Starting phenix.real_space_refine on Mon Jul 28 22:53:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5v4s_8633/07_2025/5v4s_8633.cif Found real_map, /net/cci-nas-00/data/ceres_data/5v4s_8633/07_2025/5v4s_8633.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5v4s_8633/07_2025/5v4s_8633.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5v4s_8633/07_2025/5v4s_8633.map" model { file = "/net/cci-nas-00/data/ceres_data/5v4s_8633/07_2025/5v4s_8633.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5v4s_8633/07_2025/5v4s_8633.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 24 5.16 5 C 6992 2.51 5 N 1844 2.21 5 O 1896 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10756 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2689 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 132} Link IDs: {'PTRANS': 10, 'TRANS': 376} Chain breaks: 3 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 456 Unresolved non-hydrogen angles: 579 Unresolved non-hydrogen dihedrals: 366 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 13, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 9, 'GLU:plan': 13, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 239 Restraints were copied for chains: C, B, D Time building chain proxies: 5.55, per 1000 atoms: 0.52 Number of scatterers: 10756 At special positions: 0 Unit cell: (116.067, 116.067, 109.24, 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 24 16.00 O 1896 8.00 N 1844 7.00 C 6992 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.33 Conformation dependent library (CDL) restraints added in 1.6 seconds 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2936 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 8 sheets defined 74.2% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 7 through 27 Processing helix chain 'A' and resid 28 through 32 removed outlier: 4.040A pdb=" N ILE A 31 " --> pdb=" O PRO A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 59 Processing helix chain 'A' and resid 84 through 93 Processing helix chain 'A' and resid 95 through 104 Processing helix chain 'A' and resid 114 through 120 removed outlier: 3.972A pdb=" N VAL A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 127 removed outlier: 4.416A pdb=" N LEU A 124 " --> pdb=" O THR A 121 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LYS A 125 " --> pdb=" O ARG A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 141 removed outlier: 4.024A pdb=" N GLN A 134 " --> pdb=" O SER A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 173 Processing helix chain 'A' and resid 179 through 195 Processing helix chain 'A' and resid 206 through 260 removed outlier: 4.881A pdb=" N LYS A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N MET A 249 " --> pdb=" O GLN A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 280 removed outlier: 4.172A pdb=" N ARG A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 290 Processing helix chain 'A' and resid 293 through 310 removed outlier: 3.699A pdb=" N LEU A 308 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU A 310 " --> pdb=" O ARG A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 319 through 330 Processing helix chain 'A' and resid 380 through 386 Processing helix chain 'A' and resid 407 through 417 Processing helix chain 'A' and resid 417 through 429 removed outlier: 3.884A pdb=" N ILE A 424 " --> pdb=" O PHE A 420 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER A 427 " --> pdb=" O ALA A 423 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA A 429 " --> pdb=" O GLU A 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 27 Processing helix chain 'B' and resid 28 through 32 removed outlier: 4.040A pdb=" N ILE B 31 " --> pdb=" O PRO B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 59 Processing helix chain 'B' and resid 84 through 93 Processing helix chain 'B' and resid 95 through 104 Processing helix chain 'B' and resid 114 through 120 removed outlier: 3.972A pdb=" N VAL B 120 " --> pdb=" O LEU B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 127 removed outlier: 4.416A pdb=" N LEU B 124 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LYS B 125 " --> pdb=" O ARG B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 141 removed outlier: 4.025A pdb=" N GLN B 134 " --> pdb=" O SER B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 173 Processing helix chain 'B' and resid 179 through 195 Processing helix chain 'B' and resid 206 through 260 removed outlier: 4.881A pdb=" N LYS B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N MET B 249 " --> pdb=" O GLN B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 280 removed outlier: 4.172A pdb=" N ARG B 268 " --> pdb=" O ASN B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 290 Processing helix chain 'B' and resid 293 through 310 removed outlier: 3.699A pdb=" N LEU B 308 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU B 310 " --> pdb=" O ARG B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 317 Processing helix chain 'B' and resid 319 through 330 Processing