Starting phenix.real_space_refine on Wed Jan 15 12:29:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rk4_19259/01_2025/8rk4_19259.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rk4_19259/01_2025/8rk4_19259.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rk4_19259/01_2025/8rk4_19259.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rk4_19259/01_2025/8rk4_19259.map" model { file = "/net/cci-nas-00/data/ceres_data/8rk4_19259/01_2025/8rk4_19259.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rk4_19259/01_2025/8rk4_19259.cif" } resolution = 4.74 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= 0.000 sd= 0.002 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 42 5.16 5 C 5313 2.51 5 N 1455 2.21 5 O 1563 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 8373 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2791 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Restraints were copied for chains: C, B Time building chain proxies: 4.96, per 1000 atoms: 0.59 Number of scatterers: 8373 At special positions: 0 Unit cell: (88.3616, 90.0288, 131.709, 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 42 16.00 O 1563 8.00 N 1455 7.00 C 5313 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.45 Conformation dependent library (CDL) restraints added in 1.3 seconds 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1968 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 21 sheets defined 11.3% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'B' and resid 17 through 19 No H-bonds generated for 'chain 'B' and resid 17 through 19' Processing helix chain 'B' and resid 20 through 35 removed outlier: 3.644A pdb=" N ASP B 24 " --> pdb=" O GLY B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 148 Processing helix chain 'B' and resid 217 through 228 Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'A' and resid 17 through 19 No H-bonds generated for 'chain 'A' and resid 17 through 19' Processing helix chain 'A' and resid 20 through 35 removed outlier: 3.645A pdb=" N ASP A 24 " --> pdb=" O GLY A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 148 Processing helix chain 'A' and resid 217 through 228 Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'C' and resid 17 through 19 No H-bonds generated for 'chain 'C' and resid 17 through 19' Processing helix chain 'C' and resid 20 through 35 removed outlier: 3.645A pdb=" N ASP C 24 " --> pdb=" O GLY C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 148 Processing helix chain 'C' and resid 217 through 228 Processing helix chain 'C' and resid 231 through 236 Processing sheet with id=1, first strand: chain 'B' and resid 42 through 44 Processing sheet with id=2, first strand: chain 'B' and resid 72 through 73 removed outlier: 3.956A pdb=" N ARG B 72 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU B 84 " --> pdb=" O ARG B 72 " (cutoff:3.500A) No H-bonds generated for sheet with id=2 Processing sheet with id=3, first strand: chain 'B' and resid 95 through 100 removed outlier: 3.562A pdb=" N LYS B 107 " --> pdb=" O VAL B 96 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'B' and resid 133 through 136 Processing sheet with id=5, first strand: chain 'B' and resid 189 through 190 Processing sheet with id=6, first strand: chain 'B' and resid 195 through 202 removed outlier: 6.077A pdb=" N THR B 243 " --> pdb=" O GLY B 199 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LYS B 201 " --> pdb=" O PHE B 241 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N PHE B 241 " --> pdb=" O LYS B 201 " (cutoff:3.500A) removed outlier: 10.304A pdb=" N PHE B 242 " --> pdb=" O CYS B 357 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N CYS B 357 " --> pdb=" O PHE B 242 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA B 244 " --> pdb=" O PHE B 355 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE B 355 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL B 285 " --> pdb=" O PRO B 358 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TRP B 360 " --> pdb=" O THR B 283 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR B 283 " --> pdb=" O TRP B 360 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N MET B 286 " --> pdb=" O LEU B 328 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU B 328 " --> pdb=" O MET B 286 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU B 288 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TRP B 308 " --> pdb=" O ARG B 329 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER B 331 " --> pdb=" O ARG B 306 