Starting phenix.real_space_refine on Sat Dec 28 11:15:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rk4_19259/12_2024/8rk4_19259.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rk4_19259/12_2024/8rk4_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_19259/12_2024/8rk4_19259.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rk4_19259/12_2024/8rk4_19259.map" model { file = "/net/cci-nas-00/data/ceres_data/8rk4_19259/12_2024/8rk4_19259.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rk4_19259/12_2024/8rk4_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 5.76, per 1000 atoms: 0.69 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: 2.15 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: 1.05 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: 2.27 Time building geometry restraints manager: 2.41 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 2.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 24.110 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.630 ------------------------------------------------------------------------------- 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 : 0.318 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: 0.2312 time to fit residues: 6.3735 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 : 0.439 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 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 A 156 TYR 0.014 0.001 TYR A 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 : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 227 MET cc_start: 0.8377 (mmp) cc_final: 0.6742 (tpp) REVERT: C 328 LEU cc_start: 0.9559 (pp) cc_final: 0.9341 (tp) REVERT: C 342 CYS cc_start: 0.8992 (t) cc_final: 0.8393 (t) outliers start: 1 outliers final: 0 residues processed: 30 average time/residue: 0.1323 time to fit residues: 5.2208 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 : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.2980 chunk 31 optimal weight: 0.0370 chunk 83 optimal weight: 40.0000 chunk 68 optimal weight: 0.4980 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 30.0000 chunk 109 optimal weight: 0.5980 chunk 89 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 99 optimal weight: 20.0000 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8619 Z= 0.154 Angle : 0.582 9.820 11793 Z= 0.297 Chirality : 0.042 0.126 1269 Planarity : 0.005 0.065 1524 Dihedral : 3.657 12.444 1209 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.31 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % 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: -0.97 (0.24), residues: 1113 helix: 1.17 (0.54), residues: 81 sheet: -1.30 (0.43), residues: 138 loop : -0.75 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 92 HIS 0.002 0.001 HIS B 305 PHE 0.006 0.001 PHE A 166 TYR 0.010 0.001 TYR B 344 ARG 0.002 0.000 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 3 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: 0 poor density : 30 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 157 MET cc_start: 0.8266 (tpt) cc_final: 0.6877 (ptt) REVERT: C 227 MET cc_start: 0.8343 (mmp) cc_final: 0.6863 (tpp) REVERT: C 328 LEU cc_start: 0.9535 (pp) cc_final: 0.9318 (tp) REVERT: C 342 CYS cc_start: 0.8904 (t) cc_final: 0.8221 (t) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.1318 time to fit residues: 5.2484 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 : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 67 optimal weight: 0.3980 chunk 101 optimal weight: 10.0000 chunk 107 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 89 optimal weight: 30.0000 chunk 60 optimal weight: 3.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8619 Z= 0.224 Angle : 0.598 8.681 11793 Z= 0.303 Chirality : 0.041 0.150 1269 Planarity : 0.005 0.071 1524 Dihedral : 3.973 11.007 1209 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.28 % Favored : 92.45 % Rotamer: Outliers : 0.00 % Allowed : 3.60 % 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: -1.17 (0.25), residues: 1113 helix: 0.73 (0.53), residues: 81 sheet: -1.79 (0.34), residues: 198 loop : -0.67 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 140 HIS 0.004 0.001 HIS C 305 PHE 0.011 0.002 PHE C 276 TYR 0.011 0.001 TYR C 346 ARG 0.009 0.001 ARG B 30 *********************** REFINEMENT MACRO_CYCLE 4 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 23 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 157 MET cc_start: 0.8297 (tpt) cc_final: 0.6806 (ptt) REVERT: C 227 MET cc_start: 0.8549 (mmp) cc_final: 0.7454 (tpp) REVERT: C 346 TYR cc_start: 0.9321 (m-80) cc_final: 0.9067 (m-80) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1502 time to fit residues: 4.4753 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 : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 chunk 74 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 54 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 27 optimal weight: 7.9990 chunk 36 optimal weight: 0.0040 chunk 21 optimal weight: 0.9980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 ASN