helix chain 'B' and resid 380 through 386 Processing helix chain 'B' and resid 407 through 417 Processing helix chain 'B' and resid 417 through 429 removed outlier: 3.883A pdb=" N ILE B 424 " --> pdb=" O PHE B 420 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER B 427 " --> pdb=" O ALA B 423 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA B 429 " --> pdb=" O GLU B 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 27 Processing helix chain 'C' and resid 28 through 32 removed outlier: 4.040A pdb=" N ILE C 31 " --> pdb=" O PRO C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 59 Processing helix chain 'C' and resid 84 through 93 Processing helix chain 'C' and resid 95 through 104 Processing helix chain 'C' and resid 114 through 120 removed outlier: 3.972A pdb=" N VAL C 120 " --> pdb=" O LEU C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 127 removed outlier: 4.416A pdb=" N LEU C 124 " --> pdb=" O THR C 121 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LYS C 125 " --> pdb=" O ARG C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 141 removed outlier: 4.025A pdb=" N GLN C 134 " --> pdb=" O SER C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 173 Processing helix chain 'C' and resid 179 through 195 Processing helix chain 'C' and resid 206 through 260 removed outlier: 4.881A pdb=" N LYS C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N MET C 249 " --> pdb=" O GLN C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 280 removed outlier: 4.172A pdb=" N ARG C 268 " --> pdb=" O ASN C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 290 Processing helix chain 'C' and resid 293 through 310 removed outlier: 3.699A pdb=" N LEU C 308 " --> pdb=" O LEU C 304 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU C 310 " --> pdb=" O ARG C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 317 Processing helix chain 'C' and resid 319 through 330 Processing helix chain 'C' and resid 380 through 386 Processing helix chain 'C' and resid 407 through 417 Processing helix chain 'C' and resid 417 through 429 removed outlier: 3.883A pdb=" N ILE C 424 " --> pdb=" O PHE C 420 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER C 427 " --> pdb=" O ALA C 423 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA C 429 " --> pdb=" O GLU C 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 27 Processing helix chain 'D' and resid 28 through 32 removed outlier: 4.040A pdb=" N ILE D 31 " --> pdb=" O PRO D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 59 Processing helix chain 'D' and resid 84 through 93 Processing helix chain 'D' and resid 95 through 104 Processing helix chain 'D' and resid 114 through 120 removed outlier: 3.972A pdb=" N VAL D 120 " --> pdb=" O LEU D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 127 removed outlier: 4.416A pdb=" N LEU D 124 " --> pdb=" O THR D 121 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LYS D 125 " --> pdb=" O ARG D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 141 removed outlier: 4.025A pdb=" N GLN D 134 " --> pdb=" O SER D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 173 Processing helix chain 'D' and resid 179 through 195 Processing helix chain 'D' and resid 206 through 260 removed outlier: 4.881A pdb=" N LYS D 248 " --> pdb=" O ALA D 244 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N MET D 249 " --> pdb=" O GLN D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 280 removed outlier: 4.172A pdb=" N ARG D 268 " --> pdb=" O ASN D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 290 Processing helix chain 'D' and resid 293 through 310 removed outlier: 3.699A pdb=" N LEU D 308 " --> pdb=" O LEU D 304 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU D 310 " --> pdb=" O ARG D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 317 Processing helix chain 'D' and resid 319 through 330 Processing helix chain 'D' and resid 380 through 386 Processing helix chain 'D' and resid 407 through 417 Processing helix chain 'D' and resid 417 through 429 removed outlier: 3.883A pdb=" N ILE D 424 " --> pdb=" O PHE D 420 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER D 427 " --> pdb=" O ALA D 423 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA D 429 " --> pdb=" O GLU D 425 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 331 through 335 removed outlier: 6.544A pdb=" N GLU A 401 " --> pdb=" O SER A 355 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 340 through 342 removed outlier: 6.530A pdb=" N THR A 340 " --> pdb=" O ALA A 396 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ALA A 396 " --> pdb=" O THR A 340 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 331 through 335 removed outlier: 6.544A pdb=" N GLU B 401 " --> pdb=" O SER B 355 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 340 through 342 removed outlier: 6.531A pdb=" N THR B 340 " --> pdb=" O ALA B 396 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ALA B 396 " --> pdb=" O THR B 340 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 331 through 335 removed outlier: 6.544A pdb=" N GLU C 401 " --> pdb=" O SER C 355 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 340 through 342 removed outlier: 6.531A pdb=" N THR C 340 " --> pdb=" O ALA C 396 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ALA C 396 " --> pdb=" O THR C 340 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 331 through 335 removed outlier: 6.544A pdb=" N GLU D 401 " --> pdb=" O SER D 355 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 340 through 342 removed outlier: 6.531A pdb=" N THR D 340 " --> pdb=" O ALA D 396 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ALA D 396 " --> pdb=" O THR D 340 " (cutoff:3.500A) 893 hydrogen bonds defined for protein. 