Starting phenix.real_space_refine on Thu Sep 26 19:30:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oze_17306/09_2024/8oze_17306.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oze_17306/09_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_17306/09_2024/8oze_17306.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oze_17306/09_2024/8oze_17306.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oze_17306/09_2024/8oze_17306.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oze_17306/09_2024/8oze_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-5461/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: 10.34, per 1000 atoms: 0.77 Number of scatterers: 13434 At special positions: 0 Unit cell: (153.67, 129.47, 84.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 P 74 15.00 O 2656 8.00 N 2244 7.00 C 8420 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.66 Conformation dependent library (CDL) restraints added in 1.7 seconds 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2748 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 14 sheets defined 35.9% alpha, 16.9% beta 21 base pairs and 58 stacking pairs defined. Time for finding SS restraints: 5.08 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: 4.42 Time building geometry restraints manager: 4.08 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: 0.00 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: 1.650 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: 0.530 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 37.760 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.760 ------------------------------------------------------------------------------- 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 : 1.350 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: 1.0334 time to fit residues: 222.7696 Evaluate side-chains 114 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 113 time to evaluate : 1.516 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 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= 0.248 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 *********************** 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 fitting. rotamer outliers: 28 poor density : 134 time to evaluate : 1.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 279 ASP cc_start: 0.7434 (t70) cc_final: 0.7198 (t70) REVERT: E 287 MET cc_start: 0.7846 (mmm) cc_final: 0.7166 (mmm) REVERT: E 336 MET cc_start: 0.8176 (mtt) cc_final: 0.7915 (mtt) REVERT: F 1 MET cc_start: 0.7495 (tpp) cc_final: 0.7261 (tpp) REVERT: F 161 MET cc_start: -0.0372 (ppp) cc_final: -0.1084 (pmt) REVERT: F 227 SER cc_start: 0.8142 (m) cc_final: 0.7877 (m) REVERT: F 322 ASN cc_start: 0.7511 (t0) cc_final: 0.7146 (t0) REVERT: G 279 ASP cc_start: 0.7579 (t70) cc_final: 0.7308 (t70) REVERT: G 336 MET cc_start: 0.8231 (mtt) cc_final: 0.7947 (mtt) REVERT: H 56 TYR cc_start: 0.7444 (t80) cc_final: 0.7128 (t80) REVERT: H 227 SER cc_start: 0.7963 (m) cc_final: 0.7663 (m) REVERT: H 334 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7411 (mt-10) outliers start: 28 outliers final: 14 residues processed: 150 average time/residue: 1.0518 time to fit residues: 175.8360 Evaluate side-chains 128 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 113 time to evaluate : 1.411 ------------------------------------------------------------------------------- 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 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 332 PHE 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 75 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 113 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 136 optimal weight: 0.6980 chunk 147 optimal weight: 4.9990 chunk 121 optimal weight: 0.5980 chunk 135 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.1582 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= 0.193 Angle : 0.561 8.075 19172 Z= 0.296 Chirality : 0.041 0.144 2092 Planarity : 0.005 0.054 2156 Dihedral : 18.582 174.664 2582 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.15 % Favored : 94.57 % Rotamer: Outliers : 2.39 % Allowed : 10.19 % Favored : 87.42 % 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: -0.47 (0.22), residues: 