Starting phenix.real_space_refine on Wed May 8 19:54:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c80_16467/05_2024/8c80_16467_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c80_16467/05_2024/8c80_16467.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c80_16467/05_2024/8c80_16467_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c80_16467/05_2024/8c80_16467_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c80_16467/05_2024/8c80_16467_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c80_16467/05_2024/8c80_16467.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c80_16467/05_2024/8c80_16467.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c80_16467/05_2024/8c80_16467_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c80_16467/05_2024/8c80_16467_updated.pdb" } resolution = 3.4 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= 0.019 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 55 5.16 5 C 7088 2.51 5 N 1795 2.21 5 O 2029 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 10968 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1502 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 10, 'TRANS': 173} Chain: "B" Number of atoms: 4214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4214 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 26, 'TRANS': 510} Chain: "C" Number of atoms: 4394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 4394 Classifications: {'peptide': 555} Link IDs: {'PTRANS': 29, 'TRANS': 525} Chain: "D" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 626 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "A" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 107 Unusual residues: {'ERG': 2, 'Z8A': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'ERG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'PLP': 1, 'Q7G': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 6.38, per 1000 atoms: 0.58 Number of scatterers: 10968 At special positions: 0 Unit cell: (90.552, 108.108, 126.588, 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 55 16.00 P 1 15.00 O 2029 8.00 N 1795 7.00 C 7088 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.11 Conformation dependent library (CDL) restraints added in 2.1 seconds 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2542 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 9 sheets defined 43.9% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.55 Creating SS restraints... Processing helix chain 'A' and resid 63 through 71 Processing helix chain 'A' and resid 87 through 102 Processing helix chain 'A' and resid 108 through 128 Processing helix chain 'A' and resid 138 through 140 No H-bonds generated for 'chain 'A' and resid 138 through 140' Processing helix chain 'A' and resid 159 through 178 Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 183 through 197 removed outlier: 4.539A pdb=" N PHE A 195 " --> pdb=" O PHE A 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 35 removed outlier: 3.703A pdb=" N TYR B 24 " --> pdb=" O THR B 21 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B 31 " --> pdb=" O TYR B 28 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR B 34 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 49 Processing helix chain 'B' and resid 54 through 72 removed outlier: 3.508A pdb=" N LEU B 63 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU B 65 " --> pdb=" O ILE B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 99 Processing helix chain 'B' and resid 116 through 119 No H-bonds generated for 'chain 'B' and resid 116 through 119' Processing helix chain 'B' and resid 162 through 175 Processing helix chain 'B' and resid 190 through 203 Processing helix chain 'B' and resid 214 through 216 No H-bonds generated for 'chain 'B' and resid 214 through 216' Processing helix chain 'B' and resid 218 through 225 Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 240 through 249 Processing helix chain 'B' and resid 261 through 278 Processing helix chain 'B' and resid 303 through 313 Processing helix chain 'B' and resid 335 through 338 No H-bonds generated for 'chain 'B' and resid 335 through 338' Processing helix chain 'B' and resid 343 through 346 No H-bonds generated for 'chain 'B' and resid 343 through 346' Processing helix chain 'B' and resid 369 through 378 removed outlier: 4.046A pdb=" N ILE B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 383 No H-bonds generated for 'chain 'B' and resid 380 through 383' Processing helix chain 'B' and resid 390 through 405 Processing helix chain 'B' and resid 408 through 425 Processing helix chain 'B' and resid 