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG B 306 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU B 307 " --> pdb=" O ALA B 314 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'B' and resid 255 through 257 removed outlier: 3.552A pdb=" N TYR B 265 " --> pdb=" O ALA B 347 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR B 346 " --> pdb=" O HIS B 296 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'A' and resid 42 through 44 Processing sheet with id=9, first strand: chain 'A' and resid 72 through 73 removed outlier: 3.957A pdb=" N ARG A 72 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU A 84 " --> pdb=" O ARG A 72 " (cutoff:3.500A) No H-bonds generated for sheet with id=9 Processing sheet with id=10, first strand: chain 'A' and resid 95 through 100 removed outlier: 3.562A pdb=" N LYS A 107 " --> pdb=" O VAL A 96 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'A' and resid 133 through 136 Processing sheet with id=12, first strand: chain 'A' and resid 189 through 190 Processing sheet with id=13, first strand: chain 'A' and resid 195 through 202 removed outlier: 6.077A pdb=" N THR A 243 " --> pdb=" O GLY A 199 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LYS A 201 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N PHE A 241 " --> pdb=" O LYS A 201 " (cutoff:3.500A) removed outlier: 10.304A pdb=" N PHE A 242 " --> pdb=" O CYS A 357 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N CYS A 357 " --> pdb=" O PHE A 242 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A 244 " --> pdb=" O PHE A 355 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE A 355 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL A 285 " --> pdb=" O PRO A 358 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TRP A 360 " --> pdb=" O THR A 283 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR A 283 " --> pdb=" O TRP A 360 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N MET A 286 " --> pdb=" O LEU A 328 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A 328 " --> pdb=" O MET A 286 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A 288 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TRP A 308 " --> pdb=" O ARG A 329 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A 331 " --> pdb=" O ARG A 306 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG A 306 " --> pdb=" O SER A 331 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A 307 " --> pdb=" O ALA A 314 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'A' and resid 255 through 257 removed outlier: 3.552A pdb=" N TYR A 265 " --> pdb=" O ALA A 347 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR A 346 " --> pdb=" O HIS A 296 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'C' and resid 42 through 44 Processing sheet with id=16, first strand: chain 'C' and resid 72 through 73 removed outlier: 3.956A pdb=" N ARG C 72 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU C 84 " --> pdb=" O ARG C 72 " (cutoff:3.500A) No H-bonds generated for sheet with id=16 Processing sheet with id=17, first strand: chain 'C' and resid 95 through 100 removed outlier: 3.562A pdb=" N LYS C 107 " --> pdb=" O VAL C 96 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'C' and resid 133 through 136 Processing sheet with id=19, first strand: chain 'C' and resid 189 through 190 Processing sheet with id=20, first strand: chain 'C' and resid 195 through 202 removed outlier: 6.077A pdb=" N THR C 243 " --> pdb=" O GLY C 199 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LYS C 201 " --> pdb=" O PHE C 241 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N PHE C 241 " --> pdb=" O LYS C 201 " (cutoff:3.500A) removed outlier: 10.304A pdb=" N PHE C 242 " --> pdb=" O CYS C 357 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N CYS C 357 " --> pdb=" O PHE C 242 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA C 244 " --> pdb=" O PHE C 355 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE C 355 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL C 285 " --> pdb=" O PRO C 358 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TRP C 360 " --> pdb=" O THR C 283 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR C 283 " --> pdb=" O TRP C 360 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET C 286 " --> pdb=" O LEU C 328 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU C 328 " --> pdb=" O MET C 286 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU C 288 " --> pdb=" O VAL C 326 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TRP C 308 " --> pdb=" O ARG C 329 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER C 331 " --> pdb=" O ARG C 306 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG C 306 " --> pdb=" O SER C 331 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU C 307 " --> pdb=" O ALA C 314 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'C' and resid 255 through 257 removed outlier: 3.552A pdb=" N TYR C 265 " --> pdb=" O ALA C 347 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR C 346 " --> pdb=" O HIS C 296 " (cutoff:3.500A) 180 hydrogen bonds defined for protein. 