Starting phenix.real_space_refine on Fri Jul 3 11:34:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8oze_17306/07_2026/8oze_17306.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oze_17306/07_2026/8oze_17306.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8oze_17306/07_2026/8oze_17306.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oze_17306/07_2026/8oze_17306.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8oze_17306/07_2026/8oze_17306.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oze_17306/07_2026/8oze_17306.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8oze_17306/07_2026/8oze_17306.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8oze_17306/07_2026/8oze_17306.cif" } resolution = 2.91 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= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 502 atoms to isotropic. 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 74 5.49 5 S 40 5.16 5 C 8420 2.51 5 N 2244 2.21 5 O 2656 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: 13434 Number of models: 1 Model: "" Number of chains: 4 Chain: "N" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 435 Classifications: {'RNA': 20} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 12, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 18} Chain: "P" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 339 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "E" Number of atoms: 2122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2122 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 8, 'TRANS': 242} Chain: "F" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3821 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 24, 'TRANS': 448} Chain breaks: 1 Restraints were copied for chains: A, B, G, H Time building chain proxies: 3.33, per 1000 atoms: 0.25 Number of scatterers: 13434 At special positions: 0 Unit cell: (153.67, 129.47, 84.7, 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 40 16.00 P 74 15.00 O 2656 8.00 N 2244 7.00 C 8420 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: 0.86 Conformation dependent library (CDL) restraints added in 468.0 milliseconds 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2748 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 14 sheets defined 35.9% alpha, 16.9% beta 21 base pairs and 58 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'E' and resid 190 through 194 Processing helix chain 'E' and resid 199 through 203 removed outlier: 3.556A pdb=" N GLU E 202 " --> pdb=" O ASP E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 233 removed outlier: 3.590A pdb=" N GLU E 231 " --> pdb=" O PRO E 228 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N THR E 232 " --> pdb=" O LYS E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 238 Processing helix chain 'E' and resid 243 through 249 Processing helix chain 'E' and resid 257 through 280 removed outlier: 3.504A pdb=" N ARG E 263 " --> pdb=" O ALA E 259 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU E 264 " --> pdb=" O GLU E 260 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE E 265 " --> pdb=" O CYS E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 366 Processing helix chain 'E' and resid 369 through 385 removed outlier: 3.834A pdb=" N LYS E 376 " --> pdb=" O THR E 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 17 No H-bonds generated for 'chain 'F' and resid 15 through 17' Processing helix chain 'F' and resid 22 through 30 Processing helix chain 'F' and resid 46 through 62 removed outlier: 3.643A pdb=" N ILE F 52 " --> pdb=" O GLN F 48 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS F 62 " --> pdb=" O ASP F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 83 Processing helix chain 'F' and resid 97 through 104 removed outlier: 3.717A pdb=" N PHE F 104 " --> pdb=" O ASP F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 131 removed outlier: 4.123A pdb=" N LYS F 124 " --> pdb=" O LEU F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 150 removed outlier: 3.568A pdb=" N TYR F 148 " --> pdb=" O PRO F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 162 Processing helix chain 'F' and resid 205 through 214 removed outlier: 3.574A pdb=" N LEU F 214 " --> pdb=" O PHE F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 264 Processing helix chain 'F' and resid 331 through 351 removed outlier: 3.586A pdb=" N GLN F 349 " --> pdb=" O SER F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 377 removed outlier: 3.564A pdb=" N VAL F 376 " --> pdb=" O ALA F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 430 Processing helix chain 'F' and resid 451 through 463 Processing helix chain 'F' and resid 477 through 491 Processing helix chain 'F' and resid 502 through 506 removed outlier: 3.592A pdb=" N TYR F 505 " --> pdb=" O ALA F 502 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 194 Processing helix chain 'G' and resid 199 through 203 removed outlier: 3.556A pdb=" N GLU G 202 " --> pdb=" O ASP G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 233 removed outlier: 3.590A pdb=" N GLU G 231 " --> pdb=" O PRO G 228 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR G 232 " --> pdb=" O LYS G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 238 Processing helix chain 'G' and resid 243 through 249 Processing helix chain 'G' and resid 257 through 280 removed outlier: 3.504A pdb=" N ARG G 263 " --> pdb=" O ALA G 259 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU G 264 " --> pdb=" O GLU G 260 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE G 265 " --> pdb=" O CYS G 261 " (cutoff:3.500A) Processing helix chain 'G' and resid 353 through 366 Processing helix chain 'G' and resid 369 through 385 removed outlier: 3.834A pdb=" N LYS G 376 " --> pdb=" O THR G 372 " (cutoff:3.500A) Processing helix chain 'H' and resid 15 through 17 No H-bonds generated for 'chain 'H' and resid 15 through 17' Processing helix chain 'H' and resid 22 through 30 Processing helix chain 'H' and resid 46 through 62 removed outlier: 3.642A pdb=" N ILE H 52 " --> pdb=" O GLN H 48 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS H 62 " --> pdb=" O ASP H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 83 Processing helix chain 'H' and resid 97 