451 through 458 removed outlier: 3.725A pdb=" N SER B 455 " --> pdb=" O PRO B 451 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS B 457 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 475 Processing helix chain 'B' and resid 483 through 502 Processing helix chain 'B' and resid 514 through 516 No H-bonds generated for 'chain 'B' and resid 514 through 516' Processing helix chain 'B' and resid 535 through 554 removed outlier: 3.537A pdb=" N CYS B 552 " --> pdb=" O SER B 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 25 No H-bonds generated for 'chain 'C' and resid 22 through 25' Processing helix chain 'C' and resid 58 through 85 removed outlier: 3.559A pdb=" N VAL C 77 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP C 79 " --> pdb=" O GLY C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 106 through 108 No H-bonds generated for 'chain 'C' and resid 106 through 108' Processing helix chain 'C' and resid 116 through 121 removed outlier: 4.833A pdb=" N ASP C 120 " --> pdb=" O ARG C 117 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N CYS C 121 " --> pdb=" O ILE C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 185 removed outlier: 3.593A pdb=" N VAL C 183 " --> pdb=" O ALA C 179 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASP C 184 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS C 185 " --> pdb=" O GLU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 214 Processing helix chain 'C' and resid 225 through 230 Processing helix chain 'C' and resid 233 through 235 No H-bonds generated for 'chain 'C' and resid 233 through 235' Processing helix chain 'C' and resid 251 through 260 removed outlier: 3.567A pdb=" N GLY C 256 " --> pdb=" O SER C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 285 removed outlier: 3.734A pdb=" N VAL C 284 " --> pdb=" O ARG C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 323 removed outlier: 3.570A pdb=" N GLU C 319 " --> pdb=" O PRO C 315 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS C 322 " --> pdb=" O VAL C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 349 No H-bonds generated for 'chain 'C' and resid 346 through 349' Processing helix chain 'C' and resid 379 through 388 removed outlier: 3.857A pdb=" N LEU C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 394 No H-bonds generated for 'chain 'C' and resid 391 through 394' Processing helix chain 'C' and resid 400 through 409 Processing helix chain 'C' and resid 423 through 426 No H-bonds generated for 'chain 'C' and resid 423 through 426' Processing helix chain 'C' and resid 428 through 443 Processing helix chain 'C' and resid 463 through 475 Proline residue: C 467 - end of helix removed outlier: 3.923A pdb=" N MET C 473 " --> pdb=" O PHE C 469 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU C 474 " --> pdb=" O SER C 470 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN C 475 " --> pdb=" O ARG C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 487 No H-bonds generated for 'chain 'C' and resid 485 through 487' Processing helix chain 'C' and resid 505 through 522 Processing helix chain 'C' and resid 542 through 552 Proline residue: C 550 - end of helix Processing helix chain 'D' and resid 14 through 21 removed outlier: 3.993A pdb=" N LYS D 18 " --> pdb=" O THR D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 45 removed outlier: 4.151A pdb=" N GLU D 33 " --> pdb=" O ASN D 29 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL D 34 " --> pdb=" O THR D 30 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR D 41 " --> pdb=" O LYS D 37 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TYR D 42 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N TYR D 43 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N HIS D 45 " --> pdb=" O THR D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 75 removed outlier: 3.612A pdb=" N LEU D 75 " --> pdb=" O PHE D 71 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 55 through 57 Processing sheet with id= B, first strand: chain 'B' and resid 135 through 137 removed outlier: 3.544A pdb=" N GLU B 142 " --> pdb=" O ARG B 137 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 207 through 211 removed outlier: 3.587A pdb=" N GLY B 367 " --> pdb=" O GLY B 207 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 252 through 256 removed outlier: 3.537A pdb=" N ALA B 234 " --> pdb=" O TYR B 254 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N GLU B 291 " --> pdb=" O ASP B 235 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ARG B 316 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N THR B 290 " --> pdb=" O