Starting phenix.real_space_refine on Thu Jul 2 09:21:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n96_49161/07_2026/9n96_49161.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n96_49161/07_2026/9n96_49161.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9n96_49161/07_2026/9n96_49161.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n96_49161/07_2026/9n96_49161.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n96_49161/07_2026/9n96_49161.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n96_49161/07_2026/9n96_49161.map" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.030 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: 5 Type Number sf(0) Gaussians P 43 5.49 5 S 45 5.16 5 C 4861 2.51 5 N 1393 2.21 5 O 1579 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7921 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 652 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "B" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 612 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain breaks: 1 Chain: "C" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 764 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 1, 'TRANS': 93} Chain: "D" Number of atoms: 750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 750 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain breaks: 1 Chain: "E" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 614 Classifications: {'peptide': 74} Link IDs: {'TRANS': 73} Chain: "F" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 579 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "G" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 604 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "J" Number of atoms: 2439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2439 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 12, 'TRANS': 295} Chain: "Y" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 343 Classifications: {'RNA': 16} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 5} Link IDs: {'rna2p': 2, 'rna3p': 13} Chain breaks: 1 Chain: "Z" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 564 Classifications: {'RNA': 27} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 3, 'rna3p_pur': 6, 'rna3p_pyr': 14} Link IDs: {'rna2p': 7, 'rna3p': 19} Time building chain proxies: 1.39, per 1000 atoms: 0.18 Number of scatterers: 7921 At special positions: 0 Unit cell: (81.225, 96.387, 127.794, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 45 16.00 P 43 15.00 O 1579 8.00 N 1393 7.00 C 4861 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: 0.49 Conformation dependent library (CDL) restraints added in 294.9 milliseconds 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1656 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 6 sheets defined 36.7% alpha, 25.4% beta 13 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 4 through 11 removed outlier: 3.693A pdb=" N LYS A 8 " --> pdb=" O GLY A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 78 removed outlier: 3.620A pdb=" N LEU A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 16 removed outlier: 4.159A pdb=" N ILE C 12 " --> pdb=" O LYS C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 23 removed outlier: 4.198A pdb=" N LEU C 21 " --> pdb=" O LEU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 100 Processing helix chain 'D' and resid 154 through 159 removed outlier: 3.640A pdb=" N GLU D 158 " --> pdb=" O SER D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 166 removed outlier: 3.777A pdb=" N ILE D 163 " --> pdb=" O LEU D 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 28 Processing helix chain 'F' and resid 6 through 13 Processing helix chain 'G' and resid 9 through 13 removed outlier: 3.516A pdb=" N MET G 13 " --> pdb=" O LYS G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 65 No H-bonds generated for 'chain 'G' and resid 63 through 65' Processing helix chain 'J' and resid 36 through 45 removed outlier: 3.748A pdb=" N LEU J 45 " --> pdb=" O ASN J 41 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 64 removed outlier: 4.127A pdb=" N VAL J 54 " --> pdb=" O SER J 50 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU J 61 " --> pdb=" O GLN J 57 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE J 62 " --> pdb=" O VAL J 58 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN J 64 " --> pdb=" O GLU J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 74 removed outlier: 3.570A pdb=" N PHE J 73 " --> pdb=" O LEU J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 74 through 79 removed outlier: 3.786A pdb=" N ALA J 79 " --> pdb=" O