1436 helix: 1.31 (0.25), residues: 436 sheet: -0.55 (0.33), residues: 272 loop : -1.24 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 370 HIS 0.003 0.001 HIS F 217 PHE 0.016 0.001 PHE H 30 TYR 0.016 0.001 TYR E 225 ARG 0.002 0.000 ARG H 24 *********************** 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 162 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 131 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 287 MET cc_start: 0.7699 (mmm) cc_final: 0.7014 (mmm) REVERT: E 336 MET cc_start: 0.8189 (mtt) cc_final: 0.7959 (mtt) REVERT: F 1 MET cc_start: 0.7159 (tpp) cc_final: 0.6863 (tpp) REVERT: F 227 SER cc_start: 0.8097 (m) cc_final: 0.7854 (m) REVERT: F 322 ASN cc_start: 0.7576 (t0) cc_final: 0.7186 (t0) REVERT: G 279 ASP cc_start: 0.7517 (t70) cc_final: 0.7238 (t70) REVERT: G 336 MET cc_start: 0.8278 (mtt) cc_final: 0.8022 (mtt) REVERT: H 56 TYR cc_start: 0.7423 (t80) cc_final: 0.7119 (t80) REVERT: H 161 MET cc_start: -0.0409 (ppp) cc_final: -0.1215 (pmt) REVERT: H 227 SER cc_start: 0.7899 (m) cc_final: 0.7618 (m) outliers start: 31 outliers final: 17 residues processed: 156 average time/residue: 1.0499 time to fit residues: 182.9937 Evaluate side-chains 125 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 108 time to evaluate : 1.466 ------------------------------------------------------------------------------- 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 F residue 13 LEU Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 406 LEU 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 132 GLU Chi-restraints excluded: chain H residue 267 LYS Chi-restraints excluded: chain H residue 274 VAL Chi-restraints excluded: chain H residue 507 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 91 optimal weight: 0.8980 chunk 136 optimal weight: 0.8980 chunk 144 optimal weight: 3.9990 chunk 71 optimal weight: 0.0980 chunk 129 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 205 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.1806 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= 0.186 Angle : 0.549 10.050 19172 Z= 0.289 Chirality : 0.040 0.236 2092 Planarity : 0.005 0.055 2156 Dihedral : 18.464 173.995 2580 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.94 % Favored : 94.78 % Rotamer: Outliers : 2.16 % Allowed : 11.96 % Favored : 85.88 % 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: 1.40 (0.25), residues: 436 sheet: -0.47 (0.33), residues: 272 loop : -1.19 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 219 HIS 0.003 0.001 HIS F 329 PHE 0.021 0.001 PHE E 198 TYR 0.016 0.001 TYR G 225 ARG 0.003 0.000 ARG G 186 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 122 time to evaluate : 1.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 279 ASP cc_start: 0.7452 (t70) cc_final: 0.7132 (t70) REVERT: E 287 MET cc_start: 0.7552 (mmm) cc_final: 0.6862 (mmm) REVERT: E 313 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7988 (tptm) REVERT: E 336 MET cc_start: 0.8164 (mtt) cc_final: 0.7928 (mtt) REVERT: F 1 MET cc_start: 0.7228 (tpp) cc_final: 0.6975 (tpp) REVERT: F 161 MET cc_start: -0.0759 (ppp) cc_final: -0.1350 (pmt) REVERT: F 227 SER cc_start: 0.8074 (m) cc_final: 0.7831 (m) REVERT: F 322 ASN cc_start: 0.7467 (t0) cc_final: 0.7087 (t0) REVERT: G 229 LYS cc_start: 0.7332 (pttt) cc_final: 0.7004 (pttt) REVERT: G 336 MET cc_start: 0.8257 (mtt) cc_final: 0.7996 (mtt) REVERT: H 56 TYR cc_start: 0.7408 (t80) cc_final: 0.7126 (t80) REVERT: H 227 SER cc_start: 0.7872 (m) cc_final: 0.7600 (m) outliers start: 28 outliers final: 20 residues processed: 144 average time/residue: 0.9826 time to fit residues: 158.8276 Evaluate side-chains 128 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 107 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 215 CYS Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain E residue 313 LYS Chi-restraints excluded: chain E residue 332 PHE Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 79 GLU Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 143 VAL 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 113 ARG Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain H residue 267 LYS Chi-restraints excluded: chain H residue 274 