468 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.44 Time building geometry restraints manager: 2.67 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: 2721 1.34 - 1.46: 2261 1.46 - 1.58: 3565 1.58 - 1.70: 0 1.70 - 1.82: 72 Bond restraints: 8619 Sorted by residual: bond pdb=" CB TRP A 31 " pdb=" CG TRP A 31 " ideal model delta sigma weight residual 1.498 1.453 0.045 3.10e-02 1.04e+03 2.08e+00 bond pdb=" CB TRP B 31 " pdb=" CG TRP B 31 " ideal model delta sigma weight residual 1.498 1.453 0.045 3.10e-02 1.04e+03 2.07e+00 bond pdb=" CB TRP C 31 " pdb=" CG TRP C 31 " ideal model delta sigma weight residual 1.498 1.454 0.044 3.10e-02 1.04e+03 2.03e+00 bond pdb=" CB ARG A 27 " pdb=" CG ARG A 27 " ideal model delta sigma weight residual 1.520 1.477 0.043 3.00e-02 1.11e+03 2.01e+00 bond pdb=" CB ARG B 27 " pdb=" CG ARG B 27 " ideal model delta sigma weight residual 1.520 1.478 0.042 3.00e-02 1.11e+03 2.00e+00 ... (remaining 8614 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 11298 1.57 - 3.13: 389 3.13 - 4.70: 85 4.70 - 6.26: 15 6.26 - 7.83: 6 Bond angle restraints: 11793 Sorted by residual: angle pdb=" C ARG C 30 " pdb=" N TRP C 31 " pdb=" CA TRP C 31 " ideal model delta sigma weight residual 120.44 115.23 5.21 1.36e+00 5.41e-01 1.47e+01 angle pdb=" C ARG A 30 " pdb=" N TRP A 31 " pdb=" CA TRP A 31 " ideal model delta sigma weight residual 120.44 115.23 5.21 1.36e+00 5.41e-01 1.47e+01 angle pdb=" C ARG B 30 " pdb=" N TRP B 31 " pdb=" CA TRP B 31 " ideal model delta sigma weight residual 120.44 115.24 5.20 1.36e+00 5.41e-01 1.46e+01 angle pdb=" N TRP C 31 " pdb=" CA TRP C 31 " pdb=" C TRP C 31 " ideal model delta sigma weight residual 111.14 114.76 -3.62 1.08e+00 8.57e-01 1.12e+01 angle pdb=" N TRP A 31 " pdb=" CA TRP A 31 " pdb=" C TRP A 31 " ideal model delta sigma weight residual 111.14 114.75 -3.61 1.08e+00 8.57e-01 1.11e+01 ... (remaining 11788 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.25: 4179 10.25 - 20.50: 459 20.50 - 30.76: 138 30.76 - 41.01: 54 41.01 - 51.26: 30 Dihedral angle restraints: 4860 sinusoidal: 1737 harmonic: 3123 Sorted by residual: dihedral pdb=" C ASP C 33 " pdb=" N ASP C 33 " pdb=" CA ASP C 33 " pdb=" CB ASP C 33 " ideal model delta harmonic sigma weight residual -122.60 -131.79 9.19 0 2.50e+00 1.60e-01 1.35e+01 dihedral pdb=" C ASP B 33 " pdb=" N ASP B 33 " pdb=" CA ASP B 33 " pdb=" CB ASP B 33 " ideal model delta harmonic sigma weight residual -122.60 -131.76 9.16 0 2.50e+00 1.60e-01 1.34e+01 dihedral pdb=" C ASP A 33 " pdb=" N ASP A 33 " pdb=" CA ASP A 33 " pdb=" CB ASP A 33 " ideal model delta harmonic sigma weight residual -122.60 -131.72 9.12 0 2.50e+00 1.60e-01 1.33e+01 ... (remaining 4857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1130 0.068 - 0.136: 130 0.136 - 0.204: 0 0.204 - 0.271: 2 0.271 - 0.339: 7 Chirality restraints: 1269 Sorted by residual: chirality pdb=" CA ASP C 33 " pdb=" N ASP C 33 " pdb=" C ASP C 33 " pdb=" CB ASP C 33 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" CA ASP B 33 " pdb=" N ASP B 33 " pdb=" C ASP B 33 " pdb=" CB ASP B 33 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" CA ASP A 33 " pdb=" N ASP A 33 " pdb=" C ASP A 33 " pdb=" CB ASP A 33 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.84e+00 ... (remaining 1266 not shown) Planarity restraints: 1524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 29 " -0.026 2.00e-02 2.50e+03 1.70e-02 7.21e+00 pdb=" CG TRP C 29 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP C 29 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP C 29 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP C 29 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 29 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 29 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 29 " -0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 29 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 29 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 