Starting phenix.real_space_refine on Thu Jul 31 23:07:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oze_17306/07_2025/8oze_17306.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oze_17306/07_2025/8oze_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8oze_17306/07_2025/8oze_17306.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oze_17306/07_2025/8oze_17306.map" model { file = "/net/cci-nas-00/data/ceres_data/8oze_17306/07_2025/8oze_17306.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oze_17306/07_2025/8oze_17306.cif" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.034 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13434 Number of models: 1 Model: "" Number of chains: 4 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 Chain: "A" 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: "B" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 339 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Restraints were copied for chains: P, N, G, H Time building chain proxies: 10.40, per 1000 atoms: 0.77 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: 3.66 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 8.44 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: 5.76 Time building geometry restraints manager: 4.32 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=" C ARG H 152 " pdb=" N PRO H 153 " ideal model delta sigma weight residual 1.331 1.350 -0.019 1.27e-02 6.20e+03 2.22e+00 bond pdb=" C ARG F 152 " pdb=" N PRO F 153 " ideal model delta sigma weight residual 1.331 1.350 -0.019 1.27e-02 6.20e+03 2.22e+00 bond pdb=" CB VAL H 317 " pdb=" CG1 VAL H 317 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.56e+00 bond pdb=" CB VAL F 317 " pdb=" CG1 VAL F 317 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.56e+00 bond pdb=" CG LEU H 490 " pdb=" CD1 LEU H 490 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.41e+00 ... (remaining 13927 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 18295 1.15 - 2.30: 704 2.30 - 3.45: 132 3.45 - 4.61: 29 4.61 - 5.76: 12 Bond angle restraints: 19172 Sorted by residual: angle pdb=" C PHE H 82 " pdb=" N ASP H 83 " pdb=" CA ASP H 83 " ideal model delta sigma weight residual 121.54 126.73 -5.19 1.91e+00 2.74e-01 7.37e+00 angle pdb=" C PHE F 82 " pdb=" N ASP F 83 " pdb=" CA ASP F 83 " ideal model delta sigma weight residual 121.54 126.66 -5.12 1.91e+00 2.74e-01 7.20e+00 angle pdb=" N ILE F 489 " pdb=" CA ILE F 489 " pdb=" C ILE F 489 " ideal model delta sigma weight residual 110.72 113.38 -2.66 1.01e+00 9.80e-01 6.93e+00 angle pdb=" N ILE H 489 " pdb=" CA ILE H 489 " pdb=" C ILE H 489 " ideal model delta sigma weight residual 110.72 113.34 -2.62 1.01e+00 9.80e-01 6.75e+00 angle pdb=" CA LYS G 302 " pdb=" CB LYS G 302 " pdb=" CG LYS G 302 " ideal model delta sigma weight residual 114.10 118.94 -4.84 2.00e+00 2.50e-01 5.85e+00 ... (remaining 19167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 7942 35.91 - 71.82: 318 71.82 - 107.74: 14 107.74 - 143.65: 0 143.65 - 179.56: 6 Dihedral angle restraints: 8280 sinusoidal: 4014 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 8277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1409 0.033 - 0.067: 495 0.067 - 0.100: 131 0.100 - 0.133: 52 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: 0.06 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'P' } ncs_group { reference = chain 'A' selection = chain 'N' } 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: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 42.960 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:14.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13932 Z= 0.152 Angle : 0.548 5.757 19172 Z= 0.301 Chirality : 0.039 0.166 2092 Planarity : 0.005 0.071 2156 Dihedral : 17.976 179.559 5532 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (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 TRP 0.010 0.001 TRP H 370 HIS 0.003 0.001 HIS H 329 PHE 0.014 0.001 PHE E 342 TYR 0.009 0.001 TYR H 280 ARG 0.004 0.000 ARG H 24 Details of bonding type rmsd hydrogen bonds : bond 0.18154 ( 461) hydrogen bonds : angle 7.28465 ( 1199) covalent geometry : bond 0.00337 (13932) covalent geometry : angle 0.54813 (19172) *********************** 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 : 1.411 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: 0.7419 (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: 