C 305 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8619 Z= 0.138 Angle : 0.595 10.451 11793 Z= 0.293 Chirality : 0.042 0.126 1269 Planarity : 0.004 0.044 1524 Dihedral : 3.747 11.512 1209 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.66 % Favored : 94.07 % 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: -1.10 (0.25), residues: 1113 helix: 0.91 (0.55), residues: 81 sheet: -1.81 (0.36), residues: 189 loop : -0.64 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 281 HIS 0.002 0.001 HIS C 305 PHE 0.008 0.001 PHE A 166 TYR 0.007 0.001 TYR B 237 ARG 0.003 0.000 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 5 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 22 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 157 MET cc_start: 0.8214 (tpt) cc_final: 0.6703 (ptt) REVERT: C 160 MET cc_start: 0.7482 (ptp) cc_final: 0.7251 (ptp) REVERT: C 223 LEU cc_start: 0.9708 (tp) cc_final: 0.9300 (pp) REVERT: C 227 MET cc_start: 0.8461 (mmp) cc_final: 0.6915 (tpp) REVERT: C 346 TYR cc_start: 0.9279 (m-80) cc_final: 0.9041 (m-80) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.1342 time to fit residues: 3.9213 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 : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.7980 chunk 26 optimal weight: 0.0010 chunk 107 optimal weight: 0.0040 chunk 89 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 35 optimal weight: 0.0070 chunk 56 optimal weight: 0.4980 chunk 103 optimal weight: 0.0040 chunk 12 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.1028 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 8619 Z= 0.127 Angle : 0.567 9.925 11793 Z= 0.274 Chirality : 0.041 0.130 1269 Planarity : 0.004 0.036 1524 Dihedral : 3.598 11.424 1209 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.66 % Favored : 94.07 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % 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: 1.70 (0.58), residues: 81 sheet: -1.65 (0.40), residues: 177 loop : -0.61 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 31 HIS 0.005 0.001 HIS C 305 PHE 0.005 0.001 PHE C 330 TYR 0.027 0.001 TYR B 109 ARG 0.002 0.000 ARG C 306 *********************** REFINEMENT MACRO_CYCLE 6 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 28 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 MET cc_start: 0.9023 (mmp) cc_final: 0.8755 (mmm) REVERT: B 34 PHE cc_start: 0.9248 (t80) cc_final: 0.8649 (m-80) REVERT: B 342 CYS cc_start: 0.8815 (t) cc_final: 0.8473 (t) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1623 time to fit residues: 5.7098 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 : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.3980 chunk 60 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 59 optimal weight: 0.3980 chunk 106 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8619 Z= 0.172 Angle : 0.637 9.810 11793 Z= 0.305 Chirality : 0.041 0.138 1269 Planarity : 0.004 0.034 1524 Dihedral : 3.906 13.674 1209 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.20 % Favored : 93.53 % 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: -1.14 (0.25), residues: 1113 helix: 1.21 (0.53), residues: 81 sheet: -2.12 (0.37), residues: 192 loop : -0.61 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 31 HIS 0.005 0.001 HIS C 305 PHE 0.014 0.002 PHE A 361 TYR 0.012 0.001 TYR A 109 ARG 0.002 0.000 ARG B 329 *********************** REFINEMENT MACRO_CYCLE 7 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 22 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 MET cc_start: 0.9049 (mmp) cc_final: 0.8740 (mmm) REVERT: B 34 PHE cc_start: 0.9246 (t80) cc_final: 0.8666 (m-80) REVERT: B 163 MET cc_start: 0.8853 (mmp) cc_final: 0.8648 (mmm) REVERT: B 237 TYR cc_start: 0.8761 (m-80) cc_final: 0.8500 (m-80) REVERT: B 342 CYS cc_start: 0.8854 (t) cc_final: 0.8456 (t) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.1944 time to fit residues: 5.3042 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 : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 30.0000 chunk 9 optimal weight: 8.9990 chunk 84 optimal weight: 5.9990 chunk 97 optimal weight: 0.0970 chunk 102 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.4929 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= 0.124 Angle : 0.573 9.665 11793 Z= 0.270 Chirality : 0.040 0.126 1269 Planarity : 0.004 0.033 1524 Dihedral : 3.659 14.344 1209 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.93 % Favored : 93.80 % 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: -1.18 (0.25), residues: 1113 helix: 1.91 (0.57), residues: 81 sheet: -2.38 (0.34), residues: 219 loop : -0.58 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 31 HIS 0.004 0.001 HIS C 305 PHE 0.014 0.001 PHE C 361 TYR 0.012 0.001 TYR A 109 ARG 0.002 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 8 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 22 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 MET cc_start: 0.9096 (mmp) cc_final: 0.8751 (mmm) REVERT: B 34 PHE cc_start: 0.9256 (t80) cc_final: 0.8700 (m-80) REVERT: B 123 MET cc_start: 