29 " 0.026 2.00e-02 2.50e+03 1.69e-02 7.18e+00 pdb=" CG TRP A 29 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP A 29 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP A 29 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 29 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 29 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 29 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 29 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 29 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 29 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 29 " -0.026 2.00e-02 2.50e+03 1.69e-02 7.16e+00 pdb=" CG TRP B 29 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP B 29 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP B 29 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 29 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 29 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 29 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 29 " -0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 29 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 29 " -0.002 2.00e-02 2.50e+03 ... (remaining 1521 not shown) Histogram of nonbonded interaction distances: 1.00 - 1.78: 12 1.78 - 2.56: 150 2.56 - 3.34: 11059 3.34 - 4.12: 21107 4.12 - 4.90: 36858 Warning: very small nonbonded interaction distances. Nonbonded interactions: 69186 Sorted by model distance: nonbonded pdb=" CE MET A 157 " pdb=" CE MET C 157 " model vdw 0.995 3.880 nonbonded pdb=" CE MET B 157 " pdb=" CE MET A 157 " model vdw 0.996 3.880 nonbonded pdb=" CE MET B 157 " pdb=" CE MET C 157 " model vdw 0.996 3.880 nonbonded pdb=" CE MET B 157 " pdb=" SD MET A 157 " model vdw 1.248 3.820 nonbonded pdb=" SD MET B 157 " pdb=" CE MET C 157 " model vdw 1.248 3.820 ... (remaining 69181 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } Set refine NCS operators NCS operators will be refined. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.350 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 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 : 0.003 0.045 8619 Z= 0.212 Angle : 0.721 7.831 11793 Z= 0.418 Chirality : 0.049 0.339 1269 Planarity : 0.005 0.048 1524 Dihedral : 11.118 51.261 2892 Min Nonbonded Distance : 0.995 Molprobity Statistics. All-atom Clashscore : 21.20 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.04 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.38 (0.25), residues: 1113 helix: -1.97 (0.43), residues: 99 sheet: -1.23 (0.44), residues: 129 loop : -0.77 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 29 HIS 0.006 0.002 HIS B 305 PHE 0.009 0.001 PHE A 156 TYR 0.008 0.001 TYR A 109 ARG 0.010 0.001 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.6529 (ppp) cc_final: 0.6020 (mmp) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.2123 time to fit residues: 5.8375 Evaluate side-chains 15 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 9.9990 chunk 84 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 44 optimal weight: 0.0770 chunk 87 optimal weight: 0.4980 chunk 33 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 0.0770 chunk 100 optimal weight: 20.0000 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.037045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.028280 restraints weight = 54855.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.028974 restraints weight = 43453.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.029509 restraints weight = 35938.546| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8619 Z= 0.177 Angle : 0.637 9.860 11793 Z= 0.324 Chirality : 0.044 0.143 1269 Planarity : 0.006 0.103 1524 Dihedral : 3.815 11.647 1209 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.04 % Favored : 95.69 % Rotamer: Outliers : 0.36 % Allowed : 3.24 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.92 (0.25), residues: 1113 helix: 0.16 (0.52), residues: 81 sheet: -0.78 (0.46), residues: 129 loop : -0.69 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 92 HIS 0.004 0.001 HIS C 305 PHE 0.009 0.002 PHE C 156 TYR 0.014 0.001 TYR B 344 ARG 0.005 0.001 ARG B 30 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 342 CYS cc_start: 0.7965 (t) cc_final: 0.4940 (t) REVERT: C 374 ILE cc_start: 0.6804 (mm) cc_final: 0.6588 (mm) outliers start: 1 outliers final: 0 residues processed: 30 average time/residue: 0.1231 time to fit residues: 4.8913 Evaluate side-chains 21 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 30.0000 chunk 88 optimal weight: 8.9990 chunk 8 optimal weight: 20.0000 chunk 7 optimal weight: 0.0470 chunk 86 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 91 optimal weight: 0.0270 chunk 103 optimal weight: 0.6980 chunk 48 optimal weight: 6.9990 chunk 79 optimal weight: 0.0970 chunk 49 optimal weight: 9.9990 overall best weight: 1.5736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.036487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.027879 restraints weight = 55742.