Starting phenix.real_space_refine on Fri May 16 03:00:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oze_17306/05_2025/8oze_17306.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oze_17306/05_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_17306/05_2025/8oze_17306.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oze_17306/05_2025/8oze_17306.map" model { file = "/net/cci-nas-00/data/ceres_data/8oze_17306/05_2025/8oze_17306.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oze_17306/05_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-5687/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: 10.51, per 1000 atoms: 0.78 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: 3.44 Conformation dependent library (CDL) restraints added in 1.5 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: 4.89 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: 4.66 Time building geometry restraints manager: 4.01 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: 1.210 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: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 37.760 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.560 ------------------------------------------------------------------------------- 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 : 1.376 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: 0.9837 time to fit residues: 211.8115 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 : 1.429 ------------------------------------------------------------------------------- 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 = 43)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.157425 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 : 1.436 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: 0.8591 (mmt) cc_final: 0.8224 (mmp) REVERT: F 1 MET cc_start: 0.7457 (tpp) cc_final: 0.7173 (tpp) REVERT: F 18 GLN cc_start: 0.7579 (mt0) cc_final: 0.7328 (mt0) REVERT: F 113 ARG cc_start: 0.6495 (OUTLIER) cc_final: 0.6119 (ptm-80) REVERT: F 117 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7853 (mp) REVERT: F 161 MET cc_start: -0.0416 (ppp) cc_final: -0.1715 (pmt) REVERT: F 205 GLN cc_start: 0.7174 (OUTLIER) cc_final: 0.6721 (tt0) REVERT: F 227 SER cc_start: 0.8737 (m) cc_final: 0.8457 (m) REVERT: F 322 ASN cc_start: 0.7430 (t0) cc_final: 0.7070 (t0) REVERT: F 333 LYS cc_start: 0.8831 (tttt) cc_final: 0.8584 (tptt) REVERT: G 254 ASN cc_start: 0.7757 (OUTLIER) cc_final: 0.7435 (t0) REVERT: G 294 TRP cc_start: 0.7697 (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: 0.7354 (mp10) REVERT: H 56 TYR cc_start: 0.7854 (t80) cc_final: 0.7273 (t80) REVERT: H 113 ARG cc_start: 0.6679 (OUTLIER) cc_final: 0.6323 (ptp90) REVERT: H 227 SER cc_start: 0.8674 (m) cc_final: 0.8390 (m) REVERT: H 334 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7860 (mt-10) outliers start: 28 outliers final: 14 residues processed: 150 average time/residue: 1.0216 time to fit residues: 170.8175 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 : 1.356 ------------------------------------------------------------------------------- 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: 0.9980 chunk 31 optimal weight: 1.9990 chunk 74 optimal weight: 0.4980 chunk 121 optimal weight: 2.9990 chunk 69 optimal weight: 0.0470 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: 0.4956 ------------------------------------------------------------------------------- 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 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 = 0.4338 r_free = 0.4338 target = 0.196733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.160612 restraints weight = 16626.546| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 2.44 r_work: 0.3820 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13932 Z= 0.123 Angle : 0.547 8.472 19172 Z= 0.289 Chirality : 0.040 0.131 2092 Planarity : 0.005 0.051 2156 Dihedral : 18.575 174.860 2582 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.94 % Favored : 94.78 % Rotamer: Outliers : 2.47 % Allowed : 9.80 % Favored : 87.73 % 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: -0.43 (0.22), residues: 1436 helix: 1.38 (0.25), residues: 436 sheet: -0.54 (0.33), residues: 272 loop : -1.23 (0.22), residues: 728 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 0.015 0.001 PHE H 30 TYR 0.016 0.001 TYR E 225 ARG 0.003 0.000 ARG F 24 Details of bonding type rmsd