through 104 removed outlier: 3.718A pdb=" N PHE H 104 " --> pdb=" O ASP H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 131 removed outlier: 4.123A pdb=" N LYS H 124 " --> pdb=" O LEU H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 150 removed outlier: 3.567A pdb=" N TYR H 148 " --> pdb=" O PRO H 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 158 through 162 Processing helix chain 'H' and resid 205 through 214 removed outlier: 3.575A pdb=" N LEU H 214 " --> pdb=" O PHE H 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 248 through 264 Processing helix chain 'H' and resid 331 through 351 removed outlier: 3.586A pdb=" N GLN H 349 " --> pdb=" O SER H 345 " (cutoff:3.500A) Processing helix chain 'H' and resid 366 through 377 removed outlier: 3.564A pdb=" N VAL H 376 " --> pdb=" O ALA H 372 " (cutoff:3.500A) Processing helix chain 'H' and resid 427 through 430 Processing helix chain 'H' and resid 451 through 463 Processing helix chain 'H' and resid 477 through 491 Processing helix chain 'H' and resid 502 through 506 removed outlier: 3.592A pdb=" N TYR H 505 " --> pdb=" O ALA H 502 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 169 through 180 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 169 through 180 current: chain 'E' and resid 317 through 328 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 334 through 344 current: chain 'E' and resid 400 through 412 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 2 through 6 current: chain 'F' and resid 297 through 305 removed outlier: 7.400A pdb=" N CYS F 298 " --> pdb=" O GLY F 318 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N GLY F 318 " --> pdb=" O CYS F 298 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA F 300 " --> pdb=" O GLU F 316 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 311 through 321 current: chain 'F' and resid 382 through 389 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 382 through 389 current: chain 'F' and resid 417 through 420 Processing sheet with id=AA2, first strand: chain 'E' and resid 208 through 210 Processing sheet with id=AA3, first strand: chain 'E' and resid 283 through 286 Processing sheet with id=AA4, first strand: chain 'E' and resid 304 through 305 removed outlier: 3.639A pdb=" N PHE E 305 " --> pdb=" O THR E 308 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 19 through 20 Processing sheet with id=AA6, first strand: chain 'F' and resid 92 through 95 removed outlier: 6.346A pdb=" N GLY F 42 " --> pdb=" O PHE F 140 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ILE F 142 " --> pdb=" O GLY F 42 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE F 44 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TRP F 139 " --> pdb=" O GLN F 222 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N PHE F 224 " --> pdb=" O TRP F 139 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL F 141 " --> pdb=" O PHE F 224 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 425 through 426 removed outlier: 4.035A pdb=" N THR F 431 " --> pdb=" O VAL F 426 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 169 through 180 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 169 through 180 current: chain 'G' and resid 317 through 328 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 334 through 344 current: chain 'G' and resid 400 through 412 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 2 through 6 current: chain 'H' and resid 297 through 305 removed outlier: 7.400A pdb=" N CYS H 298 " --> pdb=" O GLY H 318 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N GLY H 318 " --> pdb=" O CYS H 298 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA H 300 " --> pdb=" O GLU H 316 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 311 through 321 current: chain 'H' and resid 382 through 389 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 382 through 389 current: chain 'H' and resid 417 through 420 Processing sheet with id=AA9, first strand: chain 'G' and resid 208 through 210 Processing sheet with id=AB1, first strand: chain 'G' and resid 283 through 286 Processing sheet with id=AB2, first strand: chain 'G' and resid 304 through 305 removed outlier: 3.639A pdb=" N PHE G 305 " --> pdb=" O THR G 308 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 18 through 20 removed outlier: 3.557A pdb=" N GLN H 18 " --> pdb=" O PHE H 14 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 92 through 95 removed outlier: 6.346A pdb=" N GLY H 42 " --> pdb=" O PHE H 140 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ILE H 142 " --> pdb=" O GLY H 42 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE H 44 " --> pdb=" O ILE H 142 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TRP H 139 " --> pdb=" O GLN H 222 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N PHE H 224 " --> pdb=" O TRP H 139 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL H 141 " --> pdb=" O PHE H 224 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 425 through 426 removed outlier: 4.034A pdb=" N THR H 431 " --> pdb=" O VAL H 426 " (cutoff:3.500A) 409 hydrogen bonds defined for protein. 1095 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 52 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 58 stacking parallelities Total time for adding SS restraints: 1.75 Time building geometry restraints manager: 1.23 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: 2871 1.33 - 1.45: 3531 1.45 - 1.57: 7324 1.57 - 1.69: 144 1.69 - 1.81: 62 Bond restraints: 13932 Sorted by residual: bond pdb=" C3' DA B 19 " pdb=" C2' DA B 19 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.54e+00 bond pdb=" C3' DA P 19 " pdb=" C2' DA P 19 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.45e+00 bond pdb=" C3' DC P 17 " pdb=" C2' DC P 17 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 7.95e+00 bond pdb=" C3' DC B 17 " pdb=" C2' DC B 17 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.90e+00 bond pdb=" C3' DC P 20 " pdb=" C2' DC P 20 " ideal model delta sigma weight residual 1.516 1.534 -0.018 8.00e-03 1.56e+04 5.13e+00 ... (remaining 13927 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 18200 1.15 - 2.30: 781 2.30 - 3.45: 148 3.45 - 4.61: 31 4.61 - 5.76: 12 Bond angle restraints: 19172 Sorted