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.028594 restraints weight = 41854.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.029149 restraints weight = 33770.569| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8619 Z= 0.162 Angle : 0.574 9.741 11793 Z= 0.296 Chirality : 0.042 0.134 1269 Planarity : 0.005 0.069 1524 Dihedral : 3.730 12.131 1209 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.31 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.98 (0.25), residues: 1113 helix: 1.04 (0.55), residues: 81 sheet: -1.40 (0.42), residues: 138 loop : -0.72 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 92 HIS 0.003 0.001 HIS A 305 PHE 0.008 0.001 PHE B 276 TYR 0.011 0.001 TYR A 133 ARG 0.002 0.001 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 VAL cc_start: 0.3961 (m) cc_final: 0.2591 (t) REVERT: A 374 ILE cc_start: 0.5192 (mm) cc_final: 0.4917 (mm) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1478 time to fit residues: 4.4598 Evaluate side-chains 19 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 58 optimal weight: 0.9990 chunk 53 optimal weight: 20.0000 chunk 2 optimal weight: 6.9990 chunk 20 optimal weight: 0.0060 chunk 66 optimal weight: 0.2980 chunk 37 optimal weight: 30.0000 chunk 86 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 35 optimal weight: 0.0020 overall best weight: 1.0608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.036495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.029918 restraints weight = 53096.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.030513 restraints weight = 40413.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.030951 restraints weight = 32506.757| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8619 Z= 0.139 Angle : 0.545 9.150 11793 Z= 0.272 Chirality : 0.041 0.129 1269 Planarity : 0.004 0.043 1524 Dihedral : 3.561 12.239 1209 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.47 % Favored : 93.26 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.30 (0.24), residues: 1113 helix: 1.26 (0.52), residues: 81 sheet: -1.48 (0.38), residues: 156 loop : -1.01 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 92 HIS 0.002 0.001 HIS B 305 PHE 0.007 0.001 PHE A 166 TYR 0.030 0.001 TYR B 109 ARG 0.002 0.000 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.1583 time to fit residues: 3.7056 Evaluate side-chains 15 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 25 optimal weight: 0.0670 chunk 43 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 90 optimal weight: 0.0060 chunk 94 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 69 optimal weight: 0.0670 chunk 103 optimal weight: 5.9990 chunk 89 optimal weight: 20.0000 chunk 99 optimal weight: 0.0670 overall best weight: 0.6412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.037095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.027922 restraints weight = 50521.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.028562 restraints weight = 40278.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.029044 restraints weight = 33807.272| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8619 Z= 0.136 Angle : 0.544 8.883 11793 Z= 0.273 Chirality : 0.041 0.127 1269 Planarity : 0.006 0.082 1524 Dihedral : 3.611 12.526 1209 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.01 % Favored : 92.72 % Rotamer: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.65 (0.24), residues: 1113 helix: 0.53 (0.50), residues: 81 sheet: -1.95 (0.36), residues: 186 loop : -1.11 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 31 HIS 0.006 0.001 HIS C 305 PHE 0.009 0.001 PHE C 204 TYR 0.019 0.001 TYR C 109 ARG 0.004 0.001 ARG C 30 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: C 160 MET cc_start: 0.4542 (ptp) cc_final: 0.3982 (ptp) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.1263 time to fit residues: 5.0033 Evaluate side-chains 17 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 41 optimal weight: 0.0370 chunk 34 optimal weight: 0.0980 chunk 12 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 110 optimal weight: 20.0000 chunk 47 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 chunk 55 optimal weight: 0.0070 chunk 73 optimal weight: 20.0000 chunk 100 optimal weight: 20.0000 overall best weight: 2.