0.6179 (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: 1.0629 time to fit residues: 228.9237 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 : 1.351 ------------------------------------------------------------------------------- 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 126 optimal weight: 0.1980 chunk 113 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 60 optimal weight: 0.2980 chunk 117 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4311 r_free = 0.4311 target = 0.193802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.157426 restraints weight = 16526.647| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 2.42 r_work: 0.3787 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1263 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= 0.171 Angle : 0.604 6.334 19172 Z= 0.319 Chirality : 0.043 0.221 2092 Planarity : 0.005 0.056 2156 Dihedral : 18.723 175.843 2582 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.64 % Favored : 94.08 % Rotamer: Outliers : 2.16 % Allowed : 7.87 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.22), residues: 1436 helix: 1.16 (0.24), residues: 436 sheet: -0.63 (0.32), residues: 272 loop : -1.37 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 219 HIS 0.003 0.001 HIS F 16 PHE 0.015 0.002 PHE E 187 TYR 0.015 0.002 TYR G 225 ARG 0.003 0.001 ARG F 24 Details of bonding type rmsd hydrogen bonds : bond 0.04792 ( 461) hydrogen bonds : angle 5.00571 ( 1199) covalent geometry : bond 0.00393 (13932) covalent geometry : angle 0.60417 (19172) *********************** 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 162 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 172 ASP cc_start: 0.8293 (m-30) cc_final: 0.8064 (m-30) REVERT: E 287 MET cc_start: 0.8105 (mmm) cc_final: 0.7501 (mmm) REVERT: E 336 MET cc_start: 0.8524 (mtt) cc_final: 0.8187 (mtt) REVERT: E 395 MET cc_start: 0.8590 (mmt) cc_final: 0.8223 (mmp) REVERT: F 1 MET cc_start: 0.7455 (tpp) cc_final: 0.7171 (tpp) REVERT: F 18 GLN cc_start: 0.7578 (mt0) cc_final: 0.7328 (mt0) REVERT: F 113 ARG cc_start: 0.6496 (OUTLIER) cc_final: 0.6121 (ptm-80) REVERT: F 117 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7855 (mp) REVERT: F 161 MET cc_start: -0.0413 (ppp) cc_final: -0.1711 (pmt) REVERT: F 205 GLN cc_start: 0.7175 (OUTLIER) cc_final: 0.6723 (tt0) REVERT: F 227 SER cc_start: 0.8736 (m) cc_final: 0.8456 (m) REVERT: F 322 ASN cc_start: 0.7429 (t0) cc_final: 0.7069 (t0) REVERT: F 333 LYS cc_start: 0.8831 (tttt) cc_final: 0.8584 (tptt) REVERT: G 254 ASN cc_start: 0.7758 (OUTLIER) cc_final: 0.7435 (t0) REVERT: G 294 TRP cc_start: 0.7698 (p-90) cc_final: 0.7438 (p-90) REVERT: G 336 MET cc_start: 0.8594 (mtt) cc_final: 0.8236 (mtt) REVERT: H 18 GLN cc_start: 0.7728 (mt0) cc_final: 0.7353 (mp10) REVERT: H 56 TYR cc_start: 0.7854 (t80) cc_final: 0.7272 (t80) REVERT: H 113 ARG cc_start: 0.6681 (OUTLIER) cc_final: 0.6325 (ptp90) REVERT: H 227 SER cc_start: 0.8674 (m) cc_final: 0.8390 (m) REVERT: H 334 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7859 (mt-10) outliers start: 28 outliers final: 14 residues processed: 150 average time/residue: 1.0856 time to fit residues: 181.5164 Evaluate side-chains 134 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 1.449 ------------------------------------------------------------------------------- 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 F residue 113 ARG 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 507 ILE Chi-restraints excluded: chain G residue 215 CYS Chi-restraints excluded: chain G residue 232 THR 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 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 127 optimal weight: 0.0370 chunk 67 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 74 optimal weight: 0.0570 chunk 121 optimal weight: 2.9990 chunk 69 optimal weight: 0.3980 chunk 5 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 ASN ** G 370 ASN ** 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 = 0.4351 r_free = 0.4351 target = 0.198270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.162419 restraints weight = 16605.372| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 2.42 r_work: 0.3838 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13932 Z= 0.119 Angle : 0.542 9.537 19172 Z= 0.286 Chirality : 0.040 0.130 2092 Planarity : 0.005 0.051 