2595 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.60 Time building geometry restraints manager: 3.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2224 1.32 - 1.44: 2731 1.44 - 1.56: 5969 1.56 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 10960 Sorted by residual: bond pdb=" CA LEU A 322 " pdb=" C LEU A 322 " ideal model delta sigma weight residual 1.524 1.475 0.049 1.27e-02 6.20e+03 1.46e+01 bond pdb=" CA LEU B 322 " pdb=" C LEU B 322 " ideal model delta sigma weight residual 1.524 1.475 0.048 1.27e-02 6.20e+03 1.45e+01 bond pdb=" CA LEU C 322 " pdb=" C LEU C 322 " ideal model delta sigma weight residual 1.524 1.475 0.048 1.27e-02 6.20e+03 1.45e+01 bond pdb=" CA LEU D 322 " pdb=" C LEU D 322 " ideal model delta sigma weight residual 1.524 1.475 0.048 1.27e-02 6.20e+03 1.45e+01 bond pdb=" N PRO C 144 " pdb=" CD PRO C 144 " ideal model delta sigma weight residual 1.473 1.431 0.042 1.40e-02 5.10e+03 8.93e+00 ... (remaining 10955 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.59: 14968 6.59 - 13.19: 48 13.19 - 19.78: 8 19.78 - 26.37: 8 26.37 - 32.96: 4 Bond angle restraints: 15036 Sorted by residual: angle pdb=" N LEU B 96 " pdb=" CA LEU B 96 " pdb=" C LEU B 96 " ideal model delta sigma weight residual 110.80 143.76 -32.96 2.13e+00 2.20e-01 2.39e+02 angle pdb=" N LEU C 96 " pdb=" CA LEU C 96 " pdb=" C LEU C 96 " ideal model delta sigma weight residual 110.80 143.76 -32.96 2.13e+00 2.20e-01 2.39e+02 angle pdb=" N LEU D 96 " pdb=" CA LEU D 96 " pdb=" C LEU D 96 " ideal model delta sigma weight residual 110.80 143.76 -32.96 2.13e+00 2.20e-01 2.39e+02 angle pdb=" N LEU A 96 " pdb=" CA LEU A 96 " pdb=" C LEU A 96 " ideal model delta sigma weight residual 110.80 143.75 -32.95 2.13e+00 2.20e-01 2.39e+02 angle pdb=" N GLU C 97 " pdb=" CA GLU C 97 " pdb=" CB GLU C 97 " ideal model delta sigma weight residual 110.07 89.00 21.07 1.45e+00 4.76e-01 2.11e+02 ... (remaining 15031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.27: 6012 13.27 - 26.54: 180 26.54 - 39.81: 60 39.81 - 53.07: 12 53.07 - 66.34: 12 Dihedral angle restraints: 6276 sinusoidal: 1748 harmonic: 4528 Sorted by residual: dihedral pdb=" C ARG C 30 " pdb=" N ARG C 30 " pdb=" CA ARG C 30 " pdb=" CB ARG C 30 " ideal model delta harmonic sigma weight residual -122.60 -153.91 31.31 0 2.50e+00 1.60e-01 1.57e+02 dihedral pdb=" C ARG D 30 " pdb=" N ARG D 30 " pdb=" CA ARG D 30 " pdb=" CB ARG D 30 " ideal model delta harmonic sigma weight residual -122.60 -153.91 31.31 0 2.50e+00 1.60e-01 1.57e+02 dihedral pdb=" C ARG B 30 " pdb=" N ARG B 30 " pdb=" CA ARG B 30 " pdb=" CB ARG B 30 " ideal model delta harmonic sigma weight residual -122.60 -153.91 31.31 0 2.50e+00 1.60e-01 1.57e+02 ... (remaining 6273 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.300: 1816 0.300 - 0.599: 12 0.599 - 0.899: 4 0.899 - 1.199: 0 1.199 - 1.499: 12 Chirality restraints: 1844 Sorted by residual: chirality pdb=" CA LEU A 96 " pdb=" N LEU A 96 " pdb=" C LEU A 96 " pdb=" CB LEU A 96 " both_signs ideal model delta sigma weight residual False 2.51 1.01 1.50 2.00e-01 2.50e+01 5.62e+01 chirality pdb=" CA LEU D 96 " pdb=" N LEU D 96 " pdb=" C LEU D 96 " pdb=" CB LEU D 96 " both_signs ideal model delta sigma weight residual False 2.51 1.01 1.50 2.00e-01 2.50e+01 5.60e+01 chirality pdb=" CA LEU B 96 " pdb=" N LEU B 96 " pdb=" C LEU B 96 " pdb=" CB LEU B 96 " both_signs ideal model delta sigma weight residual False 2.51 1.01 1.50 2.00e-01 2.50e+01 5.60e+01 ... (remaining 1841 not shown) Planarity restraints: 1888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN D 141 " 0.085 5.00e-02 4.00e+02 1.29e-01 2.65e+01 pdb=" N PRO D 142 " -0.223 5.00e-02 4.00e+02 pdb=" CA PRO D 142 " 0.071 5.00e-02 4.00e+02 pdb=" CD PRO D 142 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 141 " 0.085 5.00e-02 4.00e+02 1.29e-01 2.65e+01 pdb=" N PRO C 142 " -0.223 5.00e-02 4.00e+02 pdb=" CA PRO C 142 " 0.071 5.00e-02 4.00e+02 pdb=" CD PRO C 142 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 141 " -0.085 5.00e-02 4.00e+02 1.29e-01 2.65e+01 pdb=" N PRO B 142 " 0.223 5.00e-02 4.00e+02 pdb=" CA PRO B 142 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO B 142 " -0.066 5.00e-02 4.00e+02 ... (remaining 1885 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 4445 2.86 - 3.37: 12000 3.37 - 3.88: 17535 3.88 - 4.39: 20739 4.39 - 