Starting phenix.real_space_refine on Mon Apr 8 16:47:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oze_17306/04_2024/8oze_17306.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oze_17306/04_2024/8oze_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oze_17306/04_2024/8oze_17306.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oze_17306/04_2024/8oze_17306.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oze_17306/04_2024/8oze_17306.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oze_17306/04_2024/8oze_17306.pdb" } 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 Residue "E PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 474": "OD1" <-> "OD2" Residue "F TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 474": "OD1" <-> "OD2" Residue "H TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 13434 Number of models: 1 Model: "" Number of chains: 8 Chain: "N" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 435 Classifications: {'RNA': 20} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 12, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 18} Chain: "P" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 339 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "E" Number of atoms: 2122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2122 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 8, 'TRANS': 242} Chain: "F" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3821 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 24, 'TRANS': 448} Chain breaks: 1 Chain: "G" 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: "H" 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} Time building chain proxies: 7.52, per 1000 atoms: 0.56 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 - 3.50 Amino acid : False - 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: 5.24 Conformation dependent library (CDL) restraints added in 1.9 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: 5.26 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: 5.95 Time building geometry restraints manager: 5.70 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: 100.17 - 106.95: 800 106.95 - 113.72: 7687 113.72 - 120.50: 5364 120.50 - 127.27: 5048 127.27 - 134.05: 273 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 2.440 nonbonded pdb=" OE2 GLU G 284 " pdb=" OG1 THR G 291 " model vdw 2.128 2.440 nonbonded pdb=" OH TYR G 221 " pdb=" O TYR G 233 " model vdw 2.224 2.440 nonbonded pdb=" OH TYR E 221 " pdb=" O TYR E 233 " model vdw 2.224 2.440 nonbonded pdb=" O LYS F 11 " pdb=" OG SER F 272 " model vdw 2.258 2.440 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'N' } ncs_group { reference = chain 'B' selection = chain 'P' } 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: 1.440 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: 0.020 Extract box with map and model: 6.420 Check model and map are aligned: 0.230 Set scattering table: 0.130 Process input model: 42.160 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.090 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:12.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.160 ------------------------------------------------------------------------------- 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= 0.210 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 1.539 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: 1.0728 time to fit residues: 230.6724 Evaluate side-chains 114 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 113 time to evaluate : 1.518 ------------------------------------------------------------------------------- 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: 2.9990 chunk 113 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 117 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 136 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 H 209 GLN ** H 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 344 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.1136 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= 0.251 Angle : 0.591 7.285 19172 Z= 0.312 Chirality : 0.042 0.230 2092 Planarity : 0.005 0.055 2156 Dihedral : 18.746 176.788 2582 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.85 % Favored : 93.87 % Rotamer: Outliers : 2.01 % Allowed : 8.56 % Favored : 89.43 % 