hydrogen bonds : bond 0.04053 ( 461) hydrogen bonds : angle 4.72400 ( 1199) covalent geometry : bond 0.00273 (13932) covalent geometry : angle 0.54713 (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 159 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 127 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 172 ASP cc_start: 0.8276 (m-30) cc_final: 0.8054 (m-30) REVERT: E 287 MET cc_start: 0.8018 (mmm) cc_final: 0.7391 (mmm) REVERT: E 336 MET cc_start: 0.8525 (mtt) cc_final: 0.8237 (mtt) REVERT: E 395 MET cc_start: 0.8567 (mmt) cc_final: 0.8303 (mmp) REVERT: F 18 GLN cc_start: 0.7579 (mt0) cc_final: 0.7335 (mt0) REVERT: F 113 ARG cc_start: 0.6354 (OUTLIER) cc_final: 0.5667 (mtm180) REVERT: F 227 SER cc_start: 0.8659 (m) cc_final: 0.8366 (m) REVERT: F 322 ASN cc_start: 0.7479 (t0) cc_final: 0.7110 (t0) REVERT: G 186 ARG cc_start: 0.7064 (OUTLIER) cc_final: 0.6832 (mpp80) REVERT: G 254 ASN cc_start: 0.7789 (OUTLIER) cc_final: 0.7488 (OUTLIER) REVERT: G 294 TRP cc_start: 0.7766 (p-90) cc_final: 0.7522 (p-90) REVERT: G 306 GLU cc_start: 0.7283 (mt-10) cc_final: 0.7028 (mt-10) REVERT: G 336 MET cc_start: 0.8606 (mtt) cc_final: 0.8262 (mtt) REVERT: H 18 GLN cc_start: 0.7871 (mt0) cc_final: 0.7260 (mm-40) REVERT: H 56 TYR cc_start: 0.7795 (t80) cc_final: 0.7232 (t80) REVERT: H 161 MET cc_start: 0.0080 (ppp) cc_final: -0.1277 (pmt) REVERT: H 205 GLN cc_start: 0.7172 (OUTLIER) cc_final: 0.6952 (tt0) REVERT: H 227 SER cc_start: 0.8584 (m) cc_final: 0.8296 (m) outliers start: 32 outliers final: 16 residues processed: 151 average time/residue: 1.0066 time to fit residues: 169.8265 Evaluate side-chains 130 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 1.344 ------------------------------------------------------------------------------- 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 113 ARG Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 274 VAL 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 G residue 415 SER Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain H residue 205 GLN Chi-restraints excluded: chain H residue 267 LYS Chi-restraints excluded: chain H residue 274 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 144 optimal weight: 0.4980 chunk 111 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 138 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- 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 = 0.4278 r_free = 0.4278 target = 0.190513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.153951 restraints weight = 16509.718| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.43 r_work: 0.3738 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 13932 Z= 0.230 Angle : 0.630 8.827 19172 Z= 0.330 Chirality : 0.044 0.232 2092 Planarity : 0.006 0.067 2156 Dihedral : 18.710 174.646 2582 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.43 % Favored : 94.29 % Rotamer: Outliers : 2.62 % Allowed : 10.96 % Favored : 86.42 % 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: -0.67 (0.22), residues: 1436 helix: 1.00 (0.24), residues: 436 sheet: -0.61 (0.33), residues: 272 loop : -1.28 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 86 HIS 0.006 0.001 HIS F 59 PHE 0.020 0.002 PHE E 198 TYR 0.016 0.002 TYR G 213 ARG 0.005 0.001 ARG E 362 Details of bonding type rmsd hydrogen bonds : bond 0.04460 ( 461) hydrogen bonds : angle 4.94424 ( 1199) covalent geometry : bond 0.00547 (13932) covalent geometry : angle 0.63007 (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 159 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 1.372 Fit side-chains revert: symmetry clash REVERT: E 172 ASP cc_start: 0.8332 (m-30) cc_final: 0.8106 (m-30) REVERT: E 287 MET cc_start: 0.7935 (mmm) cc_final: 0.7375 (mmm) REVERT: E 313 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7837 (tptm) REVERT: E 315 LYS cc_start: 0.7549 (mptt) cc_final: 0.7269 (mppt) REVERT: E 336 MET cc_start: 0.8544 (mtt) cc_final: 0.8277 (mtt) REVERT: E 395 MET cc_start: 0.8783 (mmt) cc_final: 0.8555 (mmp) REVERT: F 113 ARG cc_start: 0.6309 (ptm160) cc_final: 0.6036 (ptm-80) REVERT: F 161 MET cc_start: -0.0447 (ppp) cc_final: -0.1676 (pmt) REVERT: F 205 GLN cc_start: 0.7077 (OUTLIER) cc_final: 0.6647 (tt0) REVERT: F 227 SER cc_start: 0.8764 (m) cc_final: 0.8438 (m) REVERT: F 322 ASN cc_start: 0.7436 (t0) cc_final: 0.7019 (t0) REVERT: G 254 ASN cc_start: 0.7809 (OUTLIER) cc_final: 0.7579 (OUTLIER) REVERT: G 336 MET cc_start: 0.8608 (mtt) cc_final: 0.8311 (mtt) REVERT: H 18 GLN cc_start: 0.8009 (mt0) cc_final: 0.7262 (mp10) REVERT: H 56 TYR cc_start: 0.7907 (t80) cc_final: 0.7377 (t80) REVERT: H 87 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7099 (mp0) REVERT: H 205 GLN cc_start: 0.7337 (OUTLIER) cc_final: 0.7060 (tt0) REVERT: H 227 SER cc_start: 0.8688 (m) cc_final: 0.8378 (m) REVERT: H 247 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7619 (mttm) outliers start: 34 outliers final: 19 residues processed: 149 average time/residue: 0.9999 time to fit residues: 166.8377 Evaluate side-chains 135 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 225 TYR 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 313 LYS Chi-restraints excluded: chain E residue 332 PHE Chi-restraints excluded: chain E residue 415 SER 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 254 ASN Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain G residue 415 SER Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain H residue 113 ARG Chi-restraints excluded: chain H residue 205 GLN Chi-restraints excluded: chain H residue 247 LYS Chi-restraints excluded: chain H residue 267 LYS Chi-restraints excluded: chain H residue 274 VAL Chi-restraints excluded: chain H residue 322 ASN Chi-restraints excluded: chain H residue 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: 8.9990 chunk 93 optimal weight: 8.9990 chunk 94 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 144 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 109 optimal weight: 0.0000 overall best weight: 1.5590 ------------------------------------------------------------------------------- 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 = 0.4278 r_free = 0.4278 target = 0.190861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.154645 restraints weight = 16812.432| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 2.43 r_work: 0.3743 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13932 Z= 0.212 Angle : 0.617 12.378 19172 Z= 0.322 Chirality : 0.043 0.144 2092 Planarity : 0.005 0.065 2156 Dihedral : 18.623 174.644 2580 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.78 % Favored : 93.94 % Rotamer: Outliers : 2.62 % Allowed : 12.35 % Favored : 85.03 % 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: 1.05 (0.25), residues: 428 sheet: -0.60 (0.33), residues: 272 loop : -1.27 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 86 HIS 0.004 0.001 HIS F 59 PHE 0.023 0.002 PHE E 198 TYR 0.014 0.002 TYR G 225 ARG 0.003 0.001 ARG H 24 Details of bonding type rmsd hydrogen bonds : bond 0.04295 ( 461) hydrogen bonds : angle 4.92998 ( 1199) covalent geometry : bond 0.00500 (13932) covalent geometry : angle 0.61740 (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 157 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 123 time to evaluate : 3.092 Fit side-chains revert: symmetry clash REVERT: E 172 ASP cc_start: 0.8323 (m-30) cc_final: 0.8094 (m-30) REVERT: E 313 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7830 (tptm) REVERT: E 315 LYS cc_start: 0.7473 (mptt) cc_final: 0.7218 (mppt) REVERT: E 336 MET cc_start: 0.8511 (mtt) cc_final: 0.8233 (mtt) REVERT: F 18 GLN cc_start: 0.7774 (mt0) cc_final: 0.7548 (mt0) REVERT: F 91 ILE cc_start: 0.7895 (OUTLIER) cc_final: 0.7382 (pt) REVERT: F 113 ARG cc_start: 0.6274 (ptm160) cc_final: 0.6009 (ptm-80) REVERT: F 205 GLN cc_start: 0.6948 (OUTLIER) cc_final: 0.6588 (tt0) REVERT: F 227 SER cc_start: 0.8765 (m) cc_final: 0.8456 (m) REVERT: F 322 ASN cc_start: 0.7575 (t0) cc_final: 0.7152 (t0) REVERT: G 254 ASN cc_start: 0.7768 (OUTLIER) cc_final: 0.7525 (t0) REVERT: G 336 MET cc_start: 0.8544 (mtt) cc_final: 0.8229 (mtt) REVERT: H 56 TYR cc_start: 0.7896 (t80) cc_final: 0.7392 (t80) REVERT: H 87 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7134 (mp0) REVERT: H 91 ILE cc_start: 0.7643 (OUTLIER) cc_final: 0.7090 (pt) REVERT: H 161 MET cc_start: -0.0575 (ppp) cc_final: -0.1908 (pmt) REVERT: H 205 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.6982 (tt0) REVERT: H 267 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7695 (mttp) REVERT: H 380 GLU cc_start: 0.7693 (tp30) cc_final: 0.7328 (tp30) outliers start: 34 outliers final: 19 residues processed: 148 average time/residue: 1.0435 time to fit residues: 172.9334 Evaluate side-chains 138 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 313 LYS 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 91 ILE 