4.90: 30705 Nonbonded interactions: 85424 Sorted by model distance: nonbonded pdb=" OG1 THR A 101 " pdb=" OH TYR A 115 " model vdw 2.352 3.040 nonbonded pdb=" OG1 THR D 101 " pdb=" OH TYR D 115 " model vdw 2.352 3.040 nonbonded pdb=" OG1 THR C 101 " pdb=" OH TYR C 115 " model vdw 2.352 3.040 nonbonded pdb=" OG1 THR B 101 " pdb=" OH TYR B 115 " model vdw 2.352 3.040 nonbonded pdb=" O ALA A 195 " pdb=" OG1 THR A 196 " model vdw 2.436 3.040 ... (remaining 85419 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 27.410 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6509 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 : 0.012 0.062 10960 Z= 0.794 Angle : 1.557 32.963 15036 Z= 1.038 Chirality : 0.138 1.499 1844 Planarity : 0.011 0.129 1888 Dihedral : 8.803 66.342 3340 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.60 % Favored : 93.14 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 1.36 % 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: -1.95 (0.19), residues: 1516 helix: -0.89 (0.13), residues: 1068 sheet: -1.20 (0.47), residues: 68 loop : -2.00 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP C 58 HIS 0.002 0.002 HIS D 161 PHE 0.011 0.002 PHE D 21 TYR 0.034 0.005 TYR A 272 ARG 0.003 0.001 ARG C 30 Details of bonding type rmsd hydrogen bonds : bond 0.17439 ( 893) hydrogen bonds : angle 7.07769 ( 2595) covalent geometry : bond 0.01192 (10960) covalent geometry : angle 1.55716 (15036) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 ASN cc_start: 0.8099 (m-40) cc_final: 0.7890 (t0) REVERT: C 230 ASN cc_start: 0.8120 (m-40) cc_final: 0.7902 (t0) REVERT: D 230 ASN cc_start: 0.8098 (m-40) cc_final: 0.7813 (t0) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.3099 time to fit residues: 63.3915 Evaluate side-chains 83 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 119 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 138 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN B 134 GLN C 134 GLN D 134 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.053684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.042971 restraints weight = 89973.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.043339 restraints weight = 69575.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.043747 restraints weight = 61778.581| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10960 Z= 0.181 Angle : 0.571 6.875 15036 Z= 0.332 Chirality : 0.040 0.142 1844 Planarity : 0.005 0.063 1888 Dihedral : 4.216 15.615 1652 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.49 % Allowed : 3.17 % Favored : 96.34 % 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: 0.69 (0.20), residues: 1516 helix: 0.93 (0.15), residues: 1100 sheet: 0.36 (0.67), residues: 52 loop : -0.77 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 167 HIS 0.001 0.000 HIS B 161 PHE 0.020 0.002 PHE C 152 TYR 0.020 0.002 TYR B 272 ARG 0.003 0.001 ARG A 246 Details of bonding type rmsd hydrogen bonds : bond 0.05639 ( 893) hydrogen bonds : angle 4.75421 ( 2595) covalent geometry : bond 0.00350 (10960) covalent geometry : angle 0.57091 (15036) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 114 time to evaluate : 1.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 ASN cc_start: 0.9380 (m-40) cc_final: 0.8779 (t0) REVERT: A 274 MET cc_start: 0.9661 (mtm) cc_final: 0.9443 (ptp) REVERT: B 274 MET cc_start: 0.9659 (mtm) cc_final: 0.9438 (ptp) REVERT: C 230 ASN cc_start: 0.9442 (m-40) cc_final: 0.8882 (t0) REVERT: C 274 MET cc_start: 0.9662 (mtm) cc_final: 0.9440 (ptp) REVERT: D 230 ASN cc_start: 0.9362 (m-40) cc_final: 0.8880 (t0) REVERT: D 274 MET cc_start: 0.9654 (mtm) cc_final: 0.9435 (ptp) outliers start: 4 outliers final: 0 residues processed: 118 average time/residue: 0.3802 time to fit residues: 59.9506 Evaluate side-chains 73 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 112 optimal weight: 10.0000 chunk 141 optimal weight: 20.0000 chunk 101 optimal weight: 5.9990 chunk 135 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 chunk 70 optimal weight: 30.0000 chunk 111 optimal weight: 30.0000 chunk 81 optimal weight: 20.0000 chunk 49 optimal weight: 0.9990 chunk 130 optimal weight: 7.9990 chunk 90 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.051966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.040905 restraints weight = 100200.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.041257 restraints weight = 79571.