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: -0.59 (0.22), residues: 1436 helix: 1.18 (0.25), residues: 436 sheet: -0.51 (0.32), residues: 272 loop : -1.34 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 219 HIS 0.003 0.001 HIS F 16 PHE 0.014 0.002 PHE E 187 TYR 0.014 0.001 TYR G 225 ARG 0.004 0.001 ARG F 24 *********************** 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 152 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 126 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 287 MET cc_start: 0.7911 (mmm) cc_final: 0.7201 (mmm) REVERT: E 336 MET cc_start: 0.8162 (mtt) cc_final: 0.7934 (mtt) REVERT: F 1 MET cc_start: 0.7513 (tpp) cc_final: 0.7287 (tpp) REVERT: F 161 MET cc_start: -0.0579 (ppp) cc_final: -0.1299 (pmt) REVERT: F 227 SER cc_start: 0.7965 (m) cc_final: 0.7606 (m) REVERT: G 279 ASP cc_start: 0.7570 (t70) cc_final: 0.7297 (t70) REVERT: G 336 MET cc_start: 0.8216 (mtt) cc_final: 0.7924 (mtt) REVERT: H 56 TYR cc_start: 0.7428 (t80) cc_final: 0.7116 (t80) REVERT: H 227 SER cc_start: 0.7718 (m) cc_final: 0.7349 (m) REVERT: H 334 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7368 (mt-10) outliers start: 26 outliers final: 14 residues processed: 143 average time/residue: 1.1140 time to fit residues: 177.3232 Evaluate side-chains 122 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 107 time to evaluate : 1.456 ------------------------------------------------------------------------------- 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 143 VAL 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 332 PHE Chi-restraints excluded: chain G residue 415 SER Chi-restraints excluded: chain H residue 117 LEU 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 507 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 135 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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** F 344 GLN ** H 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 13932 Z= 0.439 Angle : 0.693 8.065 19172 Z= 0.360 Chirality : 0.046 0.159 2092 Planarity : 0.006 0.074 2156 Dihedral : 18.886 176.844 2582 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.55 % Favored : 93.18 % Rotamer: Outliers : 2.70 % Allowed : 11.11 % Favored : 86.19 % 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: -0.90 (0.21), residues: 1436 helix: 0.75 (0.24), residues: 434 sheet: -0.60 (0.32), residues: 272 loop : -1.44 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 86 HIS 0.005 0.001 HIS F 59 PHE 0.019 0.002 PHE E 342 TYR 0.016 0.002 TYR E 251 ARG 0.008 0.001 ARG F 113 *********************** 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 153 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 118 time to evaluate : 1.435 Fit side-chains REVERT: E 336 MET cc_start: 0.8210 (mtt) cc_final: 0.8001 (mtt) REVERT: E 349 LYS cc_start: 0.6920 (OUTLIER) cc_final: 0.6381 (pptt) REVERT: F 1 MET cc_start: 0.7202 (tpp) cc_final: 0.6961 (tpp) REVERT: F 30 PHE cc_start: 0.5818 (m-10) cc_final: 0.5612 (m-10) REVERT: F 91 ILE cc_start: 0.7424 (OUTLIER) cc_final: 0.6863 (pt) REVERT: F 227 SER cc_start: 0.8118 (m) cc_final: 0.7791 (m) REVERT: G 336 MET cc_start: 0.8278 (mtt) cc_final: 0.8060 (mtt) REVERT: H 56 TYR cc_start: 0.7592 (t80) cc_final: 0.7308 (t80) REVERT: H 91 ILE cc_start: 0.7322 (OUTLIER) cc_final: 0.6721 (pt) REVERT: H 161 MET cc_start: -0.0010 (ppp) cc_final: -0.0912 (pmt) REVERT: H 247 LYS cc_start: 0.7592 (OUTLIER) cc_final: 0.7024 (mttm) REVERT: H 334 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7535 (mt-10) outliers start: 35 outliers final: 19 residues processed: 144 average time/residue: 1.0357 time to fit residues: 167.3435 Evaluate side-chains 128 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 104 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 349 LYS 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 267 LYS Chi-restraints excluded: chain F residue 274 VAL 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 387 ASP Chi-restraints excluded: chain G residue 415 SER Chi-restraints excluded: chain H residue 66 ASN Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 117 LEU 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 334 GLU Chi-restraints excluded: chain H residue 507 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 chunk 144 optimal weight: 0.0470 chunk 71 optimal weight: 0.5980 