Starting phenix.real_space_refine on Mon Mar 11 04:39:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2z_30973/03_2024/7e2z_30973_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2z_30973/03_2024/7e2z_30973.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2z_30973/03_2024/7e2z_30973_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2z_30973/03_2024/7e2z_30973_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2z_30973/03_2024/7e2z_30973_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2z_30973/03_2024/7e2z_30973.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2z_30973/03_2024/7e2z_30973.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2z_30973/03_2024/7e2z_30973_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2z_30973/03_2024/7e2z_30973_updated.pdb" } resolution = 3.1 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 53 5.16 5 Cl 2 4.86 5 C 4494 2.51 5 N 1172 2.21 5 O 1274 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 21": "NH1" <-> "NH2" Residue "A ARG 24": "NH1" <-> "NH2" Residue "A ARG 32": "NH1" <-> "NH2" Residue "A GLU 43": "OE1" <-> "OE2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A ARG 205": "NH1" <-> "NH2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 251": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "R ARG 65": "NH1" <-> "NH2" Residue "R ARG 134": "NH1" <-> "NH2" Residue "R ARG 148": "NH1" <-> "NH2" Residue "R ARG 339": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6997 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1766 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 216} Chain breaks: 2 Chain: "B" Number of atoms: 2516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2516 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 322} Chain: "G" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 347 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 4, 'TRANS': 40} Chain: "R" Number of atoms: 2368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2368 Unusual residues: {'9SC': 1, 'CLR': 3, 'J40': 1} Classifications: {'peptide': 278, 'undetermined': 5} Link IDs: {'PTRANS': 11, 'TRANS': 266, None: 5} Not linked: pdbres="ILE R 415 " pdbres="9SC R 501 " Not linked: pdbres="9SC R 501 " pdbres="CLR R 502 " Not linked: pdbres="CLR R 502 " pdbres="CLR R 503 " Not linked: pdbres="CLR R 503 " pdbres="CLR R 504 " Not linked: pdbres="CLR R 504 " pdbres="J40 R 505 " Chain breaks: 2 Time building chain proxies: 4.19, per 1000 atoms: 0.60 Number of scatterers: 6997 At special positions: 0 Unit cell: (77.064, 115.596, 112.554, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 2 17.00 S 53 16.00 P 2 15.00 O 1274 8.00 N 1172 7.00 C 4494 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS R 109 " - pdb=" SG CYS R 187 " distance=2.03 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: 2.79 Conformation dependent library (CDL) restraints added in 1.2 seconds 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1642 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 8 sheets defined 44.5% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.956A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 227 through 231 removed outlier: 4.229A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 308 removed outlier: 3.953A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 351 removed outlier: 3.667A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 24 Processing helix chain 'B' and resid 30 through 36 removed outlier: 3.704A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 22 No H-bonds generated for 'chain 'G' and resid 19 through 22' Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'R' and resid 36 through 63 Processing helix chain 'R' and resid 70 through 88 removed outlier: 3.726A pdb=" N LEU R 74 " --> pdb=" O VAL R 70 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE R 75 " --> pdb=" O ALA R 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 90 through 99 Processing helix chain 'R' and resid 106 through 139 removed outlier: 3.682A pdb=" N LEU R 127 " --> pdb=" O SER R 123 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS R 128 " --> pdb=" O ILE R 124 " (cutoff:3.500A) Processing helix chain 'R' and resid 141 through 146 Processing helix chain 'R' and resid 150 through 174 Proline residue: R 170 - end of helix Processing helix chain 'R' and resid 193 through 203 Processing helix chain 'R' and resid 205 through 227 Processing helix chain 'R' and resid 325 through 370 removed outlier: 3.660A pdb=" N PHE R 354 " --> pdb=" O ILE R 350 " (cutoff:3.500A) Proline residue: R 360 - end of helix Proline residue: R 369 - end of helix Processing helix chain 'R' and resid 372 through 374 No H-bonds generated for 'chain 'R' and resid 372 through 374' Processing helix chain 'R' and resid 379 through 400 removed outlier: 3.816A pdb=" N ASN R 392 " --> pdb=" O LEU R 388 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N SER R 393 " --> pdb=" O GLY R 389 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU R 394 " --> pdb=" O TYR R 390 " (cutoff:3.500A) Proline residue: R 397 - end of helix Processing helix chain 'R' and resid 405 through 414 Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.808A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.010A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.971A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 7.048A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.746A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 250 through 254 Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.637A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.544A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) 340 hydrogen bonds defined for protein. 999 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.16 Time building geometry restraints manager: 2.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1116 1.31 - 1.44: 1890 1.44 - 1.56: 4042 1.56 - 1.69: 18 1.69 - 1.82: 76 Bond restraints: 7142 Sorted by residual: bond pdb=" C19 9SC R 501 " pdb=" N3 9SC R 501 " ideal model delta sigma weight residual 1.395 1.650 -0.255 2.00e-02 2.50e+03 1.62e+02 bond pdb=" C18 J40 R 505 " pdb=" C19 J40 R 505 " ideal model delta sigma weight residual 1.333 1.528 -0.195 2.00e-02 2.50e+03 9.47e+01 bond pdb=" C19 9SC R 501 " pdb=" C20 9SC R 501 " ideal model delta sigma weight residual 1.386 1.578 -0.192 2.00e-02 2.50e+03 9.18e+01 bond pdb=" C21 J40 R 505 " pdb=" C22 J40 R 505 " ideal model delta sigma weight residual 1.340 1.527 -0.187 2.00e-02 2.50e+03 8.74e+01 bond pdb=" C24 J40 R 505 " pdb=" C25 J40 R 505 " ideal model delta sigma weight residual 1.341 1.528 -0.187 2.00e-02 2.50e+03 8.70e+01 ... (remaining 7137 not shown) Histogram of bond angle deviations from ideal: 100.13 - 106.90: 165 106.90 - 113.67: 4039 113.67 - 120.44: 2678 120.44 - 127.22: 2728 127.22 - 133.99: 72 Bond angle restraints: 9682 Sorted by residual: angle pdb=" C18 J40 R 505 " pdb=" C19 J40 R 505 " pdb=" C20 J40 R 505 " ideal model delta sigma weight residual 152.67 112.88 39.79 3.00e+00 1.11e-01 1.76e+02 angle pdb=" C15 J40 R 505 " pdb=" C16 J40 R 505 " pdb=" C17 J40 R 505 " ideal model delta sigma weight residual 152.66 112.99 39.67 3.00e+00 1.11e-01 1.75e+02 angle pdb=" C21 J40 R 505 " pdb=" C22 J40 R 505 " pdb=" C23 J40 R 505 " ideal model delta sigma weight residual 152.66 113.07 39.59 3.00e+00 1.11e-01 1.74e+02 angle pdb=" C24 J40 R 505 " pdb=" C25 J40 R 505 " pdb=" C26 J40 R 505 " ideal model delta sigma weight residual 152.63 113.29 39.34 3.00e+00 1.11e-01 1.72e+02 angle pdb=" C18 9SC R 501 " pdb=" C21 9SC R 501 " pdb=" C22 9SC R 501 " ideal model delta sigma weight residual 110.23 124.06 -13.83 3.00e+00 1.11e-01 2.12e+01 ... (remaining 9677 