VAL Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 507 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 8.9990 chunk 82 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 74 optimal weight: 0.2980 chunk 130 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 13932 Z= 0.399 Angle : 0.663 10.553 19172 Z= 0.346 Chirality : 0.045 0.155 2092 Planarity : 0.006 0.070 2156 Dihedral : 18.687 174.556 2580 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.06 % Favored : 93.66 % Rotamer: Outliers : 2.24 % Allowed : 12.58 % Favored : 85.19 % 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: -0.73 (0.22), residues: 1436 helix: 0.93 (0.24), residues: 434 sheet: -0.57 (0.34), residues: 268 loop : -1.33 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 86 HIS 0.005 0.001 HIS F 59 PHE 0.024 0.002 PHE E 198 TYR 0.019 0.002 TYR E 251 ARG 0.004 0.001 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 143 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 114 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 313 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.7952 (tptm) REVERT: E 336 MET cc_start: 0.8225 (mtt) cc_final: 0.8017 (mtt) REVERT: F 1 MET cc_start: 0.7490 (tpp) cc_final: 0.7236 (tpp) REVERT: F 227 SER cc_start: 0.8244 (m) cc_final: 0.7980 (m) REVERT: F 322 ASN cc_start: 0.7631 (t0) cc_final: 0.7149 (t0) REVERT: G 229 LYS cc_start: 0.7343 (pttt) cc_final: 0.7139 (pttt) REVERT: G 279 ASP cc_start: 0.7485 (t70) cc_final: 0.7219 (t70) REVERT: G 336 MET cc_start: 0.8288 (mtt) cc_final: 0.8052 (mtt) REVERT: H 56 TYR cc_start: 0.7561 (t80) cc_final: 0.7299 (t80) REVERT: H 87 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.7105 (mp0) REVERT: H 91 ILE cc_start: 0.7200 (OUTLIER) cc_final: 0.6581 (pt) REVERT: H 161 MET cc_start: -0.0682 (ppp) cc_final: -0.1705 (pmt) REVERT: H 380 GLU cc_start: 0.7014 (tp30) cc_final: 0.6814 (tp30) outliers start: 29 outliers final: 12 residues processed: 136 average time/residue: 0.9942 time to fit residues: 151.9626 Evaluate side-chains 123 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 1.409 ------------------------------------------------------------------------------- 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 313 LYS Chi-restraints excluded: chain E residue 332 PHE Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 274 VAL 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 87 GLU Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 274 VAL 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: 9.9990 chunk 130 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 209 GLN ** H 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13932 Z= 0.311 Angle : 0.614 11.461 19172 Z= 0.321 Chirality : 0.043 0.162 2092 Planarity : 0.005 0.069 2156 Dihedral : 18.617 174.288 2580 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.64 % Favored : 94.08 % Rotamer: Outliers : 2.47 % Allowed : 13.97 % Favored : 83.56 % 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: -0.71 (0.22), residues: 1436 helix: 0.95 (0.24), residues: 434 sheet: -0.56 (0.34), residues: 268 loop : -1.32 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 86 HIS 0.003 0.001 HIS F 59 PHE 0.026 0.002 PHE E 198 TYR 0.014 0.002 TYR G 225 ARG 0.003 0.001 ARG H 24 *********************** 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 146 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 114 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 313 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7898 (tptm) REVERT: E 336 MET cc_start: 0.8211 (mtt) cc_final: 0.7998 (mtt) REVERT: F 1 MET cc_start: 0.7572 (tpp) cc_final: 0.7355 (tpp) REVERT: F 91 ILE cc_start: 0.7386 (OUTLIER) cc_final: 0.6820 (pt) REVERT: F 161 MET cc_start: -0.0761 (ppp) cc_final: -0.1662 (pmt) REVERT: F 322 ASN cc_start: 0.7674 (t0) cc_final: 0.7192 (t0) REVERT: G 287 MET cc_start: 0.7586 (mmm) cc_final: 0.7120 (mmm) REVERT: G 336 MET cc_start: 0.8275 (mtt) cc_final: 0.8030 (mtt) REVERT: H 56 TYR cc_start: 0.7564 (t80) cc_final: 0.7345 (t80) REVERT: H 91 ILE cc_start: 0.7201 (OUTLIER) cc_final: 0.6568 (pt) outliers start: 32 outliers final: 16 residues processed: 139 average time/residue: 1.0178 time to fit residues: 159.0656 Evaluate side-chains 120 