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.041743 restraints weight = 70752.127| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10960 Z= 0.265 Angle : 0.640 6.855 15036 Z= 0.373 Chirality : 0.041 0.153 1844 Planarity : 0.005 0.045 1888 Dihedral : 4.307 15.580 1652 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % 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 (0.21), residues: 1516 helix: 1.13 (0.15), residues: 1096 sheet: 1.32 (0.80), residues: 48 loop : -0.21 (0.36), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 162 HIS 0.004 0.002 HIS B 161 PHE 0.026 0.002 PHE D 154 TYR 0.027 0.002 TYR B 272 ARG 0.005 0.001 ARG A 246 Details of bonding type rmsd hydrogen bonds : bond 0.05404 ( 893) hydrogen bonds : angle 4.70494 ( 2595) covalent geometry : bond 0.00498 (10960) covalent geometry : angle 0.64003 (15036) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.9691 (ptmt) cc_final: 0.9412 (ptmt) REVERT: A 217 MET cc_start: 0.9559 (mtm) cc_final: 0.9346 (mtp) REVERT: B 125 LYS cc_start: 0.9686 (ptmt) cc_final: 0.9416 (ptmt) REVERT: B 217 MET cc_start: 0.9538 (mtm) cc_final: 0.9328 (mtp) REVERT: C 125 LYS cc_start: 0.9702 (ptmt) cc_final: 0.9419 (ptmt) REVERT: C 217 MET cc_start: 0.9558 (mtm) cc_final: 0.9347 (mtp) REVERT: D 125 LYS cc_start: 0.9786 (tptp) cc_final: 0.9547 (tppp) REVERT: D 217 MET cc_start: 0.9548 (mtm) cc_final: 0.9342 (mtp) REVERT: D 230 ASN cc_start: 0.9648 (m-40) cc_final: 0.9303 (t0) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.3502 time to fit residues: 46.7541 Evaluate side-chains 68 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 126 optimal weight: 7.9990 chunk 74 optimal weight: 20.0000 chunk 18 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 135 optimal weight: 8.9990 chunk 144 optimal weight: 50.0000 chunk 118 optimal weight: 0.2980 chunk 94 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 106 optimal weight: 50.0000 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.054940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.042783 restraints weight = 87210.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.043508 restraints weight = 66343.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.043948 restraints weight = 54123.072| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 10960 Z= 0.139 Angle : 0.475 4.979 15036 Z= 0.276 Chirality : 0.037 0.128 1844 Planarity : 0.004 0.040 1888 Dihedral : 3.979 16.061 1652 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % 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: 1.74 (0.22), residues: 1516 helix: 1.58 (0.15), residues: 1112 sheet: 1.72 (0.84), residues: 48 loop : -0.13 (0.36), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 162 HIS 0.002 0.001 HIS B 161 PHE 0.024 0.002 PHE D 154 TYR 0.016 0.002 TYR A 272 ARG 0.006 0.001 ARG B 246 Details of bonding type rmsd hydrogen bonds : bond 0.04645 ( 893) hydrogen bonds : angle 4.27815 ( 2595) covalent geometry : bond 0.00278 (10960) covalent geometry : angle 0.47510 (15036) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.9596 (ptmt) cc_final: 0.9257 (ptmt) REVERT: A 230 ASN cc_start: 0.9699 (m110) cc_final: 0.9406 (t0) REVERT: B 125 LYS cc_start: 0.9587 (ptmt) cc_final: 0.9248 (ptmt) REVERT: C 125 LYS cc_start: 0.9608 (ptmt) cc_final: 0.9259 (ptmt) REVERT: C 230 ASN cc_start: 0.9690 (m110) cc_final: 0.9356 (t0) REVERT: D 125 LYS cc_start: 0.9768 (tptp) cc_final: 0.9152 (tppp) REVERT: D 230 ASN cc_start: 0.9693 (m-40) cc_final: 0.9283 (t0) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.3012 time to fit residues: 41.8818 Evaluate side-chains 59 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 144 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 48 optimal weight: 10.0000 chunk 104 optimal weight: 50.0000 chunk 136 optimal weight: 9.9990 chunk 123 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 ASN ** D 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.053089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.041783 restraints weight = 98594.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 17)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.042119 restraints weight = 75880.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.042670 restraints weight = 67406.077| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.4812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10960 Z= 0.142 Angle : 0.472 4.497 15036 Z= 0.274 Chirality : 0.038 0.144 1844 Planarity : 0.003 0.029 1888 Dihedral : 3.749 15.904 1652 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % 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: 2.17 (0.22), residues: 1516 helix: 1.89 (0.15), residues: 1108 sheet: 2.08 (0.87), residues: 48 loop : 0.02 (0.37), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 162 HIS 0.002 0.000 HIS C 161 PHE 0.024 0.002 PHE D 154 TYR 0.015 0.001 TYR B 272 ARG 0.002 0.000 ARG B 268 Details of bonding type rmsd hydrogen bonds : bond 0.04223 ( 893) hydrogen bonds : angle 4.04716 ( 2595) covalent geometry : bond 0.00284 (10960) covalent geometry : angle 0.47167 (15036) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.9677 (ptmt) cc_final: 0.9422 (ptmt) REVERT: A 162 TRP cc_start: 0.9262 (m-90) cc_final: 0.8938 (m-90) REVERT: A 230 ASN cc_start: 0.9692 (m110) cc_final: 0.9384 (t0) REVERT: B 125 LYS cc_start: 0.9671 (ptmt) cc_final: 0.9371 (ptmt) REVERT: B 162 TRP cc_start: 0.9263 (m-90) cc_final: 0.8947 (m-90) REVERT: B 217 MET cc_start: 0.9478 (mtm) cc_final: 0.9263 (mtp) REVERT: C 125 LYS cc_start: 0.9705 (ptmt) cc_final: 0.9448 (ptmt) REVERT: C 162 TRP cc_start: 0.9264 (m-90) cc_final: 0.8933 (m100) REVERT: C 217 MET cc_start: 0.9494 (mtm) cc_final: 0.9270 (mtp) REVERT: C 230 ASN cc_start: 0.9724 (m110) cc_final: 0.9437 (t0) REVERT: D 125 LYS cc_start: 0.9756 (tptp) cc_final: 0.9395 (mttt) REVERT: D 162 TRP cc_start: 0.9254 (m-90) cc_final: 0.8940 (m-90) REVERT: D 217 MET cc_start: 0.9474 (mtm) cc_final: 0.9259 (mtp) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.2818 time to fit residues: 36.3913 Evaluate side-chains 57 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 78 optimal weight: 0.7980 chunk 91 optimal weight: 10.0000 chunk 102 optimal weight: 8.9990 chunk 125 optimal weight: 4.9990 chunk 79 optimal weight: 7.9990 chunk 83 optimal weight: 0.1980 chunk 10 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 98 optimal weight: 8.9990 chunk 62 optimal weight: 9.9990 chunk 70 optimal weight: 30.0000 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN B 59 ASN C 59 ASN C 161 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.052744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.041533 restraints weight = 102084.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.042178 restraints weight = 77611.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.042628 restraints weight = 63226.875| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.5253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10960 Z= 0.146 Angle : 0.483 5.245 15036 Z= 0.279 Chirality : 0.038 0.120 1844 Planarity : 0.003 0.027 1888 Dihedral : 3.738 16.560 1652 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % 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: 2.51 (0.22), residues: 1516 helix: 2.11 (0.15), residues: 1112 sheet: 2.31 (0.89), residues: 48 loop : 0.21 (0.39), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 162 HIS 0.001 0.001 HIS D 161 PHE 0.023 0.002 PHE D 154 TYR 0.014 0.001 TYR B 272 ARG 0.003 0.000 ARG C 268 Details of bonding type rmsd hydrogen bonds : bond 0.04047 ( 893) hydrogen bonds : angle 4.02269 ( 2595) covalent geometry : bond 0.00294 (10960) covalent geometry : angle 0.48315 (15036) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.9676 (ptmt) cc_final: 0.9353 (ptmt) REVERT: A 162 TRP cc_start: 0.9310 (m-90) cc_final: 0.8901 (m-90) REVERT: A 230 ASN cc_start: 0.9705 (m110) cc_final: 0.9397 (t0) REVERT: B 125 LYS cc_start: 0.9672 (ptmt) cc_final: 0.9361 (ptmt) REVERT: B 162 TRP cc_start: 0.9355 (m-90) cc_final: 0.8970 (m-90) REVERT: B 217 MET cc_start: 0.9530 (mtm) cc_final: 0.9321 (mtp) REVERT: C 125 LYS cc_start: 0.9687 (ptmt) cc_final: 0.9366 (ptmt) REVERT: C 149 LEU cc_start: 0.9200 (mt) cc_final: 0.8986 (mt) REVERT: C 151 LEU cc_start: 0.9780 (mt) cc_final: 0.9556 (tp) REVERT: C 162 TRP cc_start: 0.9312 (m-90) cc_final: 0.8915 (m-90) REVERT: C 217 MET cc_start: 0.9543 (mtm) cc_final: 0.9325 (mtp) REVERT: C 230 ASN cc_start: 0.9724 (m110) cc_final: 0.9440 (t0) REVERT: D 125 LYS cc_start: 0.9753 (tptp) cc_final: 0.9398 (mttt) REVERT: D 162 TRP cc_start: 0.9277 (m-90) cc_final: 0.8885 (m-90) REVERT: D 217 MET cc_start: 0.9535 (mtm) cc_final: 0.9316 (mtp) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.3409 time to fit residues: 43.2548 Evaluate side-chains 62 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 111 optimal weight: 50.0000 chunk 81 optimal weight: 20.0000 chunk 16 optimal weight: 4.9990 chunk 107 optimal weight: 50.0000 chunk 112 optimal weight: 9.9990 chunk 114 optimal weight: 20.0000 chunk 124 optimal weight: 6.9990 chunk 33 optimal weight: 50.0000 chunk 94 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN B 141 GLN ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 GLN D 141 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.051938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.041283 restraints weight = 103923.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.041933 restraints weight = 79347.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.042275 restraints weight = 64290.908| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.5942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10960 Z= 0.191 Angle : 0.521 4.988 15036 Z= 0.305 Chirality : 0.039 0.118 1844 Planarity : 0.004 0.034 1888 Dihedral : 3.919 16.936 1652 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % 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: 2.58 (0.22), residues: 1516 helix: 2.15 (0.15), residues: 1112 sheet: 2.06 (0.87), residues: 48 loop : 0.36 (0.40), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 162 HIS 0.003 0.002 HIS C 161 PHE 0.020 0.002 PHE D 154 TYR 0.014 0.002 TYR D 272 ARG 0.004 0.001 ARG A 268 Details of bonding type rmsd hydrogen bonds : bond 0.04138 ( 893) hydrogen bonds : angle 4.17628 ( 2595) covalent geometry : bond 0.00374 (10960) covalent geometry : angle 0.52149 (15036) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.9693 (ptmt) cc_final: 0.9316 (ptmt) REVERT: A 149 LEU cc_start: 0.9218 (mt) cc_final: 0.8979 (mt) REVERT: A 162 TRP cc_start: 0.9518 (m-90) cc_final: 0.9156 (m100) REVERT: A 230 ASN cc_start: 0.9710 (m110) cc_final: 0.9381 (t0) REVERT: B 125 LYS cc_start: 0.9690 (ptmt) cc_final: 