by residual: angle pdb=" N3 DT B 8 " pdb=" C4 DT B 8 " pdb=" O4 DT B 8 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.76e+01 angle pdb=" N3 DT P 18 " pdb=" C4 DT P 18 " pdb=" O4 DT P 18 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT P 8 " pdb=" C4 DT P 8 " pdb=" O4 DT P 8 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.70e+01 angle pdb=" N3 DT B 18 " pdb=" C4 DT B 18 " pdb=" O4 DT B 18 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 angle pdb=" N3 DT P 15 " pdb=" C4 DT P 15 " pdb=" O4 DT P 15 " ideal model delta sigma weight residual 119.90 122.33 -2.43 6.00e-01 2.78e+00 1.64e+01 ... (remaining 19167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 7886 35.91 - 71.82: 222 71.82 - 107.74: 14 107.74 - 143.65: 0 143.65 - 179.56: 6 Dihedral angle restraints: 8128 sinusoidal: 3862 harmonic: 4266 Sorted by residual: dihedral pdb=" O4' U N 13 " pdb=" C1' U N 13 " pdb=" N1 U N 13 " pdb=" C2 U N 13 " ideal model delta sinusoidal sigma weight residual 200.00 20.44 179.56 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U A 13 " pdb=" C1' U A 13 " pdb=" N1 U A 13 " pdb=" C2 U A 13 " ideal model delta sinusoidal sigma weight residual 200.00 20.44 179.56 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U N 9 " pdb=" C1' U N 9 " pdb=" N1 U N 9 " pdb=" C2 U N 9 " ideal model delta sinusoidal sigma weight residual -160.00 -10.62 -149.38 1 1.50e+01 4.44e-03 7.94e+01 ... (remaining 8125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1377 0.033 - 0.067: 495 0.067 - 0.100: 153 0.100 - 0.133: 62 0.133 - 0.166: 5 Chirality restraints: 2092 Sorted by residual: chirality pdb=" CB ILE E 239 " pdb=" CA ILE E 239 " pdb=" CG1 ILE E 239 " pdb=" CG2 ILE E 239 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.93e-01 chirality pdb=" CB ILE G 239 " pdb=" CA ILE G 239 " pdb=" CG1 ILE G 239 " pdb=" CG2 ILE G 239 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.78e-01 chirality pdb=" CA ILE H 388 " pdb=" N ILE H 388 " pdb=" C ILE H 388 " pdb=" CB ILE H 388 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.94e-01 ... (remaining 2089 not shown) Planarity restraints: 2156 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS H 392 " 0.047 5.00e-02 4.00e+02 7.07e-02 8.00e+00 pdb=" N PRO H 393 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO H 393 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO H 393 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 392 " -0.046 5.00e-02 4.00e+02 7.06e-02 7.97e+00 pdb=" N PRO F 393 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO F 393 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO F 393 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG F 72 " 0.038 5.00e-02 4.00e+02 5.78e-02 5.34e+00 pdb=" N PRO F 73 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO F 73 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO F 73 " 0.032 5.00e-02 4.00e+02 ... (remaining 2153 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 351 2.68 - 3.24: 12584 3.24 - 3.79: 22295 3.79 - 4.35: 31171 4.35 - 4.90: 49036 Nonbonded interactions: 115437 Sorted by model distance: nonbonded pdb=" OE2 GLU E 284 " pdb=" OG1 THR E 291 " model vdw 2.128 3.040 nonbonded pdb=" OE2 GLU G 284 " pdb=" OG1 THR G 291 " model vdw 2.128 3.040 nonbonded pdb=" OH TYR G 221 " pdb=" O TYR G 233 " model vdw 2.224 3.040 nonbonded pdb=" OH TYR E 221 " pdb=" O TYR E 233 " model vdw 2.224 3.040 nonbonded pdb=" O LYS F 11 " pdb=" OG SER F 272 " model vdw 2.258 3.040 ... (remaining 115432 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: 0.01 Found NCS groups: ncs_group { reference = chain 'N' selection = chain 'A' } ncs_group { reference = chain 'P' selection = chain 'B' } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' } 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: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.950 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 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 : 0.004 0.041 13932 Z= 0.222 Angle : 0.571 5.757 19172 Z= 0.354 Chirality : 0.041 0.166 2092 Planarity : 0.005 0.071 2156 Dihedral : 16.485 179.559 5380 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.69 % Favored : 93.04 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -0.72 (0.22), residues: 1436 helix: 0.86 (0.25), residues: 442 sheet: -0.64 (0.31), residues: 274 loop : -1.26 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 24 TYR 0.009 0.001 TYR H 280 PHE 0.014 0.001 PHE E 342 TRP 0.010 0.001 TRP H 370 HIS 0.003 0.001 HIS H 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.22 (13932) covalent geometry : angle 0.57108 / 0.35 (19172) hydrogen bonds : bond 0.18154 / 10.61 ( 461) hydrogen bonds : angle 7.28465 / 7.13 ( 1199) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: E 336 MET cc_start: 0.8148 (mtt) cc_final: 0.7877 (mtt) REVERT: F 227 SER cc_start: 0.7807 (m) cc_final: 0.7418 (m) REVERT: G 279 ASP cc_start: 0.7416 (t70) cc_final: 0.7152 (t70) REVERT: G 336 MET cc_start: 0.8195 (mtt) cc_final: 0.7983 (mtt) REVERT: G 369 TRP cc_start: 0.6536 (m100) cc_final: 0.6180 (m100) REVERT: H 56 TYR cc_start: 0.7477 (t80) cc_final: 0.7158 (t80) REVERT: H 227 SER cc_start: 0.7634 (m) cc_final: 0.7205 (m) outliers start: 0 outliers final: 1 residues processed: 193 average time/residue: 0.4391 time to fit residues: 94.2138 Evaluate side-chains 114 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 387 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 9.