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 101 time to evaluate : 1.448 ------------------------------------------------------------------------------- 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 313 LYS 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 143 VAL 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 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 274 VAL Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 459 ILE Chi-restraints excluded: chain H residue 507 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 0.9980 chunk 82 optimal weight: 0.4980 chunk 105 optimal weight: 0.5980 chunk 122 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 88 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 413 ASN ** H 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 209 GLN H 322 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.2297 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= 0.188 Angle : 0.572 12.586 19172 Z= 0.298 Chirality : 0.040 0.143 2092 Planarity : 0.005 0.065 2156 Dihedral : 18.497 172.901 2580 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.43 % Favored : 94.29 % Rotamer: Outliers : 1.54 % Allowed : 15.35 % 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: -0.40 (0.22), residues: 1436 helix: 1.19 (0.24), residues: 436 sheet: -0.21 (0.34), residues: 264 loop : -1.19 (0.23), residues: 736 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 0.029 0.001 PHE E 198 TYR 0.015 0.001 TYR G 225 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 138 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 118 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 287 MET cc_start: 0.7480 (mmm) cc_final: 0.7092 (mmm) REVERT: E 336 MET cc_start: 0.8188 (mtt) cc_final: 0.7963 (mtt) REVERT: F 91 ILE cc_start: 0.7266 (OUTLIER) cc_final: 0.6671 (pt) REVERT: F 322 ASN cc_start: 0.7575 (t0) cc_final: 0.7110 (t0) REVERT: G 287 MET cc_start: 0.7583 (mmm) cc_final: 0.7129 (mmm) REVERT: G 336 MET cc_start: 0.8245 (mtt) cc_final: 0.7993 (mtt) REVERT: G 371 ASN cc_start: 0.7290 (m-40) cc_final: 0.7045 (t0) REVERT: H 56 TYR cc_start: 0.7497 (t80) cc_final: 0.7252 (t80) REVERT: H 161 MET cc_start: -0.0721 (ppp) cc_final: -0.2059 (pmt) outliers start: 20 outliers final: 13 residues processed: 135 average time/residue: 0.9873 time to fit residues: 150.0087 Evaluate side-chains 118 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 1.556 ------------------------------------------------------------------------------- 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 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 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 132 GLU Chi-restraints excluded: chain H residue 274 VAL Chi-restraints excluded: chain H residue 322 ASN Chi-restraints excluded: chain H residue 459 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 0.9990 chunk 43 optimal weight: 0.2980 chunk 28 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 131 optimal weight: 0.3980 chunk 138 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 18 GLN ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 209 GLN H 322 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2355 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= 0.189 Angle : 0.566 11.695 19172 Z= 0.294 Chirality : 0.040 0.133 2092 Planarity : 0.005 0.063 2156 Dihedral : 18.464 172.564 2580 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.43 % Favored : 94.29 % Rotamer: Outliers : 2.08 % Allowed : 15.43 % 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: -0.35 (0.23), residues: 1436 helix: 1.29 (0.25), residues: 436 sheet: -0.45 (0.33), residues: 280 loop : -1.10 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 86 HIS 0.013 0.001 HIS F 59 PHE 0.031 0.001 PHE E 198 TYR 0.013 0.001 TYR G 225 ARG 0.002 0.000 ARG F 72 *********************** 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 136 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 109 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 287 MET cc_start: 0.7497 (mmm) cc_final: 0.7067 (mmm) REVERT: E 336 MET cc_start: 0.8195 (mtt) cc_final: 0.7974 (mtt) REVERT: F 91 ILE cc_start: 0.7403 (OUTLIER) cc_final: 0.6782 (pt) REVERT: F 161 MET cc_start: -0.1293 (ppp) cc_final: -0.2490 (pmt) REVERT: F 322 ASN cc_start: 0.7579 (t0) cc_final: 0.7103 (t0) REVERT: G 232 THR cc_start: 0.7244 (m) cc_final: 0.7003 (m) REVERT: G 279 ASP cc_start: 0.7447 (t0) cc_final: 0.7168 (t70) REVERT: G 336 MET cc_start: 0.8255 (mtt) cc_final: 0.8003 (mtt) REVERT: G 371 ASN cc_start: 0.7323 (m-40) cc_final: 0.7042 (t0) REVERT: H 56 TYR cc_start: 0.7474 (t80) cc_final: 0.7218 (t80) outliers start: 27 outliers final: 17 residues processed: 130 average time/residue: 1.0837 time to fit residues: 157.5205 Evaluate side-chains 126 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 108 time to evaluate : 1.518 ------------------------------------------------------------------------------- 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 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 G residue 215 CYS 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 132 GLU Chi-restraints excluded: chain H residue 274 VAL Chi-restraints excluded: chain H residue 322 ASN Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 459 ILE Chi-restraints excluded: chain H residue 507 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 127 optimal weight: 0.0570 chunk 88 optimal weight: 0.8980 chunk 142 optimal weight: 0.7980 chunk 86 optimal weight: 0.0670 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 18 GLN ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 370 ASN H 209 GLN H 322 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.2404 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= 0.179 Angle : 0.566 15.032 19172 Z= 0.293 Chirality : 0.040 0.196 2092 Planarity : 0.005 0.061 2156 Dihedral : 18.430 172.050 2580 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.36 % Favored : 94.36 % Rotamer: Outliers : 1.85 % Allowed : 16.05 % Favored : 82.10 % 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: -0.28 (0.23), residues: 1436 helix: 1.38 (0.25), residues: 436 sheet: -0.44 (0.33), residues: 280 loop : -1.06 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 86 HIS 0.010 0.001 HIS F 59 PHE 0.036 0.001 PHE E 198 TYR 0.014 0.001 TYR G 225 ARG 0.003 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 134 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 110 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 287 MET cc_start: 0.7550 (mmm) cc_final: 0.7129 (mmm) REVERT: E 336 MET cc_start: 0.8195 (mtt) cc_final: 0.7972 (mtt) REVERT: F 1 MET cc_start: 0.7609 (tpp) cc_final: 0.7156 (tpp) REVERT: F 91 ILE cc_start: 0.7367 (OUTLIER) cc_final: 0.6738 (pt) REVERT: F 322 ASN cc_start: 0.7206 (t0) cc_final: 0.6756 (t0) REVERT: G 232 THR cc_start: 0.7175 (OUTLIER) cc_final: 0.6942 (m) REVERT: G 279 ASP cc_start: 0.7470 (t0) cc_final: 0.7213 (t70) REVERT: G 336 MET cc_start: 0.8255 (mtt) cc_final: 0.7995 (mtt) REVERT: G 371 ASN cc_start: 0.7343 (m-40) cc_final: 0.7083 (t0) REVERT: H 56 TYR cc_start: 0.7450 (t80) cc_final: 0.7187 (t80) outliers start: 24 outliers final: 16 residues processed: 129 average time/residue: 1.0069 time to fit residues: 146.3490 Evaluate side-chains 121 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 103 time to evaluate : 1.470 ------------------------------------------------------------------------------- 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 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 406 LEU Chi-restraints excluded: chain G residue 215 CYS Chi-restraints excluded: chain G residue 232 THR 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 132 GLU 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 67 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 149 optimal weight: 2.9990 chunk 137 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 72 optimal weight: 0.1980 chunk 94 optimal weight: 0.9990 chunk 126 optimal weight: 0.0670 chunk 36 optimal weight: 2.9990 overall best weight: 0.5520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 413 ASN ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 413 ASN H 209 GLN ** 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: 0.7409 moved from start: 0.2482 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= 0.176 Angle : 0.561 14.758 19172 Z= 0.290 Chirality : 0.040 0.147 2092 Planarity : 0.005 0.061 2156 Dihedral : 18.394 171.458 2580 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.29 % Favored : 94.43 % Rotamer: Outliers : 1.54 % Allowed : 16.67 % Favored : 81.79 % 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: 1.43 (0.25), residues: 438 sheet: -0.44 (0.33), residues: 280 loop : -1.05 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 86 HIS 0.010 0.001 HIS F 59 PHE 0.035 0.001 PHE E 198 TYR 0.013 0.001 TYR G 225 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 130 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 110 time to evaluate : 1.