ASP J 75 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 83 Processing helix chain 'J' and resid 85 through 103 removed outlier: 4.300A pdb=" N ARG J 89 " --> pdb=" O SER J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 119 removed outlier: 3.594A pdb=" N ILE J 111 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ALA J 112 " --> pdb=" O LEU J 108 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASN J 113 " --> pdb=" O LYS J 109 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN J 115 " --> pdb=" O ILE J 111 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU J 117 " --> pdb=" O ASN J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 123 through 147 removed outlier: 4.040A pdb=" N GLN J 135 " --> pdb=" O LEU J 131 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LYS J 138 " --> pdb=" O THR J 134 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 171 removed outlier: 3.802A pdb=" N MET J 160 " --> pdb=" O ALA J 156 " (cutoff:3.500A) Processing helix chain 'J' and resid 172 through 174 No H-bonds generated for 'chain 'J' and resid 172 through 174' Processing helix chain 'J' and resid 176 through 194 Processing helix chain 'J' and resid 224 through 244 removed outlier: 3.647A pdb=" N LEU J 228 " --> pdb=" O GLN J 224 " (cutoff:3.500A) Processing helix chain 'J' and resid 249 through 267 removed outlier: 3.599A pdb=" N GLY J 258 " --> pdb=" O THR J 254 " (cutoff:3.500A) Processing helix chain 'J' and resid 270 through 279 removed outlier: 3.834A pdb=" N ILE J 275 " --> pdb=" O MET J 271 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N GLN J 276 " --> pdb=" O SER J 272 " (cutoff:3.500A) Processing helix chain 'J' and resid 290 through 311 Processing helix chain 'J' and resid 312 through 316 removed outlier: 4.283A pdb=" N GLU J 316 " --> pdb=" O ALA J 313 " (cutoff:3.500A) Processing helix chain 'J' and resid 317 through 326 removed outlier: 4.053A pdb=" N THR J 322 " --> pdb=" O GLN J 318 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N THR J 323 " --> pdb=" O ALA J 319 " (cutoff:3.500A) Processing helix chain 'J' and resid 327 through 329 No H-bonds generated for 'chain 'J' and resid 327 through 329' Processing helix chain 'J' and resid 331 through 336 removed outlier: 3.527A pdb=" N ILE J 335 " --> pdb=" O PRO J 331 " (cutoff:3.500A) Processing helix chain 'J' and resid 337 through 339 No H-bonds generated for 'chain 'J' and resid 337 through 339' Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 19 removed outlier: 6.675A pdb=" N GLY A 30 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE A 46 " --> pdb=" O GLY A 30 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N LEU A 32 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N SER A 44 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET A 43 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLU A 59 " --> pdb=" O ASN A 45 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 70 through 73 removed outlier: 4.219A pdb=" N LEU B 69 " --> pdb=" O LEU A 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 70 through 73 removed outlier: 4.219A pdb=" N LEU B 69 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N CYS B 43 " --> pdb=" O PHE B 31 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N PHE B 31 " --> pdb=" O CYS B 43 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N CYS B 45 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLY B 29 " --> pdb=" O CYS B 45 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLU B 47 " --> pdb=" O PHE B 27 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N PHE B 27 " --> pdb=" O GLU B 47 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ARG B 16 " --> pdb=" O GLU B 83 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER B 79 " --> pdb=" O ILE B 20 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 66 through 68 removed outlier: 3.885A pdb=" N HIS C 40 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR C 30 " --> pdb=" O HIS C 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 339 through 343 removed outlier: 6.734A pdb=" N ILE D 173 " --> pdb=" O ARG D 180 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL D 182 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL D 171 " --> pdb=" O VAL D 182 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS D 168 " --> pdb=" O ALA D 359 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU D 355 " --> pdb=" O HIS D 172 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ARG D 174 " --> pdb=" O VAL D 353 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL D 353 " --> pdb=" O ARG D 174 