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.36: 4318 34.36 - 68.71: 70 68.71 - 103.07: 10 103.07 - 137.42: 1 137.42 - 171.78: 1 Dihedral angle restraints: 4400 sinusoidal: 1869 harmonic: 2531 Sorted by residual: dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 133.58 -40.58 1 1.00e+01 1.00e-02 2.31e+01 dihedral pdb=" C19 J40 R 505 " pdb=" C20 J40 R 505 " pdb=" C21 J40 R 505 " pdb=" C22 J40 R 505 " ideal model delta sinusoidal sigma weight residual 222.83 51.05 171.78 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C12 9SC R 501 " pdb=" C11 9SC R 501 " pdb=" N2 9SC R 501 " pdb=" C8 9SC R 501 " ideal model delta sinusoidal sigma weight residual -165.81 -45.98 -119.83 1 3.00e+01 1.11e-03 1.60e+01 ... (remaining 4397 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.009: 1114 1.009 - 2.018: 0 2.018 - 3.026: 0 3.026 - 4.035: 0 4.035 - 5.044: 2 Chirality restraints: 1116 Sorted by residual: chirality pdb=" C1 J40 R 505 " pdb=" C2 J40 R 505 " pdb=" C6 J40 R 505 " pdb=" O1 J40 R 505 " both_signs ideal model delta sigma weight residual False -2.51 2.53 -5.04 2.00e-01 2.50e+01 6.36e+02 chirality pdb=" C4 J40 R 505 " pdb=" C3 J40 R 505 " pdb=" C5 J40 R 505 " pdb=" O4 J40 R 505 " both_signs ideal model delta sigma weight residual False -2.50 2.52 -5.02 2.00e-01 2.50e+01 6.29e+02 chirality pdb=" C14 CLR R 503 " pdb=" C13 CLR R 503 " pdb=" C15 CLR R 503 " pdb=" C8 CLR R 503 " both_signs ideal model delta sigma weight residual False -2.32 -2.54 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1113 not shown) Planarity restraints: 1192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C20 J40 R 505 " 0.138 2.00e-02 2.50e+03 2.37e-01 5.63e+02 pdb=" C21 J40 R 505 " -0.306 2.00e-02 2.50e+03 pdb=" C22 J40 R 505 " 0.306 2.00e-02 2.50e+03 pdb=" C23 J40 R 505 " -0.138 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C23 J40 R 505 " -0.136 2.00e-02 2.50e+03 2.32e-01 5.39e+02 pdb=" C24 J40 R 505 " 0.299 2.00e-02 2.50e+03 pdb=" C25 J40 R 505 " -0.299 2.00e-02 2.50e+03 pdb=" C26 J40 R 505 " 0.136 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 J40 R 505 " -0.146 2.00e-02 2.50e+03 1.46e-01 2.14e+02 pdb=" C18 J40 R 505 " 0.146 2.00e-02 2.50e+03 pdb=" C19 J40 R 505 " 0.147 2.00e-02 2.50e+03 pdb=" C20 J40 R 505 " -0.146 2.00e-02 2.50e+03 ... (remaining 1189 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 157 2.71 - 3.26: 6803 3.26 - 3.80: 10915 3.80 - 4.35: 13759 4.35 - 4.90: 23570 Nonbonded interactions: 55204 Sorted by model distance: nonbonded pdb=" O PHE R 403 " pdb=" O2 J40 R 505 " model vdw 2.160 2.440 nonbonded pdb=" OD1 ASP A 251 " pdb=" ND2 ASN A 255 " model vdw 2.265 2.520 nonbonded pdb=" OG1 THR A 182 " pdb=" OD1 ASN B 119 " model vdw 2.308 2.440 nonbonded pdb=" OH TYR B 145 " pdb=" OD2 ASP B 186 " model vdw 2.314 2.440 nonbonded pdb=" NH1 ARG B 22 " pdb=" O ASP B 258 " model vdw 2.324 2.520 ... (remaining 55199 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.990 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 23.100 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 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 : 0.009 0.255 7142 Z= 0.617 Angle : 1.051 39.791 9682 Z= 0.422 Chirality : 0.217 5.044 1116 Planarity : 0.011 0.237 1192 Dihedral : 14.201 171.779 2752 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 2.35 (0.30), residues: 854 helix: 3.25 (0.27), residues: 384 sheet: 1.29 (0.41), residues: 154 loop : -0.52 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 211 HIS 0.001 0.000 HIS A 213 PHE 0.009 0.001 PHE R 48 TYR 0.018 0.001 TYR A 230 ARG 0.002 0.000 ARG R 333 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.806 Fit side-chains REVERT: A 14 GLU cc_start: 0.5509 (mm-30) cc_final: 0.5270 (mm-30) REVERT: A 21 ARG cc_start: 0.7531 (mtm-85) cc_final: 0.7080 (ttm110) REVERT: B 67 SER cc_start: 0.8260 (m) cc_final: 0.7901 (t) REVERT: B 161 SER cc_start: 0.8781 (t) cc_final: 0.8285 (m) REVERT: B 331 SER cc_start: 0.8426 (t) cc_final: 0.8147 (t) REVERT: R 387 TRP cc_start: 0.6930 (m100) cc_final: 0.6443 (m100) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.2382 time to fit residues: 34.0652 Evaluate side-chains 91 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 0.0870 chunk 49 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7142 Z= 0.144 Angle : 0.574 14.088 9682 Z= 0.260 Chirality : 0.050 0.827 1116 Planarity : 0.003 0.029 1192 Dihedral : 10.109 135.067 1181 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.94 % Allowed : 8.37 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 2.34 (0.30), residues: 854 helix: 3.26 (0.27), residues: 383 sheet: 1.17 (0.40), residues: 160 loop : -0.52 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.002 0.001 HIS A 322 PHE 0.010 0.001 PHE B 292 TYR 0.008 0.001 TYR R 195 ARG 0.002 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 100 time to evaluate : 0.802 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7571 (mtm-85) cc_final: 0.7122 (ttm110) REVERT: B 161 SER cc_start: 0.8861 (t) cc_final: 0.8353 (m) REVERT: B 322 ASP cc_start: 0.6886 (OUTLIER) cc_final: 0.6618 (m-30) outliers start: 7 outliers final: 4 residues processed: 103 average time/residue: 0.2240 time to fit residues: 29.9762 Evaluate side-chains 98 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 93 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain R residue 367 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 42 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 269 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7142 Z= 0.183 Angle : 0.534 9.665 9682 Z= 0.264 Chirality : 0.041 0.296 1116 Planarity : 0.003 0.035 1192 Dihedral : 9.885 131.812 1181 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.43 % Allowed : 9.72 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 2.06 (0.29), residues: 854 helix: 2.99 (0.27), residues: 384 sheet: 0.95 (0.40), residues: 166 loop : -0.58 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS A 244 PHE 0.012 0.001 PHE R 362 TYR 0.011 0.001 TYR R 195 ARG 0.004 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 102 time to evaluate : 0.812 Fit side-chains revert: symmetry clash REVERT: B 228 ASP cc_start: 0.6154 (OUTLIER) cc_final: 0.5731 (m-30) REVERT: B 254 ASP cc_start: 0.8047 (OUTLIER) cc_final: 0.7350 (p0) REVERT: B 322 ASP cc_start: 0.6898 (OUTLIER) cc_final: 0.6626 (m-30) REVERT: R 147 LYS cc_start: 0.8340 (mmtm) cc_final: 0.8064 (mmtt) REVERT: R 228 LYS cc_start: 0.7137 (OUTLIER) cc_final: 0.6527 (ptmm) outliers start: 18 outliers final: 5 residues processed: 112 average time/residue: 0.2049 time to fit residues: 30.4161 Evaluate side-chains 100 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 91 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 228 LYS Chi-restraints excluded: chain R residue 367 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 76 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 51 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 22 optimal weight: 0.3980 chunk 68 optimal weight: 0.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7142 Z= 0.163 Angle : 0.493 8.995 9682 Z= 0.246 Chirality : 0.039 0.140 1116 Planarity : 0.003 0.035 1192 Dihedral : 9.212 132.442 1181 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.29 % Allowed : 11.88 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.97 (0.29), residues: 854 helix: 2.90 (0.27), residues: 384 sheet: 0.96 (0.40), residues: 164 loop : -0.62 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.002 0.001 HIS A 322 PHE 0.010 0.001 PHE R 362 TYR 0.007 0.001 TYR R 195 ARG 0.003 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 93 time to evaluate : 0.805 Fit side-chains revert: symmetry clash REVERT: A 198 MET