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 287 MET cc_start: 0.7557 (mmm) cc_final: 0.7137 (mmm) REVERT: E 336 MET cc_start: 0.8196 (mtt) cc_final: 0.7972 (mtt) REVERT: F 91 ILE cc_start: 0.7011 (OUTLIER) cc_final: 0.6360 (pt) REVERT: F 322 ASN cc_start: 0.7189 (t0) cc_final: 0.6758 (t0) REVERT: G 232 THR cc_start: 0.7035 (OUTLIER) cc_final: 0.6815 (m) REVERT: G 336 MET cc_start: 0.8258 (mtt) cc_final: 0.7997 (mtt) REVERT: G 371 ASN cc_start: 0.7289 (m-40) cc_final: 0.7019 (t0) REVERT: H 56 TYR cc_start: 0.7434 (t80) cc_final: 0.7155 (t80) outliers start: 20 outliers final: 14 residues processed: 125 average time/residue: 1.2260 time to fit residues: 172.2611 Evaluate side-chains 119 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 103 time to evaluate : 1.352 ------------------------------------------------------------------------------- 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 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 406 LEU Chi-restraints excluded: chain G residue 215 CYS Chi-restraints excluded: chain G residue 232 THR 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 113 ARG Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain H residue 274 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.3681 > 50: distance: 28 - 29: 7.184 distance: 29 - 30: 10.342 distance: 29 - 32: 8.558 distance: 30 - 31: 4.962 distance: 30 - 39: 18.334 distance: 32 - 33: 13.215 distance: 33 - 34: 14.504 distance: 34 - 35: 16.410 distance: 35 - 36: 10.106 distance: 36 - 37: 6.913 distance: 36 - 38: 6.173 distance: 39 - 40: 5.544 distance: 40 - 41: 3.522 distance: 40 - 43: 4.136 distance: 41 - 42: 6.462 distance: 41 - 50: 3.168 distance: 43 - 44: 4.472 distance: 44 - 45: 4.970 distance: 44 - 46: 4.593 distance: 45 - 47: 6.050 distance: 46 - 48: 5.622 distance: 47 - 49: 7.395 distance: 48 - 49: 5.800 distance: 50 - 51: 11.897 distance: 51 - 52: 11.501 distance: 51 - 54: 21.358 distance: 52 - 53: 20.274 distance: 52 - 58: 21.693 distance: 54 - 55: 19.290 distance: 55 - 56: 20.469 distance: 55 - 57: 10.264 distance: 58 - 59: 13.414 distance: 59 - 60: 6.570 distance: 59 - 62: 10.602 distance: 60 - 61: 25.992 distance: 60 - 65: 4.383 distance: 61 - 85: 58.712 distance: 62 - 63: 10.864 distance: 62 - 64: 17.827 distance: 65 - 66: 22.346 distance: 66 - 67: 12.210 distance: 66 - 69: 12.122 distance: 67 - 68: 25.425 distance: 67 - 76: 9.405 distance: 69 - 70: 14.307 distance: 70 - 71: 3.751 distance: 71 - 72: 7.030 distance: 72 - 73: 9.994 distance: 73 - 74: 4.439 distance: 73 - 75: 3.221 distance: 76 - 77: 13.965 distance: 77 - 78: 16.728 distance: 77 - 80: 18.856 distance: 78 - 79: 20.499 distance: 78 - 85: 20.057 distance: 80 - 81: 12.063 distance: 81 - 82: 6.506 distance: 82 - 83: 10.357 distance: 82 - 84: 30.897 distance: 85 - 86: 17.918 distance: 86 - 87: 10.688 distance: 86 - 89: 20.510 distance: 87 - 88: 9.332 distance: 87 - 93: 18.920 distance: 89 - 90: 22.239 distance: 90 - 91: 3.315 distance: 90 - 92: 7.448 distance: 93 - 94: 5.466 distance: 94 - 95: 18.584 distance: 94 - 97: 24.459 distance: 95 - 96: 25.205 distance: 95 - 100: 38.296 distance: 97 - 98: 5.189 distance: 100 - 101: 24.289 distance: 101 - 102: 7.729 distance: 101 - 104: 40.568 distance: 102 - 103: 19.618 distance: 102 - 111: 14.059 distance: 104 - 105: 8.775 distance: 105 - 106: 33.706 distance: 105 - 107: 14.227 distance: 106 - 108: 10.091 distance: 107 - 109: 34.433 distance: 108 - 110: 28.102 distance: 109 - 110: 33.903 distance: 111 - 112: 23.665 distance: 111 - 117: 17.265 distance: 112 - 113: 17.055 distance: 112 - 115: 10.723 distance: 113 - 114: 7.807 distance: 113 - 118: 27.566 distance: 115 - 116: 20.944 distance: 116 - 117: 17.145