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLU F 61 " --> pdb=" O LEU D 358 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N SER F 56 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N TYR F 50 " --> pdb=" O SER F 56 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N HIS F 58 " --> pdb=" O GLU F 48 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLU F 48 " --> pdb=" O HIS F 58 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N GLY F 60 " --> pdb=" O ASN F 46 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N MET F 42 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL F 36 " --> pdb=" O MET F 42 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU F 44 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL F 34 " --> pdb=" O LEU F 44 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ASN F 46 " --> pdb=" O TYR F 32 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N TYR F 32 " --> pdb=" O ASN F 46 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N MET F 27 " --> pdb=" O LEU F 23 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N GLY F 74 " --> pdb=" O PRO F 18 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N MET F 20 " --> pdb=" O ILE F 72 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ILE F 72 " --> pdb=" O MET F 20 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LYS F 22 " --> pdb=" O LEU F 70 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ARG E 76 " --> pdb=" O GLY F 74 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ALA E 61 " --> pdb=" O LEU E 74 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ARG E 76 " --> pdb=" O ASP E 59 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASP E 59 " --> pdb=" O ARG E 76 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N MET E 78 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL E 57 " --> pdb=" O MET E 78 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N LEU E 58 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ILE E 48 " --> pdb=" O LEU E 58 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ASP E 60 " --> pdb=" O CYS E 46 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N CYS E 46 " --> pdb=" O ASP E 60 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N MET E 41 " --> pdb=" O LEU E 35 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LEU E 35 " --> pdb=" O MET E 41 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU E 86 " --> pdb=" O TRP E 34 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 54 through 62 removed outlier: 7.254A pdb=" N GLN G 54 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N MET G 48 " --> pdb=" O GLN G 54 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASN G 56 " --> pdb=" O VAL G 46 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL G 46 " --> pdb=" O ASN G 56 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N GLY G 58 " --> pdb=" O GLU G 44 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU G 44 " --> pdb=" O GLY G 58 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL G 41 " --> pdb=" O ARG G 32 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N CYS G 45 " --> pdb=" O GLN G 28 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLN G 28 " --> pdb=" O CYS G 45 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N GLU G 47 " --> pdb=" O HIS G 26 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N HIS G 26 " --> pdb=" O GLU G 47 " (cutoff:3.500A) 293 hydrogen bonds defined for protein. 831 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 31 hydrogen bonds 62 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 1.01 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2156 1.33 - 1.46: 1556 1.46 - 1.58: 4256 1.58 - 1.70: 84 1.70 - 1.82: 78 Bond restraints: 8130 Sorted by residual: bond pdb=" C VAL A 5 " pdb=" N PRO A 6 " ideal model delta sigma weight residual 1.335 1.409 -0.074 1.36e-02 5.41e+03 2.96e+01 bond pdb=" C MET D 148 " pdb=" N PRO D 149 " ideal model delta sigma weight residual 1.335 1.378 -0.043 9.40e-03 1.13e+04 2.11e+01 bond pdb=" N1 U Z 13 " pdb=" C2 U Z 13 " ideal model delta sigma weight residual 1.381 1.397 -0.016 9.00e-03 1.23e+04 3.31e+00 bond pdb=" CA PHE D 193 " pdb=" C PHE D 193 " ideal model delta sigma weight residual 1.523 1.491 0.032 1.80e-02 3.09e+03 3.12e+00 bond pdb=" N1 C Z 14 " pdb=" C2 C Z 14 " ideal model delta sigma weight residual 1.397 1.414 -0.017 1.00e-02 1.00e+04 3.06e+00 ... (remaining 8125 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 10797 2.30 - 4.61: 300 4.61 - 6.91: 46 6.91 - 9.21: 20 9.21 - 11.51: 5 Bond angle restraints: 11168 Sorted by residual: angle pdb=" C1' C Z 14 " pdb=" N1 