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 371 ASN F 307 ASN ** F 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 344 GLN H 209 GLN ** H 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 344 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.193361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.157463 restraints weight = 16757.466| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 2.38 r_work: 0.3787 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 13932 Z= 0.215 Angle : 0.658 7.723 19172 Z= 0.347 Chirality : 0.046 0.255 2092 Planarity : 0.006 0.064 2156 Dihedral : 15.765 176.134 2430 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.99 % Favored : 93.73 % Rotamer: Outliers : 2.24 % Allowed : 8.18 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -0.79 (0.22), residues: 1436 helix: 0.97 (0.24), residues: 438 sheet: -0.63 (0.32), residues: 272 loop : -1.43 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 24 TYR 0.014 0.002 TYR G 225 PHE 0.020 0.002 PHE G 305 TRP 0.014 0.002 TRP G 219 HIS 0.004 0.001 HIS F 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.22 (13932) covalent geometry : angle 0.65761 / 0.35 (19172) hydrogen bonds : bond 0.05413 / 3.13 ( 461) hydrogen bonds : angle 5.20295 / 5.26 ( 1199) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 0.474 Fit side-chains revert: symmetry clash REVERT: E 287 MET cc_start: 0.8082 (mmm) cc_final: 0.7453 (mmm) REVERT: E 336 MET cc_start: 0.8541 (mtt) cc_final: 0.8171 (mtt) REVERT: F 1 MET cc_start: 0.7546 (tpp) cc_final: 0.7236 (tpp) REVERT: F 18 GLN cc_start: 0.7533 (mt0) cc_final: 0.6673 (mt0) REVERT: F 30 PHE cc_start: 0.6569 (m-10) cc_final: 0.5912 (m-10) REVERT: F 113 ARG cc_start: 0.6520 (ptm160) cc_final: 0.5802 (mtm180) REVERT: F 117 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7894 (mp) REVERT: F 205 GLN cc_start: 0.7286 (OUTLIER) cc_final: 0.6802 (tt0) REVERT: F 227 SER cc_start: 0.8753 (m) cc_final: 0.8469 (m) REVERT: F 322 ASN cc_start: 0.7404 (t0) cc_final: 0.7016 (t0) REVERT: F 333 LYS cc_start: 0.8819 (tttt) cc_final: 0.8569 (tptt) REVERT: G 336 MET cc_start: 0.8584 (mtt) cc_final: 0.8314 (mtt) REVERT: G 369 TRP cc_start: 0.7237 (m100) cc_final: 0.6129 (m100) REVERT: H 56 TYR cc_start: 0.7897 (t80) cc_final: 0.7386 (t80) REVERT: H 227 SER cc_start: 0.8669 (m) cc_final: 0.8384 (m) REVERT: H 334 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7714 (mt-10) outliers start: 29 outliers final: 19 residues processed: 144 average time/residue: 0.4825 time to fit residues: 77.5064 Evaluate side-chains 133 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 332 PHE Chi-restraints excluded: chain E residue 387 ASP Chi-restraints excluded: chain E residue 415 SER Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 205 GLN Chi-restraints excluded: chain F residue 267 LYS Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 507 ILE Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain G residue 415 SER Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 267 LYS Chi-restraints excluded: chain H residue 274 VAL Chi-restraints excluded: chain H residue 334 GLU Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 507 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 52 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 93 optimal weight: 7.9990 chunk 106 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 123 optimal weight: 0.9990 chunk 140 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 ASN ** F 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 GLN H 322 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.194176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.157887 restraints weight = 16663.544| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 2.44 r_work: 0.3791 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13932 Z= 0.144 Angle : 0.581 6.790 19172 Z= 0.311 Chirality : 0.043 0.240 2092 Planarity : 0.005 0.058 2156 Dihedral : 15.617 176.054 2430 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.22 % Favored : 94.50 % Rotamer: Outliers : 2.39 % Allowed : 10.03 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -0.58 (0.22), residues: 1436 helix: 1.18 (0.25), residues: 436 sheet: -0.60 (0.32), residues: 272 loop : -1.29 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 243 TYR 0.014 0.001 TYR G 225 PHE 0.015 0.001 PHE E 198 TRP 0.014 0.001 TRP F 370 HIS 0.005 0.001 HIS F 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (13932) covalent geometry : angle 0.58060 / 0.31 (19172) hydrogen bonds : bond 0.04613 / 2.65 ( 461) hydrogen bonds : angle 4.89781 / 4.96 ( 1199) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 125 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 287 MET cc_start: 0.7953 (mmm) cc_final: 0.7337 (mmm) REVERT: E 336 MET cc_start: 0.8526 (mtt) cc_final: 0.8261 (mtt) REVERT: F 18 GLN cc_start: 0.7517 (mt0) cc_final: 0.6685 (mt0) REVERT: F 30 PHE cc_start: 0.6705 (m-10) cc_final: 0.6069 (m-10) REVERT: F 113 ARG cc_start: 0.6445 (ptm160) cc_final: 0.5807 (mtm180) REVERT: F 117 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7820 (mp) REVERT: F 227 SER cc_start: 0.8731 (m) cc_final: 0.8432 (m) REVERT: F 322 ASN cc_start: 0.7315 (t0) cc_final: 0.6909 (t0) REVERT: F 333 LYS cc_start: 0.8818 (tttt) cc_final: 0.8569 (tptt) REVERT: G 254 ASN cc_start: 0.7757 (p0) cc_final: 0.7424 (t0) REVERT: G 336 MET cc_start: 0.8610 (mtt) cc_final: 0.8329 (mtt) REVERT: H 56 TYR cc_start: 0.7840 (t80) cc_final: 0.7308 (t80) REVERT: H 205 GLN cc_start: 0.7430 (OUTLIER) cc_final: 0.7161 (tt0) REVERT: H 227 SER cc_start: 0.8663 (m) cc_final: 0.8365 (m) REVERT: H 334 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7850 (mt-10) outliers start: 31 outliers final: 13 residues processed: 146 average time/residue: 0.4872 time to fit residues: 78.9055 Evaluate side-chains 127 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 215 CYS Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 254 ASN Chi-restraints excluded: chain E residue 332 PHE Chi-restraints excluded: chain E residue 387 ASP Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 507 ILE Chi-restraints excluded: chain G residue 215 CYS Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain H residue 205 GLN Chi-restraints excluded: chain H residue 267 LYS Chi-restraints excluded: chain H residue 274 VAL Chi-restraints excluded: chain H residue 334 GLU Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 507 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 55 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 121 optimal weight: 0.4980 chunk 122 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 142 optimal weight: 0.5980 chunk 123 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 115 optimal weight: 0.3980 chunk 117 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 ASN ** F 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 209 GLN H 322 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.195393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.159218 restraints weight = 