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 254 ASN Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain G residue 415 SER Chi-restraints excluded: chain H residue 87 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 267 LYS Chi-restraints excluded: chain H residue 274 VAL Chi-restraints excluded: chain H residue 322 ASN Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 507 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 77 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 71 optimal weight: 0.4980 chunk 132 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 137 optimal weight: 0.2980 chunk 1 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 49 optimal weight: 0.2980 chunk 50 optimal weight: 0.6980 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** E 413 ASN F 307 ASN ** F 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 GLN H 209 GLN H 322 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.195125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.159038 restraints weight = 16662.520| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 2.44 r_work: 0.3800 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13932 Z= 0.125 Angle : 0.560 11.499 19172 Z= 0.293 Chirality : 0.040 0.204 2092 Planarity : 0.005 0.061 2156 Dihedral : 18.479 173.277 2580 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.36 % Favored : 94.36 % Rotamer: Outliers : 2.39 % Allowed : 13.19 % Favored : 84.41 % 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: -0.37 (0.22), residues: 1436 helix: 1.24 (0.25), residues: 440 sheet: -0.17 (0.35), residues: 252 loop : -1.21 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 370 HIS 0.003 0.001 HIS H 217 PHE 0.026 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 0.03777 ( 461) hydrogen bonds : angle 4.70437 ( 1199) covalent geometry : bond 0.00280 (13932) covalent geometry : angle 0.56036 (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 151 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 120 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 336 MET cc_start: 0.8520 (mtt) cc_final: 0.8226 (mtt) REVERT: F 18 GLN cc_start: 0.7565 (mt0) cc_final: 0.7145 (tt0) REVERT: F 161 MET cc_start: -0.0758 (ppp) cc_final: -0.2191 (pmt) REVERT: F 205 GLN cc_start: 0.6782 (OUTLIER) cc_final: 0.6372 (tt0) REVERT: F 322 ASN cc_start: 0.7477 (t0) cc_final: 0.7058 (t0) REVERT: G 186 ARG cc_start: 0.7270 (OUTLIER) cc_final: 0.7006 (mpp80) REVERT: G 254 ASN cc_start: 0.7741 (OUTLIER) cc_final: 0.7533 (t0) REVERT: G 294 TRP cc_start: 0.7840 (p-90) cc_final: 0.7598 (p-90) REVERT: G 336 MET cc_start: 0.8572 (mtt) cc_final: 0.8235 (mtt) REVERT: H 18 GLN cc_start: 0.7672 (mt0) cc_final: 0.7164 (mm-40) REVERT: H 56 TYR cc_start: 0.7805 (t80) cc_final: 0.7329 (t80) REVERT: H 91 ILE cc_start: 0.7530 (OUTLIER) cc_final: 0.6984 (pt) REVERT: H 205 GLN cc_start: 0.7318 (OUTLIER) cc_final: 0.6878 (tt0) REVERT: H 267 LYS cc_start: 0.7769 (OUTLIER) cc_final: 0.7529 (mttp) outliers start: 31 outliers final: 17 residues processed: 144 average time/residue: 1.0231 time to fit residues: 164.8805 Evaluate side-chains 130 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 1.479 ------------------------------------------------------------------------------- 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 132 GLU Chi-restraints excluded: chain F residue 205 GLN Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 459 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 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 267 LYS Chi-restraints excluded: chain H residue 274 VAL Chi-restraints excluded: chain H residue 322 ASN Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 459 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: 0.6980 chunk 136 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 120 optimal weight: 0.0670 chunk 18 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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** ** G 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 209 GLN H 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.195807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.159582 restraints weight = 16525.641| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 2.44 r_work: 0.3804 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2188 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= 0.128 Angle : 0.560 12.788 19172 Z= 0.291 Chirality : 0.040 0.189 2092 Planarity : 0.005 0.057 