 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 B 371 GLN X 89 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 = 0.4262 r_free = 0.4262 target = 0.178988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.120027 restraints weight = 16068.654| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 3.77 r_work: 0.3455 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.5773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 11538 Z= 0.239 Angle : 0.718 15.451 15760 Z= 0.361 Chirality : 0.046 0.164 1771 Planarity : 0.005 0.051 2019 Dihedral : 5.206 33.594 1595 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.81 % Favored : 88.19 % Rotamer: Outliers : 3.82 % Allowed : 22.78 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.21), residues: 1457 helix: -0.98 (0.80), residues: 37 sheet: -1.30 (0.23), residues: 526 loop : -2.09 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 285 HIS 0.005 0.002 HIS X 188 PHE 0.013 0.002 PHE X 95 TYR 0.016 0.002 TYR X 85 ARG 0.005 0.001 ARG W 65 Details of bonding type rmsd hydrogen bonds : bond 0.04070 ( 232) hydrogen bonds : angle 6.01123 ( 576) SS BOND : bond 0.00772 ( 8) SS BOND : angle 2.17892 ( 16) covalent geometry : bond 0.00569 (11530) covalent geometry : angle 0.71521 (15744) *********************** 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 193 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 146 time to evaluate : 1.335 Fit side-chains revert: symmetry clash REVERT: A 523 ARG cc_start: 0.5211 (mtp180) cc_final: 0.4568 (mpt180) REVERT: B 238 ARG cc_start: 0.8026 (ttm110) cc_final: 0.7800 (ttm110) REVERT: B 345 LYS cc_start: 0.8219 (ptmm) cc_final: 0.7979 (tmtt) REVERT: B 473 LEU cc_start: 0.6659 (OUTLIER) cc_final: 0.5904 (tt) REVERT: B 476 ARG cc_start: 0.7201 (mtm110) cc_final: 0.6713 (ttm110) REVERT: L 166 ASP cc_start: 0.7928 (m-30) cc_final: 0.7343 (t70) REVERT: W 18 LEU cc_start: 0.8148 (mt) cc_final: 0.7920 (mt) REVERT: W 28 ASP cc_start: 0.7784 (t0) cc_final: 0.7146 (t0) REVERT: W 65 ARG cc_start: 0.7490 (ttp-110) cc_final: 0.7082 (ttp-110) REVERT: W 89 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7692 (tm-30) REVERT: W 103 PHE cc_start: 0.8135 (OUTLIER) cc_final: 0.7290 (p90) REVERT: X 89 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8372 (pp30) REVERT: X 138 PHE cc_start: 0.8137 (p90) cc_final: 0.7313 (p90) REVERT: Y 6 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7204 (mm-30) REVERT: Y 11 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8479 (mt) REVERT: Y 82 GLN cc_start: 0.7756 (tp-100) cc_final: 0.7368 (tp-100) REVERT: Y 160 TRP cc_start: 0.8136 (m100) cc_final: 0.7654 (m100) outliers start: 47 outliers final: 36 residues processed: 181 average time/residue: 0.2488 time to fit residues: 66.1816 Evaluate side-chains 181 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 141 time to evaluate : 1.227 ------------------------------------------------------------------------------- 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 B residue 354 THR Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 494 GLU 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 103 PHE Chi-restraints excluded: chain W residue 169 VAL Chi-restraints excluded: chain W residue 202 ASN 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 167 SER Chi-restraints excluded: chain X residue 183 ASP Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 22 CYS Chi-restraints excluded: chain Y residue 25 SER 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 76 optimal weight: 8.9990 chunk 93 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 66 optimal weight: 0.0020 chunk 71 optimal weight: 0.9990 overall best weight: 1.