cc_start: 0.8547 (ttm) cc_final: 0.8253 (ttp) REVERT: B 234 PHE cc_start: 0.8604 (OUTLIER) cc_final: 0.8343 (m-80) REVERT: R 147 LYS cc_start: 0.8316 (mmtm) cc_final: 0.8037 (mmtt) REVERT: R 228 LYS cc_start: 0.7333 (OUTLIER) cc_final: 0.6731 (ptmm) outliers start: 17 outliers final: 8 residues processed: 103 average time/residue: 0.2214 time to fit residues: 30.0519 Evaluate side-chains 94 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 84 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 228 LYS Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 394 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 46 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 0 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7142 Z= 0.164 Angle : 0.484 9.093 9682 Z= 0.245 Chirality : 0.039 0.146 1116 Planarity : 0.003 0.036 1192 Dihedral : 9.226 132.302 1181 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.10 % Allowed : 12.15 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.91 (0.29), residues: 854 helix: 2.85 (0.27), residues: 387 sheet: 0.92 (0.39), residues: 164 loop : -0.68 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.002 0.001 HIS A 322 PHE 0.009 0.001 PHE B 292 TYR 0.008 0.001 TYR R 195 ARG 0.003 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 92 time to evaluate : 0.761 Fit side-chains revert: symmetry clash REVERT: A 198 MET cc_start: 0.8531 (ttm) cc_final: 0.8234 (ttp) REVERT: A 269 ASN cc_start: 0.8593 (m-40) cc_final: 0.8383 (m110) REVERT: B 58 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8345 (pt) REVERT: B 228 ASP cc_start: 0.6239 (OUTLIER) cc_final: 0.5805 (m-30) REVERT: B 234 PHE cc_start: 0.8629 (OUTLIER) cc_final: 0.8186 (m-80) REVERT: B 322 ASP cc_start: 0.6923 (OUTLIER) cc_final: 0.6635 (m-30) REVERT: G 46 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7696 (ptmt) REVERT: R 147 LYS cc_start: 0.8265 (mmtm) cc_final: 0.7977 (mmtt) outliers start: 23 outliers final: 12 residues processed: 107 average time/residue: 0.2111 time to fit residues: 29.8404 Evaluate side-chains 107 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 90 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 223 ARG Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 394 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 73 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 48 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7142 Z= 0.150 Angle : 0.484 8.858 9682 Z= 0.242 Chirality : 0.039 0.138 1116 Planarity : 0.003 0.035 1192 Dihedral : 9.034 131.381 1181 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.83 % Allowed : 13.36 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.85 (0.29), residues: 854 helix: 2.80 (0.27), residues: 393 sheet: 0.89 (0.39), residues: 164 loop : -0.80 (0.33), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.002 0.001 HIS B 266 PHE 0.008 0.001 PHE R 362 TYR 0.007 0.001 TYR R 195 ARG 0.003 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 93 time to evaluate : 0.816 Fit side-chains revert: symmetry clash REVERT: A 198 MET cc_start: 0.8529 (ttm) cc_final: 0.8226 (ttp) REVERT: B 58 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8300 (pt) REVERT: B 234 PHE cc_start: 0.8579 (OUTLIER) cc_final: 0.8152 (m-80) REVERT: B 254 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7301 (p0) REVERT: B 322 ASP cc_start: 0.6894 (OUTLIER) cc_final: 0.6619 (m-30) REVERT: G 46 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7709 (ptmt) REVERT: R 147 LYS cc_start: 0.8261 (mmtm) cc_final: 0.7973 (mmtt) outliers start: 21 outliers final: 14 residues processed: 109 average time/residue: 0.2124 time to fit residues: 30.4149 Evaluate side-chains 106 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 87 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 223 ARG Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 