16552.930| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 2.43 r_work: 0.3810 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13932 Z= 0.127 Angle : 0.566 8.413 19172 Z= 0.301 Chirality : 0.042 0.248 2092 Planarity : 0.005 0.055 2156 Dihedral : 15.607 175.203 2430 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.36 % Favored : 94.36 % Rotamer: Outliers : 2.62 % Allowed : 10.42 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -0.47 (0.22), residues: 1436 helix: 1.30 (0.25), residues: 436 sheet: -0.52 (0.33), residues: 272 loop : -1.24 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 362 TYR 0.013 0.001 TYR G 225 PHE 0.018 0.001 PHE E 198 TRP 0.013 0.001 TRP G 219 HIS 0.003 0.001 HIS H 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (13932) covalent geometry : angle 0.56627 / 0.30 (19172) hydrogen bonds : bond 0.04189 / 2.39 ( 461) hydrogen bonds : angle 4.76778 / 4.82 ( 1199) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 120 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: E 229 LYS cc_start: 0.7695 (tttt) cc_final: 0.7355 (pttt) REVERT: E 287 MET cc_start: 0.7998 (mmm) cc_final: 0.7388 (mmm) REVERT: E 336 MET cc_start: 0.8513 (mtt) cc_final: 0.8244 (mtt) REVERT: F 30 PHE cc_start: 0.6699 (m-10) cc_final: 0.6277 (m-10) REVERT: F 205 GLN cc_start: 0.6999 (OUTLIER) cc_final: 0.6521 (tt0) REVERT: F 227 SER cc_start: 0.8688 (m) cc_final: 0.8379 (m) REVERT: F 322 ASN cc_start: 0.7436 (t0) cc_final: 0.7043 (t0) REVERT: G 210 TYR cc_start: 0.7232 (t80) cc_final: 0.6990 (t80) REVERT: G 236 SER cc_start: 0.6204 (t) cc_final: 0.5998 (p) REVERT: G 254 ASN cc_start: 0.7770 (OUTLIER) cc_final: 0.7433 (OUTLIER) REVERT: G 294 TRP cc_start: 0.7755 (p-90) cc_final: 0.7531 (p-90) REVERT: G 306 GLU cc_start: 0.7336 (mt-10) cc_final: 0.7132 (mt-10) REVERT: G 336 MET cc_start: 0.8603 (mtt) cc_final: 0.8241 (mtt) REVERT: H 56 TYR cc_start: 0.7827 (t80) cc_final: 0.7289 (t80) REVERT: H 205 GLN cc_start: 0.7193 (OUTLIER) cc_final: 0.6978 (tt0) REVERT: H 227 SER cc_start: 0.8612 (m) cc_final: 0.8307 (m) REVERT: H 380 GLU cc_start: 0.7715 (tp30) cc_final: 0.7344 (tp30) outliers start: 34 outliers final: 19 residues processed: 147 average time/residue: 0.4274 time to fit residues: 70.0987 Evaluate side-chains 129 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 215 CYS Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 254 ASN Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain E residue 332 PHE Chi-restraints excluded: chain E residue 387 ASP Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 205 GLN Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 507 ILE Chi-restraints excluded: chain G residue 215 CYS Chi-restraints excluded: chain G residue 254 ASN Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain H residue 205 GLN Chi-restraints excluded: chain H residue 267 LYS Chi-restraints excluded: chain H residue 274 VAL Chi-restraints excluded: chain H residue 507 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 119 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 GLN F 307 ASN ** F 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 209 GLN ** H 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.193387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.157029 restraints weight = 16611.394| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 2.42 r_work: 0.3774 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13932 Z= 0.166 Angle : 0.584 9.399 19172 Z= 0.309 Chirality : 0.043 0.275 2092 Planarity : 0.005 0.061 2156 Dihedral : 15.662 174.837 2430 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.50 % Favored : 94.22 % Rotamer: Outliers : 2.55 % Allowed : 11.11 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -0.50 (0.22), residues: 1436 helix: 1.19 (0.24), residues: 440 sheet: -0.51 (0.33), residues: 272 loop : -1.23 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 263 TYR 0.015 0.002 TYR E 251 PHE 0.020 0.002 PHE E 198 TRP 0.012 0.002 TRP G 219 HIS 0.003 0.001 HIS F 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (13932) covalent geometry : angle 0.58398 / 0.31 (19172) hydrogen bonds : bond 0.04234 / 2.43 ( 461) hydrogen bonds : angle 4.79037 / 4.87 ( 1199) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: E 192 TRP cc_start: 0.7725 (p-90) cc_final: 0.7458 (p-90) REVERT: E 229 LYS cc_start: 0.7688 (OUTLIER) cc_final: 0.7407 (pttt) REVERT: E 287 MET cc_start: 0.7912 (mmm) cc_final: 0.7269 (mmm) REVERT: E 336 MET cc_start: 0.8549 (mtt) cc_final: 0.8283 (mtt) REVERT: F 205 GLN cc_start: 0.7067 (OUTLIER) cc_final: 0.6640 (tt0) REVERT: F 227 SER cc_start: 0.8718 (m) cc_final: 0.8383 (m) REVERT: F 322 ASN cc_start: 0.7483 (t0) cc_final: 0.7067 (t0) REVERT: G 254 ASN cc_start: 0.7769 (OUTLIER) cc_final: 0.7443 (OUTLIER) REVERT: G 306 GLU cc_start: 0.7385 (mt-10) cc_final: 0.7137 (mt-10) REVERT: G 336 MET cc_start: 0.8603 (mtt) cc_final: 0.8282 (mtt) REVERT: H 56 TYR cc_start: 0.7860 (t80) cc_final: 0.7387 (t80) REVERT: H 205 GLN cc_start: 0.7244 (OUTLIER) cc_final: 0.6994 (tt0) REVERT: H 227 SER cc_start: 0.8681 (m) cc_final: 0.8430 (m) outliers start: 33 outliers final: 20 residues processed: 140 average time/residue: 0.4545 time to fit residues: 71.2298 Evaluate side-chains 130 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 215 CYS Chi-restraints excluded: chain E residue 229 LYS Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain E residue 332 PHE Chi-restraints excluded: chain E residue 387 ASP Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 205 GLN Chi-restraints excluded: chain F residue 267 LYS Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 507 ILE Chi-restraints excluded: chain G residue 215 CYS Chi-restraints excluded: chain G residue 254 ASN Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain H residue 113 ARG Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain H residue 205 GLN Chi-restraints excluded: chain H residue 267 LYS Chi-restraints excluded: chain H residue 274 VAL Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 507 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 40 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 87 optimal weight: 0.5980 chunk 124 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 114 optimal weight: 0.6980 chunk 