Starting phenix.real_space_refine on Wed Sep 25 16:56:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v4s_8633/09_2024/5v4s_8633.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v4s_8633/09_2024/5v4s_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v4s_8633/09_2024/5v4s_8633.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v4s_8633/09_2024/5v4s_8633.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v4s_8633/09_2024/5v4s_8633.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v4s_8633/09_2024/5v4s_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 5.22, per 1000 atoms: 0.49 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: 2.89 Conformation dependent library (CDL) restraints added in 1.4 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: 1.32 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: 3.85 Time building geometry restraints manager: 3.33 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' 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: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.090 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.030 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.710 ------------------------------------------------------------------------------- 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= 0.792 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.279 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: 0.2930 time to fit residues: 59.6844 Evaluate side-chains 83 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.291 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6575 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= 0.229 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 *********************** 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 fitting. rotamer outliers: 4 poor density : 114 time to evaluate : 1.307 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: 0.7662 (m-40) cc_final: 0.6512 (t0) REVERT: A 249 MET cc_start: 0.6373 (ttm) cc_final: 0.4382 (ttm) REVERT: B 249 MET cc_start: 0.6327 (ttm) cc_final: 0.4351 (ttm) REVERT: C 230 ASN cc_start: 0.7660 (m-40) cc_final: 0.6503 (t0) REVERT: C 249 MET cc_start: 0.6332 (ttm) cc_final: 0.4407 (ttm) REVERT: D 230 ASN cc_start: 0.7632 (m-40) cc_final: 0.6786 (t0) REVERT: D 249 MET cc_start: 0.6397 (ttm) cc_final: 0.4544 (ttm) outliers start: 4 outliers final: 0 residues processed: 118 average time/residue: 0.3061 time to fit residues: 47.8298 Evaluate side-chains 73 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 20.0000 chunk 42 optimal weight: 1.9990 chunk 114 optimal weight: 20.0000 chunk 93 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 138 optimal weight: 8.9990 chunk 149 optimal weight: 0.8980 chunk 123 optimal weight: 9.9990 chunk 137 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN C 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10960 Z= 0.176 Angle : 0.489 5.854 15036 Z= 0.285 Chirality : 0.037 0.130 1844 Planarity : 0.004 0.045 1888 Dihedral : 3.856 14.326 1652 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % 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: 1.82 (0.21), residues: 1516 helix: 1.74 (0.15), residues: 1092 sheet: 1.06 (0.79), residues: 48 loop : -0.27 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 162 HIS 0.003 0.001 HIS C 161 PHE 0.020 0.002 PHE C 154 TYR 0.018 0.001 TYR B 272 ARG 0.002 0.000 ARG A 270 *********************** 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 115 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.128 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 outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.2757 time to fit residues: 42.8473 Evaluate side-chains 65 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.0011 > 50: distance: 21 - 23: 15.636 distance: 23 - 24: 13.576 distance: 24 - 25: 14.823 distance: 24 - 27: 21.379 distance: 25 - 26: 15.105 distance: 25 - 28: 11.598 distance: 28 - 29: 5.533 distance: 29 - 30: 8.557 distance: 30 - 31: 12.050 distance: 30 - 33: 6.333 distance: 31 - 48: 14.063 distance: 33 - 34: 3.881 distance: 34 - 35: 6.698 distance: 34 - 37: 17.579 distance: 35 - 36: 12.231 distance: 35 - 38: 7.619 distance: 36 - 53: 9.588 distance: 38 - 39: 14.108 distance: 39 - 40: 15.846 distance: 39 - 42: 30.547 distance: 40 - 41: 28.157 distance: 40 - 43: 6.135 distance: 41 - 58: 15.365 distance: 43 - 44: 5.257 distance: 44 - 45: 12.886 distance: 44 - 47: 13.347 distance: 45 - 46: 22.280 distance: 45 - 48: 10.191 distance: 48 - 49: 10.990 distance: 49 - 50: 10.470 distance: 49 - 52: 16.607 distance: 50 - 51: 24.374 distance: 50 - 53: 10.386 distance: 53 - 54: 7.123 distance: 54 - 55: 8.853 distance: 54 - 57: 8.764 distance: 55 - 56: 10.748 distance: 55 - 58: 11.401 distance: 59 - 60: 7.369 distance: 59 - 62: 11.011 distance: 60 - 61: 12.202 distance: 60 - 63: 3.765 distance: 63 - 64: 10.979 distance: 64 - 65: 14.898 distance: 64 - 67: 19.746 distance: 65 - 66: 30.218 distance: 65 - 68: 15.259 distance: 68 - 69: 6.177 distance: 69 - 70: 10.577 distance: 69 - 72: 40.170 distance: 70 - 71: 16.332 distance: 70 - 73: 24.573