394 LEU Chi-restraints excluded: chain R residue 407 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 9 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 60 optimal weight: 0.0980 chunk 69 optimal weight: 2.9990 chunk 45 optimal weight: 0.0270 chunk 81 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.1642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7142 Z= 0.183 Angle : 0.510 9.341 9682 Z= 0.255 Chirality : 0.040 0.147 1116 Planarity : 0.003 0.035 1192 Dihedral : 9.026 132.061 1181 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.37 % Allowed : 14.30 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.80 (0.29), residues: 854 helix: 2.74 (0.27), residues: 393 sheet: 0.90 (0.40), residues: 164 loop : -0.83 (0.33), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS B 183 PHE 0.009 0.001 PHE A 274 TYR 0.009 0.001 TYR R 195 ARG 0.003 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 92 time to evaluate : 0.806 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7591 (mtm-85) cc_final: 0.7129 (ttm110) REVERT: A 198 MET cc_start: 0.8549 (ttm) cc_final: 0.8235 (ttp) REVERT: B 58 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8349 (pt) REVERT: B 234 PHE cc_start: 0.8588 (OUTLIER) cc_final: 0.7971 (m-80) REVERT: B 254 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7477 (p0) REVERT: B 322 ASP cc_start: 0.6868 (OUTLIER) cc_final: 0.6611 (m-30) REVERT: G 46 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7669 (ptmt) outliers start: 25 outliers final: 13 residues processed: 108 average time/residue: 0.2176 time to fit residues: 30.7314 Evaluate side-chains 109 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 91 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 394 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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: 56.4662 > 50: distance: 53 - 99: 27.873 distance: 73 - 155: 4.643 distance: 76 - 152: 15.520 distance: 90 - 138: 3.314 distance: 92 - 96: 9.093 distance: 96 - 97: 12.499 distance: 97 - 98: 22.280 distance: 98 - 99: 8.138 distance: 98 - 100: 31.775 distance: 100 - 101: 35.755 distance: 101 - 102: 9.780 distance: 101 - 104: 29.820 distance: 102 - 103: 5.664 distance: 102 - 105: 16.824 distance: 105 - 106: 5.969 distance: 106 - 107: 5.203 distance: 106 - 109: 10.390 distance: 107 - 108: 11.135 distance: 107 - 111: 10.481 distance: 109 - 110: 14.481 distance: 111 - 112: 9.522 distance: 112 - 113: 15.788 distance: 112 - 115: 20.409 distance: 113 - 114: 19.849 distance: 113 - 119: 19.729 distance: 115 - 116: 14.547 distance: 116 - 117: 13.703 distance: 116 - 118: 14.829 distance: 120 - 121: 9.099 distance: 120 - 123: 7.735 distance: 121 - 122: 18.501 distance: 124 - 125: 8.752 distance: 125 - 126: 10.678 distance: 125 - 128: 11.060 distance: 126 - 127: 14.212 distance: 126 - 130: 19.467 distance: 128 - 129: 9.008 distance: 130 - 209: 15.123 distance: 131 - 132: 12.454 distance: 131 - 134: 14.516 distance: 132 - 133: 7.607 distance: 132 - 135: 7.120 distance: 133 - 206: 7.758 distance: 135 - 136: 4.141 distance: 136 - 137: 3.276 distance: 136 - 139: 15.511 distance: 137 - 138: 3.364 distance: 137 - 144: 6.688 distance: 139 - 140: 19.565 distance: 140 - 141: 9.284 distance: 141 - 142: 15.366 distance: 142 - 143: 6.603 distance: 145 - 146: 9.256 distance: 145 - 148: 9.979 distance: 146 - 147: 10.737 distance: 146 - 152: 15.175 distance: 147 - 192: 13.279 distance: 148 - 149: 17.878 distance: 149 - 150: 8.232 distance: 149 - 151: 8.154 distance: 152 - 153: 6.467 distance: 153 - 154: 7.512 distance: 153 - 156: 7.117 distance: 154 - 155: 6.624 distance: 154 - 166: 5.404 distance: 156 - 157: 10.693 distance: 157 - 158: 4.948 distance: 158 - 160: 6.691 distance: 159 - 161: 7.748 distance: 159 - 162: 4.522 distance: 162 - 164: 3.142 distance: 163 - 165: 4.965 distance: 164 - 165: 3.394