chunk 129 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.1825 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= 0.180 Angle : 0.556 10.207 19172 Z= 0.293 Chirality : 0.040 0.133 2092 Planarity : 0.005 0.061 2156 Dihedral : 18.576 175.535 2582 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.01 % Favored : 94.71 % Rotamer: Outliers : 2.01 % Allowed : 12.42 % Favored : 85.57 % 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: -0.42 (0.22), residues: 1436 helix: 1.16 (0.25), residues: 436 sheet: -0.12 (0.34), residues: 252 loop : -1.23 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 219 HIS 0.004 0.001 HIS F 217 PHE 0.016 0.001 PHE E 198 TYR 0.014 0.001 TYR E 210 ARG 0.003 0.000 ARG H 24 *********************** 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 155 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 129 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 279 ASP cc_start: 0.7447 (t70) cc_final: 0.7103 (t70) REVERT: E 336 MET cc_start: 0.8146 (mtt) cc_final: 0.7924 (mtt) REVERT: E 387 ASP cc_start: 0.6866 (OUTLIER) cc_final: 0.6625 (p0) REVERT: F 1 MET cc_start: 0.7289 (tpp) cc_final: 0.7037 (tpp) REVERT: F 161 MET cc_start: -0.0456 (ppp) cc_final: -0.1031 (pmt) REVERT: F 227 SER cc_start: 0.7892 (m) cc_final: 0.7578 (m) REVERT: G 229 LYS cc_start: 0.7407 (pttt) cc_final: 0.7000 (pttt) REVERT: G 279 ASP cc_start: 0.7522 (t70) cc_final: 0.7252 (t70) REVERT: G 336 MET cc_start: 0.8238 (mtt) cc_final: 0.7989 (mtt) REVERT: H 56 TYR cc_start: 0.7428 (t80) cc_final: 0.7220 (t80) REVERT: H 227 SER cc_start: 0.7965 (m) cc_final: 0.7725 (m) outliers start: 26 outliers final: 12 residues processed: 149 average time/residue: 0.9639 time to fit residues: 162.3999 Evaluate side-chains 123 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 110 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 215 CYS Chi-restraints excluded: chain E residue 225 TYR 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 E residue 415 SER Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 507 ILE Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain G residue 415 SER 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 120 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 413 ASN ** H 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13932 Z= 0.280 Angle : 0.590 11.128 19172 Z= 0.309 Chirality : 0.042 0.135 2092 Planarity : 0.005 0.066 2156 Dihedral : 18.608 174.994 2582 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.85 % Favored : 93.87 % Rotamer: Outliers : 2.39 % Allowed : 13.27 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (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: -0.55 (0.22), residues: 1436 helix: 1.02 (0.25), residues: 436 sheet: -0.45 (0.33), residues: 268 loop : -1.19 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 86 HIS 0.003 0.001 HIS F 59 PHE 0.021 0.002 PHE E 198 TYR 0.016 0.002 TYR G 210 ARG 0.003 0.000 ARG G 361 *********************** 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 150 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 119 time to evaluate : 1.478 Fit side-chains revert: symmetry clash REVERT: E 287 MET cc_start: 0.7631 (mmm) cc_final: 0.7258 (mmm) REVERT: E 336 MET cc_start: 0.8188 (mtt) cc_final: 0.7968 (mtt) REVERT: E 349 LYS cc_start: 0.6902 (OUTLIER) cc_final: 0.6436 (pptt) REVERT: G 287 MET cc_start: 0.7536 (mmm) cc_final: 0.7289 (mmm) REVERT: G 336 MET cc_start: 0.8256 (mtt) cc_final: 0.8032 (mtt) REVERT: H 56 TYR cc_start: 0.7505 (t80) cc_final: 0.7263 (t80) REVERT: H 161 MET cc_start: -0.0809 (ppp) cc_final: -0.1777 (pmt) outliers start: 31 outliers final: 19 residues processed: 142 average time/residue: 0.9494 time to fit residues: 152.5757 Evaluate side-chains 129 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 109 time to evaluate : 1.484 ------------------------------------------------------------------------------- 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 349 LYS Chi-restraints excluded: chain E residue 387 ASP Chi-restraints excluded: chain E residue 415 SER Chi-restraints excluded: chain F residue 66 ASN Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 507 ILE Chi-restraints excluded: chain G residue 215 CYS Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain G residue 415 SER Chi-restraints excluded: chain H residue 66 