2156 Dihedral : 18.521 174.316 2582 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.74 % Favored : 94.99 % Rotamer: Outliers : 2.47 % Allowed : 9.72 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.22), residues: 1436 helix: 1.42 (0.25), residues: 436 sheet: -0.36 (0.33), residues: 270 loop : -1.19 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 370 HIS 0.003 0.001 HIS F 217 PHE 0.014 0.001 PHE E 198 TYR 0.018 0.001 TYR E 225 ARG 0.003 0.000 ARG H 24 Details of bonding type rmsd hydrogen bonds : bond 0.03986 ( 461) hydrogen bonds : angle 4.67019 ( 1199) covalent geometry : bond 0.00262 (13932) covalent geometry : angle 0.54211 (19172) *********************** 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 163 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 172 ASP cc_start: 0.8249 (m-30) cc_final: 0.8043 (m-30) REVERT: E 287 MET cc_start: 0.8079 (mmm) cc_final: 0.7468 (mmm) REVERT: E 336 MET cc_start: 0.8511 (mtt) cc_final: 0.8226 (mtt) REVERT: F 18 GLN cc_start: 0.7540 (mt0) cc_final: 0.7240 (mt0) REVERT: F 227 SER cc_start: 0.8644 (m) cc_final: 0.8350 (m) REVERT: F 322 ASN cc_start: 0.7458 (t0) cc_final: 0.7092 (t0) REVERT: G 172 ASP cc_start: 0.8174 (m-30) cc_final: 0.7959 (m-30) REVERT: G 186 ARG cc_start: 0.7081 (OUTLIER) cc_final: 0.6179 (mpp80) REVERT: G 254 ASN cc_start: 0.7771 (OUTLIER) cc_final: 0.7480 (OUTLIER) REVERT: G 294 TRP cc_start: 0.7767 (p-90) cc_final: 0.7506 (p-90) REVERT: G 306 GLU cc_start: 0.7266 (mt-10) cc_final: 0.7015 (mt-10) REVERT: G 336 MET cc_start: 0.8599 (mtt) cc_final: 0.8291 (mtt) REVERT: H 18 GLN cc_start: 0.7948 (mt0) cc_final: 0.7307 (mm-40) REVERT: H 56 TYR cc_start: 0.7913 (t80) cc_final: 0.7293 (t80) REVERT: H 161 MET cc_start: -0.0353 (ppp) cc_final: -0.1516 (pmt) REVERT: H 205 GLN cc_start: 0.7158 (OUTLIER) cc_final: 0.6957 (tt0) REVERT: H 227 SER cc_start: 0.8625 (m) cc_final: 0.8361 (m) outliers start: 32 outliers final: 12 residues processed: 156 average time/residue: 1.1027 time to fit residues: 192.0658 Evaluate side-chains 125 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 1.526 ------------------------------------------------------------------------------- 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 E residue 415 SER Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain G residue 186 ARG 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 144 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 114 optimal weight: 0.6980 chunk 138 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 74 optimal weight: 0.0060 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 307 ASN ** F 322 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.194606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.158298 restraints weight = 16413.440| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 2.42 r_work: 0.3784 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13932 Z= 0.168 Angle : 0.576 10.110 19172 Z= 0.302 Chirality : 0.041 0.218 2092 Planarity : 0.005 0.060 2156 Dihedral : 18.585 173.977 2582 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.22 % Favored : 94.50 % Rotamer: Outliers : 2.39 % Allowed : 11.03 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.22), residues: 1436 helix: 1.27 (0.24), residues: 436 sheet: -0.52 (0.33), residues: 272 loop : -1.20 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 86 HIS 0.003 0.001 HIS F 59 PHE 0.020 0.002 PHE E 198 TYR 0.016 0.001 TYR G 225 ARG 0.003 0.001 ARG F 24 Details of bonding type rmsd hydrogen bonds : bond 0.04046 ( 461) hydrogen bonds : angle 4.71079 ( 1199) covalent geometry : bond 0.00391 (13932) covalent geometry : angle 0.57631 (19172) *********************** 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 150 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 1.455 Fit side-chains revert: symmetry clash REVERT: E 287 MET cc_start: 0.7919 (mmm) cc_final: 0.7248 (mmm) REVERT: E 313 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.8041 (tptm) REVERT: E 315 LYS cc_start: 0.7590 (mptt) cc_final: 0.7323 (mppt) REVERT: E 336 MET cc_start: 0.8530 (mtt) cc_final: 0.8245 (mtt) REVERT: F 113 ARG cc_start: 0.6695 (ptm160) cc_final: 0.5920 (mtm180) REVERT: F 161 MET cc_start: -0.0730 (ppp) cc_final: -0.1759 (pmt) REVERT: F 205 GLN cc_start: 0.7055 (OUTLIER) cc_final: 0.6645 (tt0) REVERT: F 227 SER cc_start: 0.8734 (m) cc_final: 0.8429 (m) REVERT: F 322 ASN cc_start: 0.7464 (t0) cc_final: 0.7104 (t0) REVERT: G 172 ASP cc_start: 0.8187 (m-30) cc_final: 0.7972 (m-30) REVERT: G 186 ARG cc_start: 0.7303 (OUTLIER) cc_final: 0.6936 (mpp80) REVERT: G 254 ASN cc_start: 0.7796 (OUTLIER) cc_final: 0.7578 (OUTLIER) REVERT: G 304 LYS cc_start: 0.7245 (OUTLIER) cc_final: 0.6784 (tttm) REVERT: G 336 MET cc_start: 0.8600 (mtt) cc_final: 0.8301 (mtt) REVERT: H 18 GLN cc_start: 0.7913 (mt0) cc_final: 0.7247 (mm-40) REVERT: H 56 TYR cc_start: 0.7803 (t80) cc_final: 0.7258 (t80) REVERT: H 87 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7149 (mp0) REVERT: H 205 GLN cc_start: 0.7201 (OUTLIER) cc_final: 0.6849 (tt0) REVERT: H 227 SER cc_start: 0.8646 (m) cc_final: 0.8350 (m) outliers start: 31 outliers final: 17 residues processed: 141 average time/residue: 1.0756 time to fit residues: 169.2120 Evaluate side-chains 134 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 1.325 ------------------------------------------------------------------------------- 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 313 LYS 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 274 VAL Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 507 ILE Chi-restraints excluded: chain G residue 186 ARG Chi-restraints excluded: chain G residue 215 CYS Chi-restraints excluded: chain G residue 254 ASN Chi-restraints excluded: chain G residue 304 LYS Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain H residue 205 GLN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 58 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 93 optimal weight: 8.9990 chunk 94 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 144 optimal weight: 0.7980 chunk 43 optimal weight: 0.0770 chunk 102 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 18 GLN ** 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 = 0.4312 r_free = 0.4312 target = 0.193282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.157710 restraints weight = 16670.411| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 2.37 r_work: 0.3812 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13932 Z= 0.134 Angle : 0.550 10.216 19172 Z= 0.287 Chirality : 0.040 0.244 2092 Planarity : 0.005 0.055 2156 Dihedral : 18.538 173.443 2582 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.94 % Favored : 94.78 % Rotamer: Outliers : 1.85 % Allowed : 12.50 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.22), residues: 1436 helix: 1.35 (0.25), residues: 440 sheet: -0.52 (0.33), residues: 284 loop : -1.11 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 86 HIS 0.003 0.001 HIS F 329 PHE 0.023 0.001 PHE E 198 TYR 0.014 0.001 TYR G 225 ARG 0.003 0.000 ARG F 24 Details of bonding type rmsd hydrogen bonds : bond 0.03776 ( 461) hydrogen bonds : angle 4.61052 ( 1199) covalent geometry : bond 0.00307 (13932) covalent geometry : angle 0.55048 (19172) *********************** 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 149 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 287 MET cc_start: 0.7888 (mmm) cc_final: 0.7249 (mmm) REVERT: E 336 MET cc_start: 0.8504 (mtt) cc_final: 0.8204 (mtt) REVERT: F 18 GLN cc_start: 0.7265 (mt0) cc_final: 0.6965 (tt0) REVERT: F 59 HIS cc_start: 0.7464 (t-90) cc_final: 0.6965 (t70) REVERT: F 113 ARG cc_start: 0.6652 (ptm160) cc_final: 0.6438 (ptm160) REVERT: F 205 GLN cc_start: 0.6992 (OUTLIER) cc_final: 0.6625 (tt0) REVERT: F 227 SER cc_start: 0.8709 (m) cc_final: 0.8394 (m) REVERT: F 322 ASN cc_start: 0.7450 (t0) cc_final: 0.7066 (t0) REVERT: G 186 ARG cc_start: 0.7177 (OUTLIER) cc_final: 0.6969 (mpp80) REVERT: G 254 ASN cc_start: 0.7856 (OUTLIER) cc_final: 0.7619 (t0) REVERT: G 294 TRP cc_start: 0.7767 (p-90) cc_final: 0.7519 (p-90) REVERT: G 336 MET cc_start: 0.8576 (mtt) cc_final: 0.8253 (mtt) REVERT: H 18 GLN cc_start: 0.7862 (mt0) cc_final: 0.7305 (mm-40) REVERT: H 56 TYR cc_start: 0.7783 (t80) cc_final: 0.7241 (t80) REVERT: H 161 MET cc_start: -0.0556 (ppp) cc_final: -0.2028 (pmt) REVERT: H 205 GLN cc_start: 0.7302 (OUTLIER) cc_final: 0.7006 (tt0) REVERT: H 227 SER cc_start: 0.8665 (m) cc_final: 0.8437 (m) REVERT: H 380 GLU cc_start: 0.7603 (tp30) cc_final: 0.7315 (tp30) outliers start: 24 outliers final: 17 residues processed: 143 average time/residue: 1.1920 time to fit residues: 189.9332 Evaluate side-chains 131 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 1.979 ------------------------------------------------------------------------------- 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 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 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 186 ARG 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 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 77 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 49 optimal weight: 0.4980 chunk 50 optimal weight: 0.7980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.195405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.159036 restraints weight = 16687.641| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 2.45 r_work: 0.3800 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13932 Z= 0.144 Angle : 0.558 11.863 19172 Z= 0.291 Chirality : 0.041 0.174 2092 Planarity : 0.005 0.059 2156 Dihedral : 18.455 172.776 2582 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.15 % Favored : 94.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.23), residues: 1436 helix: 1.33 (0.25), residues: 442 sheet: -0.48 (0.33), residues: 284 loop : -1.08 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 86 HIS 0.003 0.001 HIS F 329 PHE 0.028 0.001 PHE E 198 TYR 0.015 0.001 TYR G 225 ARG 0.003 0.000 ARG F 24 Details of bonding type rmsd hydrogen bonds : bond 0.03749 ( 461) hydrogen bonds : angle 4.59006 ( 1199) covalent geometry : bond 0.00332 (13932) covalent geometry : angle 0.55809 (19172) *********************** 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 148 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 117 time to evaluate : 2.885 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 287 MET cc_start: 0.7922 (mmm) cc_final: 0.7273 (mmm) REVERT: E 336 MET cc_start: 0.8509 (mtt) cc_final: 0.8206 (mtt) REVERT: F 18 GLN cc_start: 0.7377 (mt0) cc_final: 0.6989 (tt0) REVERT: F 57 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.6812 (tt) REVERT: F 59 HIS cc_start: 0.7480 (t-90) cc_final: 0.6973 (t70) REVERT: F 161 MET cc_start: -0.1205 (ppp) cc_final: -0.2529 (pmt) REVERT: F 205 GLN cc_start: 0.6946 (OUTLIER) cc_final: 0.6587 (tt0) REVERT: F 227 SER cc_start: 0.8719 (m) cc_final: 0.8402 (m) REVERT: F 322 ASN cc_start: 0.7471 (t0) cc_final: 0.7076 (t0) REVERT: G 186 ARG cc_start: 0.7276 (OUTLIER) cc_final: 0.7040 (mpp80) REVERT: G 254 ASN cc_start: 0.7828 (OUTLIER) cc_final: 0.7617 (t0) REVERT: G 294 TRP cc_start: 0.7798 (p-90) cc_final: 0.7491 (p-90) REVERT: G 336 MET cc_start: 0.8581 (mtt) cc_final: 0.8247 (mtt) REVERT: H 18 GLN cc_start: 0.7917 (mt0) cc_final: 0.7358 (mm-40) REVERT: H 56 TYR cc_start: 0.7773 (t80) cc_final: 0.7312 (t80) REVERT: H 57 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.6834 (tt) REVERT: H 91 ILE cc_start: 0.7503 (OUTLIER) cc_final: 0.6926 (pt) REVERT: H 205 GLN cc_start: 0.7288 (OUTLIER) cc_final: 0.6936 (tt0) REVERT: H 380 GLU cc_start: 0.7729 (tp30) cc_final: 0.7407 (tp30) outliers start: 31 outliers final: 19 residues processed: 141 average time/residue: 1.4317 time to fit residues: 224.9241 Evaluate side-chains 134 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 1.482 ------------------------------------------------------------------------------- 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 332 PHE Chi-restraints excluded: chain F residue 13 LEU 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 186 ARG 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 57 LEU Chi-restraints excluded: chain H residue 79 GLU 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 205 GLN 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 85 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 307 ASN ** F 322 ASN ** 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 = 0.4298 r_free = 0.4298 target = 0.192701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.156133 restraints weight = 16630.274| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 2.44 r_work: 0.3767 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13932 Z= 0.205 Angle : 0.603 12.902 19172 Z= 0.313 Chirality : 0.043 0.157 2092 Planarity : 0.005 0.064 2156 Dihedral : 18.529 172.849 2580 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.43 % Favored : 94.29 % Rotamer: Outliers : 2.47 % Allowed : 13.66 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.22), residues: 1436 helix: 1.17 (0.24), residues: 440 sheet: -0.42 (0.34), residues: 272 loop : -1.17 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 86 HIS 0.006 0.001 HIS H 329 PHE 0.032 0.002 PHE E 198 TYR 0.015 0.002 TYR G 225 ARG 0.003 0.001 ARG F 24 Details of bonding type rmsd hydrogen bonds : bond 0.04052 ( 461) hydrogen bonds : angle 4.71153 ( 1199) covalent geometry : bond 0.00482 (13932) covalent geometry : angle 0.60343 (19172) *********************** 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 145 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 1.474 Fit side-chains revert: symmetry clash REVERT: E 287 MET cc_start: 0.7932 (mmm) cc_final: 0.7319 (mmm) REVERT: E 336 MET cc_start: 0.8564 (mtt) cc_final: 0.8294 (mtt) REVERT: F 18 GLN cc_start: 0.7702 (mt0) cc_final: 0.7440 (tt0) REVERT: F 57 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.6923 (tt) REVERT: F 205 GLN cc_start: 0.7004 (OUTLIER) cc_final: 0.6624 (tt0) REVERT: F 227 SER cc_start: 0.8764 (m) cc_final: 0.8435 (m) REVERT: F 322 ASN cc_start: 0.7538 (t0) cc_final: 0.7110 (t0) REVERT: G 186 ARG cc_start: 0.7304 (OUTLIER) cc_final: 0.7066 (mpp80) REVERT: G 254 ASN cc_start: 0.7930 (OUTLIER) cc_final: 0.7661 (t0) REVERT: G 336 MET cc_start: 0.8622 (mtt) cc_final: 0.8318 (mtt) REVERT: H 18 GLN cc_start: 0.7931 (mt0) cc_final: 0.7440 (mm-40) REVERT: H 56 TYR cc_start: 0.7903 (t80) cc_final: 0.7405 (t80) REVERT: H 57 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.6926 (tt) REVERT: H 91 ILE cc_start: 0.7607 (OUTLIER) cc_final: 0.7050 (pt) REVERT: H 161 MET cc_start: -0.0699 (ppp) cc_final: -0.2417 (pmt) outliers start: 32 outliers final: 18 residues processed: 138 average time/residue: 1.1655 time to fit residues: 180.6059 Evaluate side-chains 137 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 1.866 ------------------------------------------------------------------------------- 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 332 PHE Chi-restraints excluded: chain F residue 13 LEU 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 507 ILE Chi-restraints excluded: chain G residue 186 ARG 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 G residue 415 SER Chi-restraints excluded: chain H residue 57 LEU 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 322 ASN Chi-restraints excluded: chain H residue 406 LEU 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 40 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 133 optimal weight: 0.7980 chunk 143 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 413 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.194241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.157897 restraints weight = 16688.502| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 2.44 r_work: 0.3785 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13932 Z= 0.152 Angle : 0.578 14.543 19172 Z= 0.299 Chirality : 0.041 0.146 2092 Planarity : 0.005 0.063 2156 Dihedral : 18.488 172.561 2580 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.43 % Favored : 94.29 % Rotamer: Outliers : 2.08 % Allowed : 14.51 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.22), residues: 1436 helix: 1.25 (0.24), residues: 440 sheet: -0.40 (0.34), residues: 268 loop : -1.14 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 86 HIS 0.003 0.001 HIS H 329 PHE 0.034 0.001 PHE E 198 TYR 0.016 0.001 TYR G 210 ARG 0.003 0.000 ARG F 24 Details of bonding type rmsd hydrogen bonds : bond 0.03792 ( 461) hydrogen bonds : angle 4.64346 ( 1199) covalent geometry : bond 0.00351 (13932) covalent geometry : angle 0.57848 (19172) *********************** 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 142 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 287 MET cc_start: 0.7921 (mmm) cc_final: 0.7340 (mmm) REVERT: E 336 MET cc_start: 0.8550 (mtt) cc_final: 0.8269 (mtt) REVERT: F 18 GLN cc_start: 0.7588 (mt0) cc_final: 0.7215 (tt0) REVERT: F 91 ILE cc_start: 0.7691 (OUTLIER) cc_final: 0.7151 (pt) REVERT: F 205 GLN cc_start: 0.6946 (OUTLIER) cc_final: 0.6602 (tt0) REVERT: F 227 SER cc_start: 0.8769 (m) cc_final: 0.8451 (m) REVERT: F 322 ASN cc_start: 0.7502 (t0) cc_final: 0.7079 (t0) REVERT: G 186 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.7067 (mpp80) REVERT: G 222 ASP cc_start: 0.7992 (m-30) cc_final: 0.7700 (m-30) REVERT: G 254 ASN cc_start: 0.7882 (OUTLIER) cc_final: 0.7628 (t0) REVERT: G 294 TRP cc_start: 0.7836 (p-90) cc_final: 