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.034762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.026561 restraints weight = 58447.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.027202 restraints weight = 43852.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.027678 restraints weight = 35401.398| |-----------------------------------------------------------------------------| r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8619 Z= 0.192 Angle : 0.602 9.495 11793 Z= 0.300 Chirality : 0.042 0.163 1269 Planarity : 0.006 0.085 1524 Dihedral : 4.112 15.836 1209 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.09 % Favored : 91.64 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.73 (0.25), residues: 1113 helix: -0.41 (0.49), residues: 81 sheet: -2.21 (0.37), residues: 186 loop : -1.01 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 360 HIS 0.008 0.003 HIS A 21 PHE 0.015 0.002 PHE A 361 TYR 0.019 0.001 TYR C 109 ARG 0.008 0.001 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 LEU cc_start: 0.7347 (mp) cc_final: 0.7110 (mp) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.1520 time to fit residues: 4.1144 Evaluate side-chains 16 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 35 optimal weight: 0.3980 chunk 30 optimal weight: 0.1980 chunk 13 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 109 optimal weight: 0.3980 chunk 97 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 26 optimal weight: 0.0770 chunk 68 optimal weight: 0.4980 chunk 41 optimal weight: 0.0030 overall best weight: 0.2148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.035939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.027429 restraints weight = 57007.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.028105 restraints weight = 42889.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.028625 restraints weight = 34803.361| |-----------------------------------------------------------------------------| r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.4615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8619 Z= 0.132 Angle : 0.561 9.916 11793 Z= 0.271 Chirality : 0.041 0.122 1269 Planarity : 0.005 0.050 1524 Dihedral : 3.695 14.994 1209 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.55 % Favored : 92.18 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.61 (0.25), residues: 1113 helix: 0.67 (0.57), residues: 81 sheet: -2.39 (0.33), residues: 213 loop : -0.89 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 29 HIS 0.006 0.001 HIS C 305 PHE 0.007 0.001 PHE C 204 TYR 0.017 0.001 TYR C 109 ARG 0.004 0.000 ARG C 30 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 MET cc_start: 0.9077 (ppp) cc_final: 0.8832 (ppp) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.1451 time to fit residues: 3.9659 Evaluate side-chains 15 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 52 optimal weight: 20.0000 chunk 45 optimal weight: 9.9990 chunk 19 optimal weight: 0.0000 chunk 99 optimal weight: 0.8980 chunk 110 optimal weight: 6.9990 chunk 15 optimal weight: 20.0000 chunk 55 optimal weight: 0.5980 chunk 89 optimal weight: 20.0000 chunk 68 optimal weight: 1.9990 chunk 24 optimal weight: 0.0470 chunk 90 optimal weight: 20.0000 overall best weight: 0.7084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.036043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.027465 restraints weight = 56441.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.028119 restraints weight = 42975.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.028603 restraints weight = 35121.991| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.4857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 8619 Z= 0.122 Angle : 0.539 9.465 11793 Z= 0.261 Chirality : 0.041 0.125 1269 Planarity : 0.004 0.045 1524 Dihedral : 3.637 13.279 1209 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.28 % Favored : 92.45 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.59 (0.25), residues: 1113 helix: 0.85 (0.58), residues: 81 sheet: -2.56 (0.31), residues: 213 loop : -0.84 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 29 HIS 0.004 0.001 HIS C 305 PHE 0.006 0.001 PHE C 166 TYR 0.016 0.001 TYR C 109 ARG 0.004 0.000 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.1518 time to fit residues: 4.1636 Evaluate side-chains 17 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 49 optimal weight: 0.0050 chunk 7 optimal weight: 5.9990 chunk 19 optimal weight: 0.0000 chunk 47 optimal weight: 10.0000 chunk 5 optimal weight: 0.0070 chunk 31 optimal weight: 3.9990 chunk 72 optimal weight: 0.3980 chunk 98 optimal weight: 0.9980 chunk 75 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 overall best weight: 0.2816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.036312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.028855 restraints weight = 52173.