0.9365 (ptmt) REVERT: B 162 TRP cc_start: 0.9519 (m-90) cc_final: 0.9159 (m100) REVERT: B 217 MET cc_start: 0.9526 (mtm) cc_final: 0.9274 (mtp) REVERT: C 125 LYS cc_start: 0.9704 (ptmt) cc_final: 0.9371 (ptmt) REVERT: C 149 LEU cc_start: 0.9159 (mt) cc_final: 0.8928 (mt) REVERT: C 151 LEU cc_start: 0.9764 (mt) cc_final: 0.9546 (tp) REVERT: C 162 TRP cc_start: 0.9486 (m-90) cc_final: 0.9051 (m-90) REVERT: C 217 MET cc_start: 0.9565 (mtm) cc_final: 0.9325 (mtp) REVERT: C 230 ASN cc_start: 0.9733 (m110) cc_final: 0.9425 (t0) REVERT: D 162 TRP cc_start: 0.9497 (m-90) cc_final: 0.9060 (m-90) REVERT: D 217 MET cc_start: 0.9558 (mtm) cc_final: 0.9328 (mtp) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.2542 time to fit residues: 30.5494 Evaluate side-chains 67 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 3 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 65 optimal weight: 40.0000 chunk 96 optimal weight: 9.9990 chunk 33 optimal weight: 50.0000 chunk 60 optimal weight: 0.5980 chunk 72 optimal weight: 10.0000 chunk 136 optimal weight: 9.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.052576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.041690 restraints weight = 105976.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.042312 restraints weight = 79562.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.042677 restraints weight = 64239.813| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.6077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10960 Z= 0.142 Angle : 0.490 5.470 15036 Z= 0.282 Chirality : 0.038 0.160 1844 Planarity : 0.003 0.025 1888 Dihedral : 3.781 16.893 1652 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % 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: 2.83 (0.23), residues: 1516 helix: 2.34 (0.15), residues: 1112 sheet: -0.40 (0.64), residues: 88 loop : 1.02 (0.44), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP C 162 HIS 0.003 0.002 HIS B 161 PHE 0.020 0.001 PHE D 154 TYR 0.015 0.001 TYR B 272 ARG 0.002 0.000 ARG D 246 Details of bonding type rmsd hydrogen bonds : bond 0.03948 ( 893) hydrogen bonds : angle 4.07788 ( 2595) covalent geometry : bond 0.00285 (10960) covalent geometry : angle 0.48962 (15036) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.9697 (ptmt) cc_final: 0.9370 (ptmt) REVERT: A 149 LEU cc_start: 0.9232 (mt) cc_final: 0.9016 (mt) REVERT: A 154 PHE cc_start: 0.9457 (t80) cc_final: 0.9233 (t80) REVERT: A 162 TRP cc_start: 0.9374 (m-90) cc_final: 0.9067 (m100) REVERT: A 230 ASN cc_start: 0.9718 (m110) cc_final: 0.9412 (t0) REVERT: B 125 LYS cc_start: 0.9693 (ptmt) cc_final: 0.9357 (ptmt) REVERT: B 162 TRP cc_start: 0.9379 (m-90) cc_final: 0.9085 (m100) REVERT: B 217 MET cc_start: 0.9514 (mtm) cc_final: 0.9306 (mtp) REVERT: C 125 LYS cc_start: 0.9710 (ptmt) cc_final: 0.9382 (ptmt) REVERT: C 149 LEU cc_start: 0.9246 (mt) cc_final: 0.9018 (mt) REVERT: C 162 TRP cc_start: 0.9355 (m-90) cc_final: 0.9062 (m100) REVERT: C 217 MET cc_start: 0.9530 (mtm) cc_final: 0.9312 (mtp) REVERT: C 230 ASN cc_start: 0.9741 (m110) cc_final: 0.9458 (t0) REVERT: D 125 LYS cc_start: 0.9766 (tptp) cc_final: 0.9443 (mttt) REVERT: D 162 TRP cc_start: 0.9349 (m-90) cc_final: 0.9044 (m100) REVERT: D 217 MET cc_start: 0.9522 (mtm) cc_final: 0.9301 (mtp) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.3417 time to fit residues: 41.1754 Evaluate side-chains 69 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 102 optimal weight: 20.0000 chunk 136 optimal weight: 8.9990 chunk 103 optimal weight: 40.0000 chunk 58 optimal weight: 1.9990 chunk 72 optimal weight: 50.0000 chunk 63 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 76 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.051780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.041207 restraints weight = 111600.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.041849 restraints weight = 83121.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.042335 restraints weight = 65643.877| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.6469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10960 Z= 0.185 Angle : 0.530 5.545 15036 Z= 0.310 Chirality : 0.039 0.139 1844 Planarity : 0.004 0.029 1888 Dihedral : 3.919 17.607 1652 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: 2.70 (0.23), residues: 1516 helix: 2.20 (0.15), residues: 1116 sheet: -0.60 (0.62), residues: 88 loop : 1.21 (0.45), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP C 162 HIS 0.003 0.002 HIS B 161 PHE 0.023 0.002 PHE D 154 TYR 0.024 0.002 TYR A 272 ARG 0.003 0.000 ARG C 246 Details of bonding type rmsd hydrogen bonds : bond 0.04092 ( 893) hydrogen bonds : angle 4.30537 ( 2595) covalent geometry : bond 0.00365 (10960) covalent geometry : angle 0.53038 (15036) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.9702 (ptmt) cc_final: 0.9375 (ptmt) REVERT: A 149 LEU cc_start: 0.9306 (mt) cc_final: 0.9096 (mt) REVERT: A 162 TRP cc_start: 0.9446 (m-90) cc_final: 0.9098 (m100) REVERT: A 230 ASN cc_start: 0.9735 (m110) cc_final: 0.9420 (t0) REVERT: B 125 LYS cc_start: 0.9697 (ptmt) cc_final: 0.9333 (ptmt) REVERT: B 162 TRP cc_start: 0.9455 (m-90) cc_final: 0.9104 (m100) REVERT: B 217 MET cc_start: 0.9595 (mtm) cc_final: 0.9356 (mtp) REVERT: C 125 LYS cc_start: 0.9705 (ptmt) cc_final: 0.9371 (ptmt) REVERT: C 149 LEU cc_start: 0.9290 (mt) cc_final: 0.9073 (mt) REVERT: C 162 TRP cc_start: 0.9412 (m-90) cc_final: 0.9093 (m100) REVERT: C 217 MET cc_start: 0.9617 (mtm) cc_final: 0.9389 (mtp) REVERT: C 230 ASN cc_start: 0.9769 (m110) cc_final: 0.9494 (t0) REVERT: D 162 TRP cc_start: 0.9423 (m-90) cc_final: 0.9088 (m100) REVERT: D 217 MET cc_start: 0.9590 (mtm) cc_final: 0.9352 (mtp) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.3671 time to fit residues: 43.3771 Evaluate side-chains 67 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 5 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 130 optimal weight: 0.0470 chunk 54 optimal weight: 6.9990 chunk 117 optimal weight: 1.9990 chunk 10 optimal weight: 0.0050 overall best weight: 1.2096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.052922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.041698 restraints weight = 100061.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.042317 restraints weight = 74795.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.042689 restraints weight = 60478.392| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.6597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10960 Z= 0.105 Angle : 0.465 5.320 15036 Z= 0.264 Chirality : 0.038 0.147 1844 Planarity : 0.003 0.022 1888 Dihedral : 3.559 16.618 1652 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % 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: 3.00 (0.23), residues: 1516 helix: 2.51 (0.15), residues: 1124 sheet: -0.39 (0.65), residues: 88 loop : 0.81 (0.44), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP C 162 HIS 0.001 0.001 HIS C 161 PHE 0.021 0.002 PHE D 154 TYR 0.014 0.001 TYR B 272 ARG 0.004 0.000 ARG D 246 Details of bonding type rmsd hydrogen bonds : bond 0.03645 ( 893) hydrogen bonds : angle 3.95896 ( 2595) covalent geometry : bond 0.00216 (10960) covalent geometry : angle 0.46493 (15036) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.9727 (ptmt) cc_final: 0.9451 (ptmt) REVERT: A 149 LEU cc_start: 0.9251 (mt) cc_final: 0.9038 (mt) REVERT: A 154 PHE cc_start: 0.9572 (t80) cc_final: 0.9302 (t80) REVERT: A 162 TRP cc_start: 0.9368 (m-90) cc_final: 0.8914 (m100) REVERT: A 230 ASN cc_start: 0.9717 (m110) cc_final: 0.9389 (t0) REVERT: B 125 LYS cc_start: 0.9715 (ptmt) cc_final: 0.9391 (ptmt) REVERT: B 162 TRP cc_start: 0.9423 (m-90) cc_final: 0.9015 (m100) REVERT: B 217 MET cc_start: 0.9526 (mtm) cc_final: 0.9290 (mtp) REVERT: B 242 LYS cc_start: 0.9663 (mmpt) cc_final: 0.9435 (ptpt) REVERT: C 125 LYS cc_start: 0.9739 (ptmt) cc_final: 0.9407 (ptmt) REVERT: C 149 LEU cc_start: 0.9256 (mt) cc_final: 0.9048 (mt) REVERT: C 162 TRP cc_start: 0.9359 (m-90) cc_final: 0.8978 (m100) REVERT: C 217 MET cc_start: 0.9516 (mtm) cc_final: 0.9285 (mtp) REVERT: C 230 ASN cc_start: 0.9752 (m110) cc_final: 0.9455 (t0) REVERT: D 162 TRP cc_start: 0.9339 (m-90) cc_final: 0.8883 (m100) REVERT: D 217 MET cc_start: 0.9503 (mtm) cc_final: 0.9263 (mtp) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.2760 time to fit residues: 35.1049 Evaluate side-chains 68 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 66 optimal weight: 50.0000 chunk 146 optimal weight: 2.9990 chunk 91 optimal weight: 0.0570 chunk 111 optimal weight: 50.0000 chunk 113 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 125 optimal weight: 5.9990 chunk 28 optimal weight: 50.0000 chunk 137 optimal weight: 7.9990 chunk 144 optimal weight: 50.0000 chunk 96 optimal weight: 0.0570 overall best weight: 2.2222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.052724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.041808 restraints weight = 101108.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.042116 restraints weight = 75838.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.042686 restraints weight = 67097.561| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.6751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10960 Z= 0.116 Angle : 0.464 5.119 15036 Z= 0.267 Chirality : 0.038 0.143 1844 Planarity : 0.003 0.022 1888 Dihedral : 3.518 16.425 1652 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % 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: 3.09 (0.23), residues: 1516 helix: 2.57 (0.15), residues: 1124 sheet: -0.42 (0.63), residues: 88 loop : 0.88 (0.44), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP C 162 HIS 0.002 0.001 HIS C 161 PHE 0.022 0.002 PHE D 154 TYR 0.016 0.001 TYR A 272 ARG 0.003 0.000 ARG D 246 Details of bonding type rmsd hydrogen bonds : bond 0.03561 ( 893) hydrogen bonds : angle 3.94437 ( 2595) covalent geometry : bond 0.00241 (10960) covalent geometry : angle 0.46380 (15036) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3350.82 seconds wall clock time: 61 minutes 33.97 seconds (3693.97 seconds total)