0.7564 (p-90) REVERT: G 336 MET cc_start: 0.8584 (mtt) cc_final: 0.8265 (mtt) REVERT: H 18 GLN cc_start: 0.7876 (mt0) cc_final: 0.7358 (mm-40) REVERT: H 56 TYR cc_start: 0.7865 (t80) cc_final: 0.7368 (t80) REVERT: H 57 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.6853 (tt) REVERT: H 91 ILE cc_start: 0.7564 (OUTLIER) cc_final: 0.7019 (pt) REVERT: H 380 GLU cc_start: 0.7758 (tp30) cc_final: 0.7387 (tp30) outliers start: 27 outliers final: 19 residues processed: 136 average time/residue: 1.6318 time to fit residues: 246.8635 Evaluate side-chains 135 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 1.620 ------------------------------------------------------------------------------- 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 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 507 ILE Chi-restraints excluded: chain G residue 186 ARG 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 G residue 415 SER Chi-restraints excluded: chain H residue 57 LEU 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 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 4 optimal weight: 0.0980 chunk 84 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 128 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 142 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 370 ASN ** H 34 ASN ** 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 = 0.4341 r_free = 0.4341 target = 0.197111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.161163 restraints weight = 16560.940| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 2.44 r_work: 0.3820 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13932 Z= 0.122 Angle : 0.556 13.634 19172 Z= 0.287 Chirality : 0.040 0.155 2092 Planarity : 0.005 0.060 2156 Dihedral : 18.400 171.469 2580 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.22 % Favored : 94.50 % Rotamer: Outliers : 1.85 % Allowed : 15.12 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.23), residues: 1436 helix: 1.42 (0.25), residues: 442 sheet: -0.45 (0.33), residues: 284 loop : -1.00 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 86 HIS 0.003 0.001 HIS H 329 PHE 0.033 0.001 PHE E 198 TYR 0.018 0.001 TYR G 210 ARG 0.002 0.000 ARG F 24 Details of bonding type rmsd hydrogen bonds : bond 0.03563 ( 461) hydrogen bonds : angle 4.50111 ( 1199) covalent geometry : bond 0.00273 (13932) covalent geometry : angle 0.55641 (19172) *********************** 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 151 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 1.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 255 PHE cc_start: 0.7602 (t80) cc_final: 0.7270 (t80) REVERT: E 287 MET cc_start: 0.7916 (mmm) cc_final: 0.7323 (mmm) REVERT: E 336 MET cc_start: 0.8513 (mtt) cc_final: 0.8205 (mtt) REVERT: F 18 GLN cc_start: 0.7466 (mt0) cc_final: 0.7214 (tt0) REVERT: F 59 HIS cc_start: 0.7367 (t-90) cc_final: 0.6930 (t70) REVERT: F 91 ILE cc_start: 0.7493 (OUTLIER) cc_final: 0.6927 (pt) REVERT: F 205 GLN cc_start: 0.6767 (OUTLIER) cc_final: 0.6430 (tt0) REVERT: F 227 SER cc_start: 0.8707 (m) cc_final: 0.8383 (m) REVERT: F 322 ASN cc_start: 0.7445 (t0) cc_final: 0.7040 (t0) REVERT: G 186 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.6593 (mpp80) REVERT: G 254 ASN cc_start: 0.7830 (OUTLIER) cc_final: 0.7623 (t0) REVERT: G 287 MET cc_start: 0.7689 (mmm) cc_final: 0.7144 (mmm) REVERT: G 294 TRP cc_start: 0.7823 (p-90) cc_final: 0.7524 (p-90) REVERT: G 336 MET cc_start: 0.8494 (mtt) cc_final: 0.8135 (mtt) REVERT: H 18 GLN cc_start: 0.7888 (mt0) cc_final: 0.7371 (mm-40) REVERT: H 56 TYR cc_start: 0.7794 (t80) cc_final: 0.7235 (t80) REVERT: H 91 ILE cc_start: 0.7073 (OUTLIER) cc_final: 0.6512 (pt) REVERT: H 324 LYS cc_start: 0.8086 (mttp) cc_final: 0.7525 (mtpp) outliers start: 24 outliers final: 16 residues processed: 145 average time/residue: 1.4970 time to fit residues: 242.6252 Evaluate side-chains 134 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 1.718 ------------------------------------------------------------------------------- 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 239 ILE 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 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 G residue 186 ARG 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 53 optimal weight: 0.0670 chunk 100 optimal weight: 0.4980 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 