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.029520 restraints weight = 38685.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.029996 restraints weight = 31097.404| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.5015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8619 Z= 0.133 Angle : 0.570 9.301 11793 Z= 0.284 Chirality : 0.042 0.218 1269 Planarity : 0.005 0.048 1524 Dihedral : 3.587 14.532 1209 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.82 % Favored : 91.91 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.82 (0.24), residues: 1113 helix: -0.73 (0.48), residues: 81 sheet: -2.69 (0.30), residues: 231 loop : -0.78 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 31 HIS 0.004 0.001 HIS C 305 PHE 0.006 0.001 PHE C 166 TYR 0.015 0.001 TYR B 109 ARG 0.004 0.000 ARG C 30 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.8300 (mmm) cc_final: 0.8052 (mmp) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1418 time to fit residues: 4.3108 Evaluate side-chains 18 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 82 optimal weight: 0.8980 chunk 59 optimal weight: 0.0670 chunk 31 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 chunk 85 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.036073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.027805 restraints weight = 50051.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.028656 restraints weight = 35314.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.029277 restraints weight = 27542.700| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.5215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8619 Z= 0.130 Angle : 0.554 8.996 11793 Z= 0.275 Chirality : 0.042 0.149 1269 Planarity : 0.004 0.050 1524 Dihedral : 3.495 13.822 1209 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.74 % Favored : 92.99 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.84 (0.24), residues: 1113 helix: -1.17 (0.46), residues: 81 sheet: -2.60 (0.32), residues: 216 loop : -0.83 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP C 31 HIS 0.004 0.001 HIS C 305 PHE 0.005 0.001 PHE A 166 TYR 0.014 0.001 TYR A 109 ARG 0.003 0.001 ARG B 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 160 MET cc_start: 0.7036 (ptp) cc_final: 0.6834 (ptp) REVERT: C 163 MET cc_start: 0.7253 (mmm) cc_final: 0.6711 (mmt) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.1358 time to fit residues: 3.9851 Evaluate side-chains 16 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 67 optimal weight: 0.2980 chunk 6 optimal weight: 9.9990 chunk 61 optimal weight: 0.0770 chunk 100 optimal weight: 6.9990 chunk 18 optimal weight: 0.0670 chunk 25 optimal weight: 0.0570 chunk 30 optimal weight: 0.2980 chunk 105 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 45 optimal weight: 8.9990 chunk 94 optimal weight: 20.0000 overall best weight: 0.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.037581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.031452 restraints weight = 50664.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.032056 restraints weight = 37726.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.032508 restraints weight = 30354.120| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.5393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 8619 Z= 0.122 Angle : 0.562 9.086 11793 Z= 0.271 Chirality : 0.042 0.148 1269 Planarity : 0.004 0.049 1524 Dihedral : 3.370 12.164 1209 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.55 % Favored : 92.18 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.77 (0.24), residues: 1113 helix: -0.87 (0.49), residues: 81 sheet: -2.33 (0.35), residues: 201 loop : -0.92 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 31 HIS 0.004 0.001 HIS C 305 PHE 0.005 0.001 PHE B 355 TYR 0.012 0.001 TYR B 109 ARG 0.004 0.000 ARG C 30 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1850.67 seconds wall clock time: 34 minutes 13.68 seconds (2053.68 seconds total)