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN W 170 HIS ** 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 = 0.4292 r_free = 0.4292 target = 0.181350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.124207 restraints weight = 15815.987| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 3.67 r_work: 0.3517 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 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 : 0.003 0.034 11538 Z= 0.129 Angle : 0.643 15.004 15760 Z= 0.321 Chirality : 0.044 0.344 1771 Planarity : 0.005 0.048 2019 Dihedral : 4.838 31.582 1595 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 2.85 % Allowed : 24.00 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.21), residues: 1457 helix: -0.68 (0.83), residues: 37 sheet: -1.26 (0.23), residues: 525 loop : -1.92 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Y 47 HIS 0.004 0.001 HIS X 188 PHE 0.009 0.001 PHE A 509 TYR 0.012 0.001 TYR W 151 ARG 0.007 0.000 ARG W 65 Details of bonding type rmsd hydrogen bonds : bond 0.03204 ( 232) hydrogen bonds : angle 5.64966 ( 576) SS BOND : bond 0.00444 ( 8) SS BOND : angle 1.75336 ( 16) covalent geometry : bond 0.00305 (11530) covalent geometry : angle 0.64078 (15744) ********************** 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 187 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 152 time to evaluate : 3.105 Fit side-chains revert: symmetry clash REVERT: B 238 ARG cc_start: 0.7999 (ttm110) cc_final: 0.7799 (ttm110) REVERT: B 345 LYS cc_start: 0.8193 (ptmm) cc_final: 0.7696 (pttp) REVERT: B 476 ARG cc_start: 0.7146 (mtm110) cc_final: 0.6642 (ttm110) REVERT: L 166 ASP cc_start: 0.7908 (m-30) cc_final: 0.7188 (t70) REVERT: W 18 LEU cc_start: 0.8120 (mt) cc_final: 0.7652 (mp) REVERT: W 28 ASP cc_start: 0.7733 (t0) cc_final: 0.7164 (t0) REVERT: W 65 ARG cc_start: 0.7453 (ttp-110) cc_final: 0.7051 (ttp-110) REVERT: W 89 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7675 (tm-30) REVERT: W 90 ASP cc_start: 0.7917 (m-30) cc_final: 0.7428 (m-30) REVERT: W 103 PHE cc_start: 0.7869 (OUTLIER) cc_final: 0.7096 (p90) REVERT: X 138 PHE cc_start: 0.8099 (p90) cc_final: 0.7237 (p90) REVERT: X 167 SER cc_start: 0.4830 (OUTLIER) cc_final: 0.4273 (p) REVERT: Y 3 LYS cc_start: 0.5948 (mmtm) cc_final: 0.5398 (ttpt) REVERT: Y 11 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8451 (mt) REVERT: Y 160 TRP cc_start: 0.8081 (m100) cc_final: 0.7657 (m100) outliers start: 35 outliers final: 30 residues processed: 180 average time/residue: 0.3721 time to fit residues: 104.4654 Evaluate side-chains 180 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 3.430 ------------------------------------------------------------------------------- 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 508 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 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 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 167 SER Chi-restraints excluded: chain X residue 183 ASP Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 22 CYS 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 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 103 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 chunk 135 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.4304 r_free = 0.4304 target = 0.182343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.125089 restraints weight = 15902.411| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 3.61 r_work: 0.3524 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.5980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11538 Z= 0.163 Angle : 0.662 14.996 15760 Z= 0.331 Chirality : 0.045 0.323 1771 Planarity : 0.005 0.049 2019 Dihedral : 4.880 33.476 1595 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 3.34 % Allowed : 23.84 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.21), residues: 1457 helix: -0.59 (0.83), residues: 37 sheet: -1.13 (0.23), residues: 535 loop : -2.00 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 520 HIS 0.004 0.001 HIS X 188 PHE 0.011 0.001 PHE A 509 TYR 0.012 0.001 TYR W 151 ARG 0.007 0.000 ARG W 65 Details of bonding type rmsd hydrogen bonds : bond 0.03484 ( 232) hydrogen bonds : angle 5.70743 ( 576) SS BOND : bond 0.00602 ( 8) SS BOND : angle 1.68418 ( 16) covalent geometry : bond 0.00389 (11530) covalent geometry : angle 0.65969 (15744) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7548.50 seconds wall clock time: 136 minutes 16.53 seconds (8176.53 seconds total)