2156 Dihedral : 18.443 172.699 2580 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.22 % Favored : 94.50 % Rotamer: Outliers : 2.01 % Allowed : 14.89 % Favored : 83.10 % 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: -0.31 (0.23), residues: 1436 helix: 1.33 (0.25), residues: 440 sheet: -0.42 (0.34), residues: 272 loop : -1.08 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 86 HIS 0.003 0.001 HIS H 217 PHE 0.028 0.001 PHE E 198 TYR 0.014 0.001 TYR G 225 ARG 0.002 0.000 ARG F 24 Details of bonding type rmsd hydrogen bonds : bond 0.03700 ( 461) hydrogen bonds : angle 4.62196 ( 1199) covalent geometry : bond 0.00290 (13932) covalent geometry : angle 0.55996 (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 143 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 192 TRP cc_start: 0.7736 (p-90) cc_final: 0.7484 (p-90) REVERT: E 287 MET cc_start: 0.7921 (mmm) cc_final: 0.7307 (mmm) REVERT: E 336 MET cc_start: 0.8521 (mtt) cc_final: 0.8229 (mtt) REVERT: F 18 GLN cc_start: 0.7526 (mt0) cc_final: 0.7112 (tt0) REVERT: F 59 HIS cc_start: 0.7370 (t-90) cc_final: 0.6885 (t70) REVERT: F 113 ARG cc_start: 0.6223 (ptm160) cc_final: 0.5739 (mtm180) REVERT: F 205 GLN cc_start: 0.6782 (OUTLIER) cc_final: 0.6425 (tt0) REVERT: F 322 ASN cc_start: 0.7475 (t0) cc_final: 0.7048 (t0) REVERT: G 186 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.6942 (mpp80) REVERT: G 254 ASN cc_start: 0.7867 (OUTLIER) cc_final: 0.7607 (t0) REVERT: G 294 TRP cc_start: 0.7844 (p-90) cc_final: 0.7572 (p-90) REVERT: G 336 MET cc_start: 0.8570 (mtt) cc_final: 0.8232 (mtt) REVERT: H 18 GLN cc_start: 0.7609 (mt0) cc_final: 0.7088 (mm-40) REVERT: H 56 TYR cc_start: 0.7758 (t80) cc_final: 0.7244 (t80) REVERT: H 91 ILE cc_start: 0.7430 (OUTLIER) cc_final: 0.6869 (pt) REVERT: H 161 MET cc_start: -0.0767 (ppp) cc_final: -0.2397 (pmt) REVERT: H 267 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7515 (mttp) REVERT: H 324 LYS cc_start: 0.8052 (mttp) cc_final: 0.7528 (mtpp) REVERT: H 380 GLU cc_start: 0.7585 (tp30) cc_final: 0.7263 (tp30) outliers start: 26 outliers final: 13 residues processed: 136 average time/residue: 1.2014 time to fit residues: 183.8127 Evaluate side-chains 125 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 1.490 ------------------------------------------------------------------------------- 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 132 GLU 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 G residue 415 SER Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 113 ARG Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain H residue 267 LYS Chi-restraints excluded: chain H residue 274 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 40 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 54 optimal weight: 0.0770 chunk 12 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- 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 H 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.190238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.153851 restraints weight = 16865.510| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 2.45 r_work: 0.3733 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 13932 Z= 0.237 Angle : 0.643 13.030 19172 Z= 0.333 Chirality : 0.044 0.167 2092 Planarity : 0.006 0.069 2156 Dihedral : 18.624 173.604 2580 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.92 % Favored : 93.80 % Rotamer: Outliers : 2.62 % Allowed : 14.43 % Favored : 82.95 % 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: -0.63 (0.22), residues: 1436 helix: 1.08 (0.25), residues: 428 sheet: -0.55 (0.34), residues: 272 loop : -1.28 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 86 HIS 0.004 0.001 HIS F 59 PHE 0.032 0.002 PHE E 198 TYR 0.018 0.002 TYR G 251 ARG 0.004 0.001 ARG G 362 Details of bonding type rmsd hydrogen bonds : bond 0.04353 ( 461) hydrogen bonds : angle 4.89017 ( 1199) covalent geometry : bond 0.00561 (13932) covalent geometry : angle 0.64319 (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 143 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 109 time to evaluate : 1.589 Fit side-chains revert: symmetry clash REVERT: E 287 MET cc_start: 0.7820 (OUTLIER) cc_final: 0.7347 (mtt) REVERT: E 336 MET cc_start: 0.8512 (mtt) cc_final: 0.8252 (mtt) REVERT: E 349 LYS cc_start: 0.7009 (OUTLIER) cc_final: 0.6417 (pptt) REVERT: F 18 GLN cc_start: 0.7778 (mt0) cc_final: 0.7498 (mt0) REVERT: F 161 MET cc_start: -0.1190 (ppp) cc_final: -0.2885 (pmt) REVERT: F 205 GLN cc_start: 0.6985 (OUTLIER) cc_final: 0.6679 (tt0) REVERT: G 186 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.7005 (mpp80) REVERT: G 254 ASN cc_start: 0.7879 (OUTLIER) cc_final: 0.7622 (t0) REVERT: G 336 MET cc_start: 0.8547 (mtt) cc_final: 0.8260 (mtt) REVERT: H 18 GLN cc_start: 0.7828 (mt0) cc_final: 0.7270 (mm-40) REVERT: H 56 TYR cc_start: 0.7923 (t80) cc_final: 0.7487 (t80) REVERT: H 57 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7015 (tt) REVERT: H 91 ILE cc_start: 0.7688 (OUTLIER) cc_final: 0.7131 (pt) REVERT: H 267 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7711 (mttp) outliers start: 34 outliers final: 16 residues processed: 133 average time/residue: 1.0180 time to fit residues: 151.8287 Evaluate side-chains 131 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 254 ASN Chi-restraints excluded: chain E residue 287 MET Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 332 PHE Chi-restraints excluded: chain E residue 349 LYS Chi-restraints excluded: chain F residue 13 LEU 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 254 ASN Chi-restraints excluded: chain G residue 291 THR 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 267 LYS Chi-restraints excluded: chain H residue 274 VAL 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: 2.9990 chunk 84 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 142 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 G 413 ASN H 209 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.193590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.157894 restraints weight = 16692.531| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 2.41 r_work: 0.3787 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2361 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= 0.141 Angle : 0.577 14.208 19172 Z= 0.298 Chirality : 0.041 0.152 2092 Planarity : 0.005 0.059 2156 Dihedral : 18.481 172.615 2580 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.08 % Favored : 94.64 % Rotamer: Outliers : 2.01 % Allowed : 15.35 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (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 (0.23), residues: 1436 helix: 1.32 (0.25), residues: 428 sheet: -0.17 (0.34), residues: 264 loop : -1.19 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 86 HIS 0.003 0.001 HIS F 217 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 0.03750 ( 461) hydrogen bonds : angle 4.68818 ( 1199) covalent geometry : bond 0.00323 (13932) covalent geometry : angle 0.57677 (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 139 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 287 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7209 (mmm) REVERT: E 336 MET cc_start: 0.8479 (mtt) cc_final: 0.8189 (mtt) REVERT: F 18 GLN cc_start: 0.7554 (mt0) cc_final: 0.7235 (tt0) REVERT: F 59 HIS cc_start: 0.7455 (t-90) cc_final: 0.6937 (t70) REVERT: F 91 ILE cc_start: 0.7730 (OUTLIER) cc_final: 0.7202 (pt) REVERT: F 205 GLN cc_start: 0.6771 (OUTLIER) cc_final: 0.6442 (tt0) REVERT: G 186 ARG cc_start: 0.7259 (OUTLIER) cc_final: 0.6988 (mpp80) REVERT: G 287 MET cc_start: 0.7748 (mmm) cc_final: 0.7152 (mmm) REVERT: G 294 TRP cc_start: 0.7844 (p-90) cc_final: 0.7605 (p-90) REVERT: G 336 MET cc_start: 0.8524 (mtt) cc_final: 0.8183 (mtt) REVERT: H 18 GLN cc_start: 0.7686 (mt0) cc_final: 0.7182 (mm-40) REVERT: H 91 ILE cc_start: 0.7412 (OUTLIER) cc_final: 0.6841 (pt) REVERT: H 267 LYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7519 (mttp) outliers start: 26 outliers final: 14 residues processed: 132 average time/residue: 1.0863 time to fit residues: 159.6822 Evaluate side-chains 125 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 287 MET 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 205 GLN Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain G residue 186 ARG Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain G residue 415 SER Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain H residue 267 LYS Chi-restraints excluded: chain H residue 274 VAL Chi-restraints excluded: chain H residue 459 ILE Chi-restraints excluded: chain H residue 507 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 71 optimal weight: 0.0010 chunk 120 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 99 optimal weight: 0.4980 chunk 53 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 overall best weight: 0.6186 ------------------------------------------------------------------------------- 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 = 0.4323 r_free = 0.4323 target = 0.194916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.159068 restraints weight = 16746.615| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 2.44 r_work: 0.3810 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.2436 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= 0.129 Angle : 0.564 13.379 19172 Z= 0.291 Chirality : 0.040 0.137 2092 Planarity : 0.005 0.061 2156 Dihedral : 18.422 171.545 2580 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.22 % Favored : 94.50 % Rotamer: Outliers : 1.70 % Allowed : 15.74 % Favored : 82.56 % 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: -0.24 (0.23), residues: 1436 helix: 1.48 (0.25), residues: 430 sheet: -0.18 (0.35), residues: 252 loop : -1.14 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 86 HIS 0.003 0.001 HIS F 217 PHE 0.034 0.001 PHE E 198 TYR 0.019 0.001 TYR E 210 ARG 0.002 0.000 ARG F 72 Details of bonding type rmsd hydrogen bonds : bond 0.03624 ( 461) hydrogen bonds : angle 4.58486 ( 1199) covalent geometry : bond 0.00293 (13932) covalent geometry : angle 0.56387 (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 131 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 287 MET cc_start: 0.7914 (mmm) cc_final: 0.7323 (mmm) REVERT: E 336 MET cc_start: 0.8485 (mtt) cc_final: 0.8187 (mtt) REVERT: E 395 MET cc_start: 0.7551 (mmp) cc_final: 0.7332 (mmp) REVERT: F 18 GLN cc_start: 0.7495 (mt0) cc_final: 0.7190 (tt0) REVERT: F 59 HIS cc_start: 0.7471 (t-90) cc_final: 0.7026 (t70) REVERT: F 91 ILE cc_start: 0.7882 (OUTLIER) cc_final: 0.7337 (pt) REVERT: F 205 GLN cc_start: 0.6747 (OUTLIER) cc_final: 0.6443 (tt0) REVERT: F 322 ASN cc_start: 0.7122 (t0) cc_final: 0.6705 (t0) REVERT: G 186 ARG cc_start: 0.7235 (OUTLIER) cc_final: 0.6961 (mpp80) REVERT: G 232 THR cc_start: 0.8145 (m) cc_final: 0.7925 (m) REVERT: G 294 TRP cc_start: 0.7909 (p-90) cc_final: 0.7641 (p-90) REVERT: G 336 MET cc_start: 0.8531 (mtt) cc_final: 0.8194 (mtt) REVERT: H 18 GLN cc_start: 0.7694 (mt0) cc_final: 0.7201 (mm-40) REVERT: H 91 ILE cc_start: 0.7261 (OUTLIER) cc_final: 0.6686 (pt) REVERT: H 267 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7522 (mttp) outliers start: 22 outliers final: 16 residues processed: 127 average time/residue: 1.0466 time to fit residues: 148.4193 Evaluate side-chains 127 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 239 ILE 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 205 GLN Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain G residue 186 ARG Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain G residue 415 SER Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain H residue 267 LYS Chi-restraints excluded: chain H residue 274 VAL Chi-restraints excluded: chain H residue 322 ASN Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 459 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 123 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 145 optimal weight: 0.9980 chunk 117 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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** ** H 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.193961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.157967 restraints weight = 16798.054| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 2.44 r_work: 0.3795 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2460 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= 0.146 Angle : 0.572 14.416 19172 Z= 0.296 Chirality : 0.040 0.141 2092 Planarity : 0.005 0.060 2156 Dihedral : 18.427 171.680 2580 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.50 % Favored : 94.22 % Rotamer: Outliers : 1.77 % Allowed : 15.74 % 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: -0.27 (0.23), residues: 1436 helix: 1.46 (0.25), residues: 430 sheet: -0.19 (0.35), residues: 252 loop : -1.17 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 86 HIS 0.002 0.001 HIS H 217 PHE 0.036 0.002 PHE E 198 TYR 0.017 0.001 TYR E 210 ARG 0.003 0.000 ARG F 113 Details of bonding type rmsd hydrogen bonds : bond 0.03675 ( 461) hydrogen bonds : angle 4.61003 ( 1199) covalent geometry : bond 0.00337 (13932) covalent geometry : angle 0.57240 (19172) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7065.60 seconds wall clock time: 123 minutes 21.83 seconds (7401.83 seconds total)