108 optimal weight: 0.5980 chunk 99 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 370 ASN F 18 GLN F 307 ASN ** F 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 209 GLN H 322 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.194750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.158432 restraints weight = 16624.534| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 2.45 r_work: 0.3797 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13932 Z= 0.136 Angle : 0.570 11.517 19172 Z= 0.302 Chirality : 0.042 0.259 2092 Planarity : 0.005 0.057 2156 Dihedral : 15.630 174.156 2430 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.36 % Favored : 94.36 % Rotamer: Outliers : 2.78 % Allowed : 11.96 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -0.42 (0.22), residues: 1436 helix: 1.26 (0.25), residues: 440 sheet: -0.53 (0.33), residues: 284 loop : -1.15 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 72 TYR 0.014 0.001 TYR G 225 PHE 0.022 0.001 PHE E 198 TRP 0.013 0.001 TRP G 219 HIS 0.002 0.001 HIS F 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (13932) covalent geometry : angle 0.56971 / 0.30 (19172) hydrogen bonds : bond 0.04001 / 2.29 ( 461) hydrogen bonds : angle 4.68965 / 4.75 ( 1199) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 123 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: E 229 LYS cc_start: 0.7678 (OUTLIER) cc_final: 0.7425 (pttt) REVERT: E 287 MET cc_start: 0.7902 (mmm) cc_final: 0.7253 (mmm) REVERT: E 336 MET cc_start: 0.8498 (mtt) cc_final: 0.8219 (mtt) REVERT: F 113 ARG cc_start: 0.6572 (ptm160) cc_final: 0.6302 (ptm160) REVERT: F 205 GLN cc_start: 0.6912 (OUTLIER) cc_final: 0.6460 (tt0) REVERT: F 227 SER cc_start: 0.8717 (m) cc_final: 0.8398 (m) REVERT: F 322 ASN cc_start: 0.7456 (t0) cc_final: 0.7046 (t0) REVERT: G 254 ASN cc_start: 0.7788 (OUTLIER) cc_final: 0.7516 (OUTLIER) REVERT: G 294 TRP cc_start: 0.7748 (p-90) cc_final: 0.7459 (p-90) REVERT: G 306 GLU cc_start: 0.7360 (mt-10) cc_final: 0.7118 (mt-10) REVERT: G 336 MET cc_start: 0.8574 (mtt) cc_final: 0.8262 (mtt) REVERT: H 56 TYR cc_start: 0.7821 (t80) cc_final: 0.7359 (t80) REVERT: H 91 ILE cc_start: 0.7582 (OUTLIER) cc_final: 0.6989 (pt) REVERT: H 227 SER cc_start: 0.8668 (m) cc_final: 0.8421 (m) REVERT: H 380 GLU cc_start: 0.7666 (tp30) cc_final: 0.7305 (tp30) outliers start: 36 outliers final: 23 residues processed: 147 average time/residue: 0.4388 time to fit residues: 72.3715 Evaluate side-chains 136 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 215 CYS Chi-restraints excluded: chain E residue 229 LYS Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 332 PHE Chi-restraints excluded: chain E residue 387 ASP Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 205 GLN Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 507 ILE Chi-restraints excluded: chain G residue 215 CYS Chi-restraints excluded: chain G residue 254 ASN Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 113 ARG Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain H residue 267 LYS Chi-restraints excluded: chain H residue 274 VAL Chi-restraints excluded: chain H residue 322 ASN Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 507 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 6 optimal weight: 6.9990 chunk 144 optimal weight: 0.0770 chunk 119 optimal weight: 0.1980 chunk 71 optimal weight: 1.9990 chunk 149 optimal weight: 8.9990 chunk 58 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 127 optimal weight: 0.9990 overall best weight: 0.8542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 413 ASN F 18 GLN F 307 ASN ** F 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 209 GLN H 322 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.195083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.158898 restraints weight = 16554.865| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 2.43 r_work: 0.3794 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13932 Z= 0.145 Angle : 0.576 11.339 19172 Z= 0.304 Chirality : 0.042 0.263 2092 Planarity : 0.005 0.060 2156 Dihedral : 15.666 174.008 2430 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.50 % Favored : 94.22 % Rotamer: Outliers : 2.55 % Allowed : 12.73 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -0.41 (0.22), residues: 1436 helix: 1.26 (0.25), residues: 440 sheet: -0.43 (0.34), residues: 272 loop : -1.17 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 72 TYR 0.014 0.001 TYR G 251 PHE 0.026 0.001 PHE E 198 TRP 0.016 0.002 TRP E 192 HIS 0.005 0.001 HIS E 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (13932) covalent geometry : angle 0.57584 / 0.30 (19172) hydrogen bonds : bond 0.04022 / 2.31 ( 461) hydrogen bonds : angle 4.67919 / 4.75 ( 1199) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 116 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 192 TRP cc_start: 0.7449 (p-90) cc_final: 0.7132 (p-90) REVERT: E 287 MET cc_start: 0.7914 (mmm) cc_final: 0.7247 (mmm) REVERT: E 303 ASP cc_start: 0.6002 (OUTLIER) cc_final: 0.5762 (p0) REVERT: E 336 MET cc_start: 0.8522 (mtt) cc_final: 0.8230 (mtt) REVERT: F 57 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.6836 (tt) REVERT: F 113 ARG cc_start: 0.6616 (ptm160) cc_final: 0.6298 (ptm160) REVERT: F 205 GLN cc_start: 0.6885 (OUTLIER) cc_final: 0.6457 (tt0) REVERT: F 227 SER cc_start: 0.8722 (m) cc_final: 0.8397 (m) REVERT: F 322 ASN cc_start: 0.7477 (t0) cc_final: 0.7050 (t0) REVERT: G 192 TRP cc_start: 0.7649 (p-90) cc_final: 0.7376 (p-90) REVERT: G 210 TYR cc_start: 0.7377 (t80) cc_final: 0.7147 (t80) REVERT: G 254 ASN cc_start: 0.7769 (OUTLIER) cc_final: 0.7524 (OUTLIER) REVERT: G 294 TRP cc_start: 0.7783 (p-90) cc_final: 0.7547 (p-90) REVERT: G 306 GLU cc_start: 0.7365 (mt-10) cc_final: 0.7119 (mt-10) REVERT: G 336 MET cc_start: 0.8580 (mtt) cc_final: 0.8271 (mtt) REVERT: H 56 TYR cc_start: 0.7831 (t80) cc_final: 0.7388 (t80) REVERT: H 91 ILE cc_start: 0.7601 (OUTLIER) cc_final: 0.7005 (pt) REVERT: H 227 SER cc_start: 0.8670 (m) cc_final: 0.8423 (m) REVERT: H 380 GLU cc_start: 0.7611 (tp30) cc_final: 0.7296 (tp30) outliers start: 33 outliers final: 22 residues processed: 140 average time/residue: 0.4551 time to fit residues: 71.2518 Evaluate side-chains 136 