C Z 14 " pdb=" C2 C Z 14 " ideal model delta sigma weight residual 118.80 124.19 -5.39 1.10e+00 8.26e-01 2.40e+01 angle pdb=" CA LYS C 8 " pdb=" CB LYS C 8 " pdb=" CG LYS C 8 " ideal model delta sigma weight residual 114.10 123.83 -9.73 2.00e+00 2.50e-01 2.37e+01 angle pdb=" C1' U Z 13 " pdb=" N1 U Z 13 " pdb=" C2 U Z 13 " ideal model delta sigma weight residual 117.70 123.21 -5.51 1.20e+00 6.94e-01 2.11e+01 angle pdb=" N GLU J 230 " pdb=" CA GLU J 230 " pdb=" CB GLU J 230 " ideal model delta sigma weight residual 110.40 117.65 -7.25 1.63e+00 3.76e-01 1.98e+01 angle pdb=" CA GLN J 332 " pdb=" CB GLN J 332 " pdb=" CG GLN J 332 " ideal model delta sigma weight residual 114.10 122.48 -8.38 2.00e+00 2.50e-01 1.75e+01 ... (remaining 11163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 4404 17.87 - 35.74: 449 35.74 - 53.61: 99 53.61 - 71.48: 51 71.48 - 89.35: 15 Dihedral angle restraints: 5018 sinusoidal: 2474 harmonic: 2544 Sorted by residual: dihedral pdb=" CA GLN A 42 " pdb=" C GLN A 42 " pdb=" N MET A 43 " pdb=" CA MET A 43 " ideal model delta harmonic sigma weight residual -180.00 -158.16 -21.84 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA MET F 40 " pdb=" C MET F 40 " pdb=" N ASN F 41 " pdb=" CA ASN F 41 " ideal model delta harmonic sigma weight residual 180.00 158.18 21.82 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA TRP F 25 " pdb=" C TRP F 25 " pdb=" N GLY F 26 " pdb=" CA GLY F 26 " ideal model delta harmonic sigma weight residual 180.00 160.01 19.99 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 5015 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 901 0.044 - 0.088: 304 0.088 - 0.131: 106 0.131 - 0.175: 21 0.175 - 0.219: 5 Chirality restraints: 1337 Sorted by residual: chirality pdb=" CB VAL A 5 " pdb=" CA VAL A 5 " pdb=" CG1 VAL A 5 " pdb=" CG2 VAL A 5 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB VAL C 88 " pdb=" CA VAL C 88 " pdb=" CG1 VAL C 88 " pdb=" CG2 VAL C 88 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA GLU E 37 " pdb=" N GLU E 37 " pdb=" C GLU E 37 " pdb=" CB GLU E 37 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.32e-01 ... (remaining 1334 not shown) Planarity restraints: 1266 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS J 245 " -0.063 5.00e-02 4.00e+02 9.53e-02 1.45e+01 pdb=" N PRO J 246 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO J 246 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO J 246 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 84 " 0.053 5.00e-02 4.00e+02 8.16e-02 1.06e+01 pdb=" N PRO C 85 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO C 85 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO C 85 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 80 " -0.050 5.00e-02 4.00e+02 7.69e-02 9.45e+00 pdb=" N PRO A 81 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 81 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 81 " -0.042 5.00e-02 4.00e+02 ... (remaining 1263 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 3864 3.01 - 3.49: 7694 3.49 - 3.96: 12599 3.96 - 4.43: 14590 4.43 - 4.90: 23140 Nonbonded interactions: 61887 Sorted by model distance: nonbonded pdb=" O5' U Z 29 " pdb=" O4' U Z 29 " model vdw 2.543 2.432 nonbonded pdb=" O4' C Z 14 " pdb=" C6 C Z 14 " model vdw 2.547 2.672 nonbonded pdb=" O ASP G 14 " pdb=" OD1 ASP G 14 " model vdw 2.556 3.040 nonbonded pdb=" O4' U Z 13 " pdb=" C6 U Z 13 " model vdw 2.562 2.672 nonbonded pdb=" O5' A Z 8 " pdb=" O4' A Z 8 " model vdw 2.567 2.432 ... (remaining 61882 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.730 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.130 Find NCS groups from input model: 0.040 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 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 : 0.005 0.075 8130 Z= 0.237 Angle : 0.974 11.514 11168 Z= 0.548 Chirality : 0.051 0.219 1337 Planarity : 0.008 0.095 1266 Dihedral : 16.342 89.349 3362 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.27), residues: 859 helix: -1.31 (0.27), residues: 281 sheet: -1.52 (0.39), residues: 177 loop : -1.19 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 161 TYR 0.021 0.002 TYR F 71 PHE 0.018 0.002 PHE A 70 TRP 0.024 0.003 TRP F 25 HIS 0.005 0.001 HIS D 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.24 ( 8130) covalent geometry : angle 0.97405 / 0.55 (11168) hydrogen bonds : bond 0.16176 / 11.11 ( 317) hydrogen bonds : angle 7.51625 / 5.05 ( 893) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: C 44 ASP cc_start: 0.7725 (m-30) cc_final: 0.7462 (m-30) REVERT: D 196 MET cc_start: 0.8102 (mpp) cc_final: 0.7466 (mtm) REVERT: E 71 ARG cc_start: 0.7979 (mmp-170) cc_final: 0.7741 (mmt180) REVERT: G 13 MET cc_start: 0.7989 (mmt) cc_final: 0.7777 (mmm) REVERT: G 48 MET cc_start: 0.7564 (mmm) cc_final: 0.7288 (mmm) REVERT: J 73 PHE cc_start: 0.9056 (m-80) cc_final: 0.8817 (m-80) REVERT: J 84 LYS cc_start: 0.8064 (ttpt) cc_final: 0.7798 (pttp) REVERT: J 142 GLN cc_start: 0.8199 (tm-30) cc_final: 0.7859 (tm-30) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.0773 time to fit residues: 16.1023 Evaluate side-chains 134 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.1980 chunk 74 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN D 344 ASN ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 276 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.188035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.143012 restraints weight = 9492.833| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.30 r_work: 0.3661 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8130 Z= 0.165 Angle : 0.630 8.729 11168 Z= 0.331 Chirality : 0.043 0.168 1337 Planarity : 0.005 0.063 1266 Dihedral : 14.940 76.469 1585 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.27 % Allowed : 8.03 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.29), residues: 859 helix: -0.44 (0.30), residues: 296 sheet: -1.52 (0.39), residues: 176 loop : -0.97 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 29 TYR 0.017 0.002 TYR F 71 PHE 0.018 0.002 PHE A 70 TRP 0.007 0.001 TRP J 158 HIS 0.006 0.001 HIS A 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 ( 8130) covalent geometry : angle 0.62960 / 0.33 (11168) hydrogen bonds : bond 0.05065 / 3.56 ( 317) hydrogen bonds : angle 5.61711 / 3.88 ( 893) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 142 time to evaluate : 0.249 Fit side-chains REVERT: D 161 ARG cc_start: 0.7483 (ttp-110) cc_final: 0.7149 (ttp-110) REVERT: D 202 ASP cc_start: 0.7877 (p0) cc_final: 0.7652 (p0) REVERT: G 13 MET cc_start: 0.7787 (mmt) cc_final: 0.7540 (mmm) REVERT: G 48 MET cc_start: 0.7270 (mmm) cc_final: 0.6971 (mmm) REVERT: J 73 PHE cc_start: 0.8729 (m-80) cc_final: 0.8506 (m-80) REVERT: J 84 LYS cc_start: 0.7992 (ttpt) cc_final: 0.7756 (pttp) REVERT: J 142 GLN cc_start: 0.8025 (tm-30) cc_final: 0.7632 (tm-30) REVERT: J 231 GLU cc_start: 0.8188 (tp30) cc_final: 0.7867 (tp30) outliers start: 10 outliers final: 4 residues processed: 147 average time/residue: 0.0936 time to fit residues: 18.1125 Evaluate side-chains 135 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 131 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 CYS Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain J residue 335 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 0.9980 chunk 51 optimal weight: 0.0870 chunk 39 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 85 optimal weight: 20.0000 chunk 2 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN D 344 ASN ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.186062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.142068 restraints weight = 9580.417| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.18 r_work: 0.3664 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3527 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8130 Z= 0.150 Angle : 0.598 7.482 11168 Z= 0.313 Chirality : 0.042 0.196 1337 Planarity : 0.004 0.055 1266 Dihedral : 14.777 76.031 1585 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.40 % Allowed : 10.45 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.29), residues: 859 helix: -0.13 (0.30), residues: 296 sheet: -1.43 (0.39), residues: 186 loop : -0.77 (0.34), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 29 TYR 0.013 0.001 TYR F 71 PHE 0.018 0.002 PHE A 70 TRP 0.009 0.001 TRP J 229 HIS 0.006 0.001 HIS D 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 ( 8130) covalent geometry : angle 0.59782 / 0.31 (11168) hydrogen bonds : bond 0.04697 / 3.33 ( 317) hydrogen bonds : angle 5.28150 / 3.65 ( 893) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 0.183 Fit side-chains REVERT: A 39 MET cc_start: 0.8140 (mmm) cc_final: 0.7798 (mmm) REVERT: D 161 ARG cc_start: 0.7783 (ttp-110) cc_final: 0.7530 (ttp-110) REVERT: D 196 MET cc_start: 0.8129 (mpp) cc_final: 0.7480 (mpp) REVERT: D 202 ASP cc_start: 0.8162 (p0) cc_final: 0.7586 (p0) REVERT: G 48 MET cc_start: 0.7553 (mmm) cc_final: 0.7277 (mmm) REVERT: J 73 PHE cc_start: 0.8821 (m-80) cc_final: 0.8559 (m-80) REVERT: J 84 LYS cc_start: 0.8142 (ttpt) cc_final: 0.7797 (pttp) REVERT: J 142 GLN cc_start: 0.8274 (tm-30) cc_final: 0.7869 (tm-30) outliers start: 11 outliers final: 9 residues processed: 