ASN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 145 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 139 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 413 ASN ** H 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.2100 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= 0.205 Angle : 0.559 11.924 19172 Z= 0.293 Chirality : 0.040 0.153 2092 Planarity : 0.005 0.062 2156 Dihedral : 18.505 174.332 2582 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.94 % Favored : 94.78 % Rotamer: Outliers : 2.31 % Allowed : 13.73 % Favored : 83.95 % 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: -0.34 (0.22), residues: 1436 helix: 1.20 (0.25), residues: 436 sheet: -0.04 (0.35), residues: 248 loop : -1.17 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 192 HIS 0.003 0.001 HIS H 217 PHE 0.026 0.001 PHE E 198 TYR 0.016 0.001 TYR E 210 ARG 0.003 0.000 ARG F 72 *********************** 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 147 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 117 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 287 MET cc_start: 0.7660 (OUTLIER) cc_final: 0.7282 (mmm) REVERT: E 336 MET cc_start: 0.8195 (mtt) cc_final: 0.7974 (mtt) REVERT: F 161 MET cc_start: -0.0633 (ppp) cc_final: -0.1527 (pmt) REVERT: G 279 ASP cc_start: 0.7525 (t70) cc_final: 0.7226 (t70) REVERT: G 287 MET cc_start: 0.7671 (OUTLIER) cc_final: 0.7398 (mmm) REVERT: G 336 MET cc_start: 0.8245 (mtt) cc_final: 0.8003 (mtt) REVERT: H 56 TYR cc_start: 0.7476 (t80) cc_final: 0.7218 (t80) REVERT: H 91 ILE cc_start: 0.7029 (OUTLIER) cc_final: 0.6384 (pt) REVERT: H 227 SER cc_start: 0.7991 (m) cc_final: 0.7750 (m) outliers start: 30 outliers final: 20 residues processed: 140 average time/residue: 0.9803 time to fit residues: 155.2375 Evaluate side-chains 132 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 109 time to evaluate : 1.355 ------------------------------------------------------------------------------- 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 287 MET 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 E residue 415 SER Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 66 ASN Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 507 ILE Chi-restraints excluded: chain G residue 215 CYS Chi-restraints excluded: chain G residue 287 MET 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 88 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 413 ASN F 18 GLN G 413 ASN ** H 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.2187 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= 0.217 Angle : 0.572 12.528 19172 Z= 0.298 Chirality : 0.040 0.177 2092 Planarity : 0.005 0.062 2156 Dihedral : 18.491 173.709 2582 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.43 % Favored : 94.29 % Rotamer: Outliers : 2.01 % Allowed : 14.66 % Favored : 83.33 % 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: -0.36 (0.22), residues: 1436 helix: 1.20 (0.25), residues: 436 sheet: -0.11 (0.35), residues: 252 loop : -1.17 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 86 HIS 0.003 0.001 HIS H 217 PHE 0.030 0.001 PHE E 198 TYR 0.018 0.001 TYR E 210 ARG 0.002 0.000 ARG F 72 *********************** 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 137 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 111 time to evaluate : 1.566 Fit side-chains revert: symmetry clash REVERT: E 287 MET cc_start: 0.7543 (OUTLIER) cc_final: 0.7069 (mmm) REVERT: E 303 ASP cc_start: 0.5879 (p0) cc_final: 0.5676 (p0) REVERT: E 336 MET cc_start: 0.8198 (mtt) cc_final: 0.7985 (mtt) REVERT: E 387 ASP cc_start: 0.6830 (OUTLIER) cc_final: 0.6263 (p0) REVERT: F 19 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7805 (mttp) REVERT: G 287 MET cc_start: 0.7670 (OUTLIER) cc_final: 0.7392 (mmm) REVERT: G 336 MET cc_start: 0.8250 (mtt) cc_final: 0.7997 (mtt) REVERT: H 56 TYR cc_start: 0.7433 (t80) cc_final: 0.7172 (t80) REVERT: H 91 ILE cc_start: 0.7138 (OUTLIER) cc_final: 0.6497 (pt) REVERT: H 161 MET cc_start: -0.0583 (ppp) cc_final: -0.1982 (pmt) REVERT: H 227 SER cc_start: 0.8029 (m) cc_final: 0.7790 (m) outliers start: 26 outliers final: 18 residues processed: 130 average time/residue: 1.0097 time to fit residues: 147.5663 Evaluate side-chains 125 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 102 time to evaluate : 1.389 ------------------------------------------------------------------------------- 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 287 MET 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 E residue 415 SER Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain F residue 66 ASN Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 507 ILE Chi-restraints excluded: chain G residue 215 CYS Chi-restraints excluded: chain G residue 287 MET Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain H residue 66 ASN Chi-restraints excluded: chain H residue 91 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 0.0470 chunk 43 optimal weight: 0.0470 chunk 28 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 131 optimal weight: 0.6980 chunk 138 optimal weight: 0.5980 chunk 126 optimal weight: 0.3980 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 413 ASN ** H 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13932 Z= 0.154 Angle : 0.544 13.497 19172 Z= 0.283 Chirality : 0.039 0.139 2092 Planarity : 0.005 0.057 2156 Dihedral : 18.361 172.610 2582 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.08 % Favored : 94.64 % Rotamer: Outliers : 1.93 % Allowed : 15.20 % Favored : 82.87 % 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: -0.12 (0.23), residues: 1436 helix: 1.43 (0.25), residues: 442 sheet: -0.14 (0.33), residues: 278 loop : -1.02 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 192 HIS 0.004 0.001 HIS H 217 PHE 0.031 0.001 PHE E 198 TYR 0.020 0.001 TYR E 210 ARG 0.003 0.000 ARG F 24 *********************** 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 144 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 119 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 287 MET cc_start: 0.7587 (mmm) cc_final: 0.7156 (mmm) REVERT: E 336 MET cc_start: 0.8147 (mtt) cc_final: 0.7914 (mtt) REVERT: E 387 ASP cc_start: 0.6842 (OUTLIER) cc_final: 0.6335 (p0) REVERT: F 161 MET cc_start: -0.0731 (ppp) cc_final: -0.1980 (pmt) REVERT: G 287 MET cc_start: 0.7532 (mmm) cc_final: 0.7300 (mmm) REVERT: G 336 MET cc_start: 0.8214 (mtt) cc_final: 0.7942 (mtt) REVERT: H 56 TYR cc_start: 0.7374 (t80) cc_final: 0.7109 (t80) REVERT: H 227 SER cc_start: 0.7857 (m) cc_final: 0.7628 (m) outliers start: 25 outliers final: 14 residues processed: 137 average time/residue: 1.0306 time to fit residues: 158.7441 Evaluate side-chains 121 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 106 time to evaluate : 1.391 ------------------------------------------------------------------------------- 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 132 GLU Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 507 ILE Chi-restraints excluded: chain G residue 215 CYS Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain H residue 66 ASN 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 507 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.5980 chunk 138 optimal weight: 0.1980 chunk 81 optimal weight: 8.9990 chunk 58 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 142 optimal weight: 0.2980 chunk 86 optimal weight: 0.0370 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 413 ASN H 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.2381 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= 0.159 Angle : 0.550 14.726 19172 Z= 0.284 Chirality : 0.039 0.157 2092 Planarity : 0.005 0.057 2156 Dihedral : 18.315 171.617 2582 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.43 % Favored : 94.29 % Rotamer: Outliers : 1.39 % Allowed : 16.13 % 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: -0.06 (0.23), residues: 1436 helix: 1.55 (0.25), residues: 438 sheet: -0.11 (0.33), residues: 278 loop : -1.01 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 192 HIS 0.013 0.001 HIS F 59 PHE 0.034 0.001 PHE E 198 TYR 0.022 0.001 TYR E 210 ARG 0.002 0.000 ARG F 24 *********************** 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 125 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 107 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 287 MET cc_start: 0.7658 (mmm) cc_final: 0.7313 (mmm) REVERT: E 336 MET cc_start: 0.8151 (mtt) cc_final: 0.7922 (mtt) REVERT: E 387 ASP cc_start: 0.6775 (OUTLIER) cc_final: 0.6236 (p0) REVERT: G 287 MET cc_start: 0.7536 (mmm) cc_final: 0.7286 (mmm) REVERT: G 336 MET cc_start: 0.8220 (mtt) cc_final: 0.7943 (mtt) REVERT: H 56 TYR cc_start: 