413 ASN ** F 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 413 ASN H 209 GLN H 322 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.195097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.158880 restraints weight = 16640.488| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 2.44 r_work: 0.3800 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13932 Z= 0.149 Angle : 0.575 15.053 19172 Z= 0.296 Chirality : 0.040 0.142 2092 Planarity : 0.005 0.062 2156 Dihedral : 18.421 171.445 2580 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.43 % Favored : 94.29 % Rotamer: Outliers : 1.70 % Allowed : 15.82 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.23), residues: 1436 helix: 1.36 (0.25), residues: 442 sheet: -0.47 (0.33), residues: 284 loop : -1.02 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 86 HIS 0.002 0.001 HIS F 329 PHE 0.035 0.001 PHE E 198 TYR 0.017 0.001 TYR E 210 ARG 0.003 0.000 ARG G 263 Details of bonding type rmsd hydrogen bonds : bond 0.03654 ( 461) hydrogen bonds : angle 4.53423 ( 1199) covalent geometry : bond 0.00346 (13932) covalent geometry : angle 0.57480 (19172) ********************** 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 136 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 287 MET cc_start: 0.7917 (mmm) cc_final: 0.7297 (mmm) REVERT: E 336 MET cc_start: 0.8526 (mtt) cc_final: 0.8224 (mtt) REVERT: F 18 GLN cc_start: 0.7516 (mt0) cc_final: 0.7237 (tt0) REVERT: F 59 HIS cc_start: 0.7512 (t-90) cc_final: 0.7062 (t70) REVERT: F 91 ILE cc_start: 0.7818 (OUTLIER) cc_final: 0.7261 (pt) REVERT: F 205 GLN cc_start: 0.6889 (OUTLIER) cc_final: 0.6556 (tt0) REVERT: F 227 SER cc_start: 0.8743 (m) cc_final: 0.8420 (m) REVERT: F 322 ASN cc_start: 0.7505 (t0) cc_final: 0.7086 (t0) REVERT: G 186 ARG cc_start: 0.7283 (OUTLIER) cc_final: 0.6582 (mpp80) REVERT: G 232 THR cc_start: 0.8254 (m) cc_final: 0.8006 (m) REVERT: G 294 TRP cc_start: 0.7830 (p-90) cc_final: 0.7587 (p-90) REVERT: G 336 MET cc_start: 0.8590 (mtt) cc_final: 0.8258 (mtt) REVERT: H 18 GLN cc_start: 0.7877 (mt0) cc_final: 0.7355 (mm-40) REVERT: H 56 TYR cc_start: 0.7833 (t80) cc_final: 0.7289 (t80) REVERT: H 91 ILE cc_start: 0.7141 (OUTLIER) cc_final: 0.6572 (pt) REVERT: H 324 LYS cc_start: 0.7968 (mttp) cc_final: 0.7434 (mtpp) REVERT: H 380 GLU cc_start: 0.7621 (tp30) cc_final: 0.7351 (tp30) outliers start: 22 outliers final: 15 residues processed: 131 average time/residue: 1.0874 time to fit residues: 158.5996 Evaluate side-chains 131 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 1.437 ------------------------------------------------------------------------------- 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 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 G residue 186 ARG Chi-restraints excluded: chain G residue 215 CYS 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 123 optimal weight: 0.2980 chunk 113 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 145 optimal weight: 0.1980 chunk 117 optimal weight: 0.5980 chunk 97 optimal weight: 3.9990 chunk 59 optimal weight: 0.4980 chunk 67 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 209 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.195723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.159626 restraints weight = 16702.960| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 2.45 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: 0.7503 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13932 Z= 0.135 Angle : 0.572 13.953 19172 Z= 0.294 Chirality : 0.040 0.140 2092 Planarity : 0.005 0.060 2156 Dihedral : 18.397 171.146 2580 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.22 % Favored : 94.50 % Rotamer: Outliers : 1.70 % Allowed : 15.90 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.23), residues: 1436 helix: 1.43 (0.25), residues: 440 sheet: -0.45 (0.33), residues: 284 loop : -1.04 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 86 HIS 0.003 0.001 HIS H 329 PHE 0.034 0.001 PHE E 198 TYR 0.018 0.001 TYR E 210 ARG 0.003 0.000 ARG F 24 Details of bonding type rmsd hydrogen bonds : bond 0.03563 ( 461) hydrogen bonds : angle 4.49189 ( 1199) covalent geometry : bond 0.00309 (13932) covalent geometry : angle 0.57213 (19172) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8322.82 seconds wall clock time: 151 minutes 7.18 seconds (9067.18 seconds total)