147 average time/residue: 0.1017 time to fit residues: 19.4340 Evaluate side-chains 144 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 135 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 CYS Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 335 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 23 optimal weight: 0.0980 chunk 71 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 ASN ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 220 HIS ** 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 = 0.4242 r_free = 0.4242 target = 0.185532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.140254 restraints weight = 9411.677| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.26 r_work: 0.3618 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8130 Z= 0.172 Angle : 0.606 6.963 11168 Z= 0.318 Chirality : 0.043 0.165 1337 Planarity : 0.004 0.048 1266 Dihedral : 14.653 75.628 1585 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.04 % Allowed : 11.97 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.29), residues: 859 helix: 0.02 (0.30), residues: 296 sheet: -0.97 (0.41), residues: 160 loop : -0.93 (0.33), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 29 TYR 0.013 0.002 TYR F 71 PHE 0.022 0.002 PHE B 31 TRP 0.009 0.001 TRP J 229 HIS 0.007 0.001 HIS D 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 ( 8130) covalent geometry : angle 0.60575 / 0.32 (11168) hydrogen bonds : bond 0.04653 / 3.28 ( 317) hydrogen bonds : angle 5.15472 / 3.57 ( 893) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 0.281 Fit side-chains REVERT: A 39 MET cc_start: 0.8110 (mmm) cc_final: 0.7710 (mmm) REVERT: D 161 ARG cc_start: 0.7784 (ttp-110) cc_final: 0.7241 (ttp-110) REVERT: D 196 MET cc_start: 0.8114 (mpp) cc_final: 0.7643 (mpp) REVERT: D 202 ASP cc_start: 0.8093 (p0) cc_final: 0.7504 (p0) REVERT: G 48 MET cc_start: 0.7293 (mmm) cc_final: 0.7020 (mmm) REVERT: J 84 LYS cc_start: 0.8235 (ttpt) cc_final: 0.7801 (pttp) REVERT: J 142 GLN cc_start: 0.8178 (tm-30) cc_final: 0.7704 (tm-30) outliers start: 16 outliers final: 12 residues processed: 153 average time/residue: 0.0932 time to fit residues: 18.8880 Evaluate side-chains 145 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 133 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 CYS Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 335 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.5369 > 50: distance: 48 - 56: 34.447 distance: 56 - 57: 36.783 distance: 56 - 184: 37.948 distance: 57 - 58: 39.646 distance: 57 - 60: 45.408 distance: 58 - 59: 56.897 distance: 58 - 64: 54.407 distance: 59 - 181: 32.876 distance: 60 - 61: 46.328 distance: 61 - 62: 13.447 distance: 61 - 63: 34.575 distance: 64 - 65: 43.419 distance: 65 - 66: 11.933 distance: 65 - 68: 44.673 distance: 66 - 67: 42.558 distance: 66 - 72: 42.202 distance: 68 - 69: 20.750 distance: 68 - 70: 21.443 distance: 69 - 71: 22.958 distance: 72 - 73: 37.854 distance: 72 - 170: 25.716 distance: 73 - 74: 18.721 distance: 73 - 76: 51.611 distance: 74 - 75: 40.153 distance: 74 - 80: 16.969 distance: 76 - 77: 57.231 distance: 77 - 78: 12.786 distance: 77 - 79: 50.216 distance: 80 - 81: 24.387 distance: 80 - 86: 33.894 distance: 81 - 82: 23.415 distance: 81 - 84: 41.475 distance: 82 - 83: 16.316 distance: 82 - 87: 26.068 distance: 84 - 85: 8.575 distance: 85 - 86: 29.659 distance: 87 - 88: 8.903 distance: 88 - 89: 20.946 distance: 88 - 91: 36.014 distance: 89 - 90: 27.732 distance: 89 - 95: 39.833 distance: 90 - 111: 18.901 distance: 91 - 92: 11.074 distance: 92 - 93: 19.457 distance: 92 - 94: 18.191 distance: 95 - 96: 29.175 distance: 96 - 97: 25.046 distance: 96 - 99: 33.568 distance: 97 - 98: 33.053 distance: 97 - 103: 15.941 distance: 99 - 100: 46.361 distance: 100 - 101: 28.348 distance: 101 - 102: 23.645 distance: 103 - 104: 23.340 distance: 104 - 107: 33.971 distance: 105 - 106: 44.805 distance: 105 - 111: 38.265 distance: 107 - 108: 20.971 distance: 108 - 109: 34.854 distance: 108 - 110: 27.659 distance: 111 - 112: 28.414 distance: 112 - 113: 23.095 distance: 112 - 115: 26.920 distance: 113 - 114: 55.595 distance: 113 - 120: 30.942 distance: 115 - 116: 29.838 distance: 116 - 117: 31.839 distance: 117 - 118: 35.705 distance: 118 - 119: 32.954 distance: 120 - 121: 38.101 distance: 121 - 122: 46.629 distance: 121 - 124: 51.953 distance: 122 - 123: 43.649 distance: 122 - 128: 14.970 distance: 124 - 125: 40.312 distance: 125 - 126: 32.591 distance: 125 - 127: 37.402 distance: 128 - 129: 53.157 distance: 129 - 130: 24.416 distance: 129 - 132: 38.813 distance: 130 - 131: 26.127 distance: 130 - 133: 20.511