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 215 CYS Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 332 PHE Chi-restraints excluded: chain E residue 387 ASP Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 205 GLN Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 507 ILE Chi-restraints excluded: chain G residue 215 CYS Chi-restraints excluded: chain G residue 254 ASN Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 113 ARG Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain H residue 267 LYS Chi-restraints excluded: chain H residue 274 VAL Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 459 ILE Chi-restraints excluded: chain H residue 507 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 74 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 144 optimal weight: 0.7980 chunk 43 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 116 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 125 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 18 GLN F 307 ASN ** F 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 209 GLN ** H 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.194748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.158471 restraints weight = 16459.885| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 2.43 r_work: 0.3797 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13932 Z= 0.141 Angle : 0.570 13.149 19172 Z= 0.300 Chirality : 0.042 0.262 2092 Planarity : 0.005 0.058 2156 Dihedral : 15.523 173.454 2430 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.43 % Favored : 94.29 % Rotamer: Outliers : 2.39 % Allowed : 13.04 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -0.39 (0.22), residues: 1436 helix: 1.25 (0.24), residues: 442 sheet: -0.48 (0.33), residues: 284 loop : -1.13 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 24 TYR 0.016 0.001 TYR G 225 PHE 0.033 0.001 PHE E 198 TRP 0.014 0.002 TRP F 86 HIS 0.003 0.001 HIS F 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (13932) covalent geometry : angle 0.57016 / 0.30 (19172) hydrogen bonds : bond 0.03925 / 2.25 ( 461) hydrogen bonds : angle 4.64463 / 4.69 ( 1199) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 192 TRP cc_start: 0.7395 (p-90) cc_final: 0.7059 (p-90) REVERT: E 287 MET cc_start: 0.7914 (mmm) cc_final: 0.7303 (mmm) REVERT: E 303 ASP cc_start: 0.6046 (OUTLIER) cc_final: 0.5719 (p0) REVERT: E 336 MET cc_start: 0.8520 (mtt) cc_final: 0.8221 (mtt) REVERT: F 57 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.6832 (tt) REVERT: F 59 HIS cc_start: 0.7416 (t-90) cc_final: 0.6926 (t70) REVERT: F 113 ARG cc_start: 0.6455 (ptm160) cc_final: 0.5883 (mtm180) REVERT: F 205 GLN cc_start: 0.6846 (OUTLIER) cc_final: 0.6454 (tt0) REVERT: F 227 SER cc_start: 0.8725 (m) cc_final: 0.8407 (m) REVERT: F 322 ASN cc_start: 0.7476 (t0) cc_final: 0.7056 (t0) REVERT: G 254 ASN cc_start: 0.7753 (OUTLIER) cc_final: 0.7516 (OUTLIER) REVERT: G 294 TRP cc_start: 0.7774 (p-90) cc_final: 0.7493 (p-90) REVERT: G 306 GLU cc_start: 0.7300 (mt-10) cc_final: 0.7057 (mt-10) REVERT: G 336 MET cc_start: 0.8588 (mtt) cc_final: 0.8282 (mtt) REVERT: H 56 TYR cc_start: 0.7881 (t80) cc_final: 0.7382 (t80) REVERT: H 91 ILE cc_start: 0.7610 (OUTLIER) cc_final: 0.7037 (pt) REVERT: H 227 SER cc_start: 0.8682 (m) cc_final: 0.8432 (m) REVERT: H 324 LYS cc_start: 0.8131 (mttp) cc_final: 0.7569 (mtpp) outliers start: 31 outliers final: 20 residues processed: 145 average time/residue: 0.4362 time to fit residues: 70.8447 Evaluate side-chains 135 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 215 CYS Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 332 PHE Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 205 GLN Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 507 ILE Chi-restraints excluded: chain G residue 215 CYS Chi-restraints excluded: chain G residue 254 ASN Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain H residue 274 VAL Chi-restraints excluded: chain H residue 322 ASN Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 459 ILE Chi-restraints excluded: chain H residue 507 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 105 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 74 optimal weight: 0.0970 chunk 60 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 18 GLN F 307 ASN ** F 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 209 GLN ** H 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.194565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.158033 restraints weight = 16666.515| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 2.45 r_work: 0.3792 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13932 Z= 0.150 Angle : 0.587 12.600 19172 Z= 0.308 Chirality : 0.042 0.265 2092 Planarity : 0.005 0.060 2156 Dihedral : 15.542 173.217 2428 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.71 % Favored : 94.01 % Rotamer: Outliers : 2.31 % Allowed : 13.97 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -0.39 (0.22), residues: 1436 helix: 1.34 (0.25), residues: 430 sheet: -0.47 (0.33), residues: 284 loop : -1.17 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 24 TYR 0.015 0.001 TYR G 225 PHE 0.036 0.001 PHE E 198 TRP 0.015 0.002 TRP F 86 HIS 0.003 0.001 HIS H 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (13932) covalent geometry : angle 0.58658 / 0.31 (19172) hydrogen bonds : bond 0.03947 / 2.27 ( 461) hydrogen bonds : angle 4.65400 / 4.71 ( 1199) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 192 TRP cc_start: 0.7517 (p-90) cc_final: 0.7114 (p-90) REVERT: E 287 MET cc_start: 0.7918 (mmm) cc_final: 0.7316 (mmm) REVERT: E 303 ASP cc_start: 0.5981 (OUTLIER) cc_final: 0.5655 (p0) REVERT: E 336 MET cc_start: 0.8531 (mtt) cc_final: 0.8243 (mtt) REVERT: E 395 MET cc_start: 0.7851 (mmp) cc_final: 0.7619 (mmp) REVERT: F 57 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.6827 (tt) REVERT: F 79 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.8065 (tm-30) REVERT: F 91 ILE cc_start: 0.7749 (OUTLIER) cc_final: 0.7207 (pt) REVERT: F 113 ARG cc_start: 0.6364 (ptm160) cc_final: 0.5854 (mtm180) REVERT: F 205 GLN cc_start: 0.6836 (OUTLIER) cc_final: 0.6446 (tt0) REVERT: F 227 SER cc_start: 0.8739 (m) cc_final: 0.8415 (m) REVERT: F 322 ASN cc_start: 0.7482 (t0) cc_final: 0.7059 (t0) REVERT: G 254 ASN cc_start: 0.7765 (OUTLIER) cc_final: 0.7543 (t0) REVERT: G 294 TRP cc_start: 0.7840 (p-90) cc_final: 0.7544 (p-90) REVERT: G 306 GLU cc_start: 0.7306 (mt-10) cc_final: 0.7059 (mt-10) REVERT: G 336 MET cc_start: 0.8593 (mtt) cc_final: 0.8290 (mtt) REVERT: H 56 TYR cc_start: 0.7858 (t80) cc_final: 0.7338 (t80) REVERT: H 91 ILE cc_start: 0.7495 (OUTLIER) cc_final: 0.6939 (pt) REVERT: H 227 SER cc_start: 0.8703 (m) cc_final: 0.8488 (m) REVERT: H 324 LYS cc_start: 0.8125 (mttp) cc_final: 0.7561 (mtpp) REVERT: H 380 GLU cc_start: 0.7637 (tp30) cc_final: 0.7303 (tp30) outliers start: 30 outliers final: 20 residues processed: 141 average time/residue: 0.4948 time to fit residues: 78.0178 Evaluate side-chains 137 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 215 CYS Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 254 ASN Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 332 PHE Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 79 GLU Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 205 GLN Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 507 ILE Chi-restraints excluded: chain G residue 215 CYS Chi-restraints excluded: chain G residue 254 ASN Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain H residue 274 VAL Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 459 ILE Chi-restraints excluded: chain H residue 507 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 63 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 54 optimal weight: 0.0970 chunk 70 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 131 optimal weight: 0.6980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 18 GLN ** F 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 322 ASN ** 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 = 0.4298 r_free = 0.4298 target = 0.192440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.156526 restraints weight = 16774.259| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 2.42 r_work: 0.3770 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13932 Z= 0.188 Angle : 0.622 13.861 19172 Z= 0.323 Chirality : 0.044 0.286 2092 Planarity : 0.005 0.061 2156 Dihedral : 15.634 173.313 2428 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.92 % Favored : 93.80 % Rotamer: Outliers : 2.24 % Allowed : 14.04 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -0.43 (0.22), residues: 1436 helix: 1.22 (0.25), residues: 430 sheet: -0.10 (0.35), residues: 252 loop : -1.28 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 263 TYR 0.017 0.002 TYR G 225 PHE 0.037 0.002 PHE E 198 TRP 0.032 0.002 TRP F 86 HIS 0.003 0.001 HIS F 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 (13932) covalent geometry : angle 0.62235 / 0.32 (19172) hydrogen bonds : bond 0.04141 / 2.39 ( 461) hydrogen bonds : angle 4.75246 / 4.83 ( 1199) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 113 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 192 TRP cc_start: 0.7658 (p-90) cc_final: 0.7364 (p-90) REVERT: E 303 ASP cc_start: 0.6053 (OUTLIER) cc_final: 0.5669 (p0) REVERT: E 336 MET cc_start: 0.8501 (mtt) cc_final: 0.8227 (mtt) REVERT: E 387 ASP cc_start: 0.7849 (p0) cc_final: 0.7610 (p0) REVERT: E 395 MET cc_start: 0.8013 (mmp) cc_final: 0.7690 (mmp) REVERT: F 91 ILE cc_start: 0.7819 (OUTLIER) cc_final: 0.7262 (pt) REVERT: F 113 ARG cc_start: 0.6344 (ptm160) cc_final: 0.5902 (mtm180) REVERT: F 205 GLN cc_start: 0.6874 (OUTLIER) cc_final: 0.6515 (tt0) REVERT: F 227 SER cc_start: 0.8768 (m) cc_final: 0.8430 (m) REVERT: F 322 ASN cc_start: 0.7511 (t0) cc_final: 0.7091 (t0) REVERT: G 254 ASN cc_start: 0.7876 (OUTLIER) cc_final: 0.7629 (t0) REVERT: G 306 GLU cc_start: 0.7329 (mt-10) cc_final: 0.7085 (mt-10) REVERT: G 336 MET cc_start: 0.8558 (mtt) cc_final: 0.8253 (mtt) REVERT: H 56 TYR cc_start: 0.7896 (t80) cc_final: 0.7431 (t80) REVERT: H 91 ILE cc_start: 0.7605 (OUTLIER) cc_final: 0.7030 (pt) outliers start: 29 outliers final: 20 residues processed: 133 average time/residue: 0.4805 time to fit residues: 71.4433 Evaluate side-chains 137 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 215 CYS Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 332 PHE Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 205 GLN Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 507 ILE Chi-restraints excluded: chain G residue 215 CYS Chi-restraints excluded: chain G residue 254 ASN Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 113 ARG Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain H residue 274 VAL Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 459 ILE Chi-restraints excluded: chain H residue 507 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 87 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 114 optimal weight: 0.5980 chunk 82 optimal weight: 0.7980 chunk 105 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 108 optimal weight: 0.2980 chunk 113 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 GLN ** F 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 322 ASN ** 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 = 0.4328 r_free = 0.4328 target = 0.195403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.159271 restraints weight = 16546.072| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 2.43 r_work: 0.3802 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13932 Z= 0.130 Angle : 0.586 13.059 19172 Z= 0.307 Chirality : 0.042 0.252 2092 Planarity : 0.005 0.058 2156 Dihedral : 15.536 172.750 2428 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.64 % Favored : 94.08 % Rotamer: Outliers : 1.77 % Allowed : 14.58 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -0.30 (0.23), residues: 1436 helix: 1.38 (0.25), residues: 430 sheet: -0.14 (0.35), residues: 264 loop : -1.19 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 24 TYR 0.018 0.001 TYR E 210 PHE 0.036 0.001 PHE E 198 TRP 0.023 0.002 TRP F 86 HIS 0.002 0.001 HIS H 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (13932) covalent geometry : angle 0.58582 / 0.31 (19172) hydrogen bonds : bond 0.03822 / 2.19 ( 461) hydrogen bonds : angle 4.60805 / 4.66 ( 1199) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3306.49 seconds wall clock time: 57 minutes 31.11 seconds (3451.11 seconds total)