0.7354 (t80) cc_final: 0.7083 (t80) REVERT: H 227 SER cc_start: 0.7842 (m) cc_final: 0.7610 (m) outliers start: 18 outliers final: 16 residues processed: 120 average time/residue: 1.0119 time to fit residues: 136.3759 Evaluate side-chains 119 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 102 time to evaluate : 1.472 ------------------------------------------------------------------------------- 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 66 ASN Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 507 ILE Chi-restraints excluded: chain G residue 215 CYS Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain G residue 415 SER Chi-restraints excluded: chain H residue 66 ASN 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 507 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 149 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 94 optimal weight: 10.0000 chunk 126 optimal weight: 0.0970 chunk 36 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 307 ASN G 413 ASN H 205 GLN H 302 GLN ** H 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13932 Z= 0.246 Angle : 0.578 13.137 19172 Z= 0.299 Chirality : 0.041 0.149 2092 Planarity : 0.005 0.062 2156 Dihedral : 18.402 171.963 2582 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.64 % Favored : 94.08 % Rotamer: Outliers : 1.39 % Allowed : 16.36 % Favored : 82.25 % 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: -0.29 (0.23), residues: 1436 helix: 1.38 (0.25), residues: 436 sheet: -0.37 (0.34), residues: 268 loop : -1.11 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 86 HIS 0.013 0.001 HIS F 59 PHE 0.036 0.002 PHE E 198 TYR 0.022 0.001 TYR E 210 ARG 0.002 0.000 ARG F 24 ********************** 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 126 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 108 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 287 MET cc_start: 0.7657 (mmm) cc_final: 0.7286 (mmm) REVERT: E 336 MET cc_start: 0.8209 (mtt) cc_final: 0.7994 (mtt) REVERT: E 387 ASP cc_start: 0.6967 (OUTLIER) cc_final: 0.6353 (p0) REVERT: G 336 MET cc_start: 0.8263 (mtt) cc_final: 0.8019 (mtt) REVERT: H 227 SER cc_start: 0.7946 (m) cc_final: 0.7707 (m) outliers start: 18 outliers final: 16 residues processed: 122 average time/residue: 1.0304 time to fit residues: 141.3648 Evaluate side-chains 122 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 105 time to evaluate : 1.485 ------------------------------------------------------------------------------- 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 66 ASN Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 507 ILE Chi-restraints excluded: chain G residue 215 CYS Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain G residue 415 SER Chi-restraints excluded: chain H residue 66 ASN 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 507 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 119 optimal weight: 0.3980 chunk 49 optimal weight: 7.9990 chunk 122 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 21 optimal weight: 0.0670 chunk 104 optimal weight: 1.9990 chunk 6 optimal weight: 0.0370 chunk 86 optimal weight: 3.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 413 ASN F 18 GLN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 302 GLN F 307 ASN H 322 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.196652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.160996 restraints weight = 16485.870| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 2.40 r_work: 0.3827 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2481 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= 0.165 Angle : 0.555 12.320 19172 Z= 0.286 Chirality : 0.039 0.136 2092 Planarity : 0.005 0.057 2156 Dihedral : 18.300 171.334 2582 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.22 % Favored : 94.50 % Rotamer: Outliers : 1.39 % Allowed : 16.59 % Favored : 82.02 % 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: -0.08 (0.23), residues: 1436 helix: 1.51 (0.25), residues: 438 sheet: -0.11 (0.33), residues: 278 loop : -1.02 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 86 HIS 0.013 0.001 HIS F 59 PHE 0.033 0.001 PHE E 198 TYR 0.021 0.001 TYR E 210 ARG 0.002 0.000 ARG F 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3814.54 seconds wall clock time: 70 minutes 10.95 seconds (4210.95 seconds total)