0.2217 (ppp) cc_final: 0.1826 (pmm) REVERT: B 342 CYS cc_start: 0.8878 (t) cc_final: 0.8493 (t) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.2196 time to fit residues: 5.8617 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 : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 10.0000 chunk 60 optimal weight: 0.0570 chunk 43 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 90 optimal weight: 30.0000 chunk 94 optimal weight: 0.6980 chunk 99 optimal weight: 0.0470 chunk 65 optimal weight: 0.2980 chunk 105 optimal weight: 0.0050 chunk 64 optimal weight: 3.9990 overall best weight: 0.2010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.5127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 8619 Z= 0.119 Angle : 0.564 9.687 11793 Z= 0.264 Chirality : 0.040 0.129 1269 Planarity : 0.004 0.032 1524 Dihedral : 3.431 13.549 1209 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.39 % Favored : 94.34 % 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: -1.15 (0.25), residues: 1113 helix: 2.11 (0.58), residues: 81 sheet: -2.27 (0.33), residues: 219 loop : -0.61 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 31 HIS 0.004 0.001 HIS C 305 PHE 0.010 0.001 PHE B 361 TYR 0.011 0.001 TYR A 109 ARG 0.002 0.000 ARG C 236 *********************** REFINEMENT MACRO_CYCLE 9 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 23 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 MET cc_start: 0.9148 (mmp) cc_final: 0.8826 (mmm) REVERT: B 34 PHE cc_start: 0.9265 (t80) cc_final: 0.8729 (m-80) REVERT: B 123 MET cc_start: 0.2610 (ppp) cc_final: 0.2259 (pmm) REVERT: B 286 MET cc_start: 0.8227 (tmm) cc_final: 0.7179 (tmm) REVERT: B 342 CYS cc_start: 0.8834 (t) cc_final: 0.8437 (t) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1840 time to fit residues: 5.2557 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 : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 0.0060 chunk 110 optimal weight: 0.0020 chunk 101 optimal weight: 5.9990 chunk 88 optimal weight: 8.9990 chunk 9 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 53 optimal weight: 20.0000 chunk 69 optimal weight: 20.0000 chunk 93 optimal weight: 0.0570 chunk 26 optimal weight: 20.0000 overall best weight: 0.4122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.5221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 8619 Z= 0.114 Angle : 0.535 9.556 11793 Z= 0.251 Chirality : 0.040 0.128 1269 Planarity : 0.004 0.034 1524 Dihedral : 3.364 12.132 1209 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.66 % Favored : 94.07 % 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: -1.06 (0.25), residues: 1113 helix: 2.28 (0.57), residues: 81 sheet: -2.21 (0.33), residues: 219 loop : -0.56 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 31 HIS 0.004 0.001 HIS C 305 PHE 0.009 0.001 PHE B 361 TYR 0.012 0.001 TYR A 109 ARG 0.001 0.000 ARG A 306 ********************** REFINEMENT MACRO_CYCLE 10 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 24 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 MET cc_start: 0.9135 (mmp) cc_final: 0.8786 (mmm) REVERT: B 34 PHE cc_start: 0.9264 (t80) cc_final: 0.8753 (m-80) REVERT: B 123 MET cc_start: 0.2756 (ppp) cc_final: 0.2441 (pmm) REVERT: B 286 MET cc_start: 0.8278 (tmm) cc_final: 0.7269 (tmm) REVERT: B 342 CYS cc_start: 0.8847 (t) cc_final: 0.8464 (t) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1747 time to fit residues: 5.2597 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 : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 0.2980 chunk 88 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 90 optimal weight: 0.0030 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 0.0030 chunk 77 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 overall best weight: 1.8604 ------------------------------------------------------------------------------- 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 = 0.3068 r_free = 0.3068 target = 0.033253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.025509 restraints weight = 54625.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.026277 restraints weight = 38424.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.026833 restraints weight = 29951.442| |-----------------------------------------------------------------------------| r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.5295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 8619 Z= 0.136 Angle : 0.530 9.328 11793 Z= 0.254 Chirality : 0.040 0.127 1269 Planarity : 0.004 0.028 1524 Dihedral : 3.383 11.575 1209 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.85 % Favored : 94.88 % 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: -1.02 (0.25), residues: 1113 helix: 2.01 (0.55), residues: 84 sheet: -2.21 (0.36), residues: 204 loop : -0.53 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 31 HIS 0.004 0.001 HIS C 305 PHE 0.007 0.001 PHE C 361 TYR 0.014 0.001 TYR A 109 ARG 0.003 0.000 ARG A 306 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1561.95 seconds wall clock time: 29 minutes 34.24 seconds (1774.24 seconds total)