ARG B 316 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N PHE B 318 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE B 349 " --> pdb=" O VAL B 319 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 434 through 436 removed outlier: 3.558A pdb=" N ILE B 435 " --> pdb=" O GLN B 448 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 133 through 137 removed outlier: 3.523A pdb=" N CYS C 136 " --> pdb=" O TYR C 155 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR C 155 " --> pdb=" O CYS C 136 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 139 through 142 removed outlier: 4.093A pdb=" N TYR C 147 " --> pdb=" O HIS C 142 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 218 through 222 removed outlier: 3.536A pdb=" N ASP C 218 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY C 373 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE C 359 " --> pdb=" O LEU C 328 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU C 242 " --> pdb=" O LEU C 298 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N CYS C 300 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE C 244 " --> pdb=" O CYS C 300 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA C 263 " --> pdb=" O VAL C 243 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N SER C 245 " --> pdb=" O ALA C 263 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ARG C 265 " --> pdb=" O SER C 245 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 455 through 460 removed outlier: 3.587A pdb=" N SER C 493 " --> pdb=" O LEU C 460 " (cutoff:3.500A) 385 hydrogen bonds defined for protein. 1110 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: 2.84 Time building geometry restraints manager: 4.49 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: 2964 1.33 - 1.45: 2008 1.45 - 1.57: 6179 1.57 - 1.69: 4 1.69 - 1.81: 83 Bond restraints: 11238 Sorted by residual: bond pdb=" C19 Z8A A 302 " pdb=" N1 Z8A A 302 " ideal model delta sigma weight residual 1.492 1.369 0.123 2.00e-02 2.50e+03 3.78e+01 bond pdb=" N ILE D 27 " pdb=" CA ILE D 27 " ideal model delta sigma weight residual 1.459 1.503 -0.044 1.25e-02 6.40e+03 1.23e+01 bond pdb=" N ASN B 188 " pdb=" CA ASN B 188 " ideal model delta sigma weight residual 1.455 1.498 -0.044 1.27e-02 6.20e+03 1.18e+01 bond pdb=" N ASN A 144 " pdb=" CA ASN A 144 " ideal model delta sigma weight residual 1.458 1.489 -0.031 9.00e-03 1.23e+04 1.16e+01 bond pdb=" N GLN C 23 " pdb=" CA GLN C 23 " ideal model delta sigma weight residual 1.457 1.501 -0.044 1.32e-02 5.74e+03 1.13e+01 ... (remaining 11233 not shown) Histogram of bond angle deviations from ideal: 99.05 - 106.05: 335 106.05 - 113.04: 6156 113.04 - 120.03: 3954 120.03 - 127.02: 4705 127.02 - 134.02: 123 Bond angle restraints: 15273 Sorted by residual: angle pdb=" N LEU D 28 " pdb=" CA LEU D 28 " pdb=" C LEU D 28 " ideal model delta sigma weight residual 113.16 100.40 12.76 1.24e+00 6.50e-01 1.06e+02 angle pdb=" N THR A 194 " pdb=" CA THR A 194 " pdb=" C THR A 194 " ideal model delta sigma weight residual 110.97 120.01 -9.04 1.09e+00 8.42e-01 6.88e+01 angle pdb=" C ILE D 31 " pdb=" N GLU D 32 " pdb=" CA GLU D 32 " ideal model delta sigma weight residual 120.38 111.58 8.80 1.37e+00 5.33e-01 4.12e+01 angle pdb=" C THR D 30 " pdb=" N ILE D 31 " pdb=" CA ILE D 31 " ideal model delta sigma weight residual 122.66 116.60 6.06 9.70e-01 1.06e+00 3.90e+01 angle pdb=" N ILE D 31 " pdb=" CA ILE D 31 " pdb=" C ILE D 31 " ideal model delta sigma weight residual 111.90 107.04 4.86 8.10e-01 1.52e+00 3.60e+01 ... (remaining 15268 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.51: 6740 27.51 - 55.01: 232 55.01 - 82.52: 35 82.52 - 110.03: 14 110.03 - 137.53: 9 Dihedral angle restraints: 7030 sinusoidal: 3080 harmonic: 3950 Sorted by residual: dihedral pdb=" C5A PLP C 601 " pdb=" O4P PLP C 601 " pdb=" P PLP C 601 " pdb=" O1P PLP C 601 " ideal model delta sinusoidal sigma weight residual 76.43 174.49 -98.06 1 2.00e+01 2.50e-03 2.74e+01 dihedral pdb=" C2B Q7G C 602 " pdb=" C1B Q7G C 602 " pdb=" O5B Q7G C 602 " pdb=" C5B Q7G C 602 " ideal model delta sinusoidal sigma weight residual -63.14 74.39 -137.53 1 3.00e+01 1.11e-03 1.85e+01 dihedral pdb=" C5B Q7G C 602 " pdb=" C1B Q7G C 602 " pdb=" O5B Q7G C 602 " pdb=" O1B Q7G C 602 " ideal model delta sinusoidal sigma weight residual 301.16 167.13 134.03 1 3.00e+01 1.11e-03 1.81e+01 ... (remaining 7027 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1508 0.072 - 0.143: 203 0.143 - 0.215: 15 0.215 - 0.286: 13 0.286 - 0.358: 1 Chirality restraints: 1740 Sorted by residual: chirality pdb=" CA LEU D 28 " pdb=" N LEU D 28 " pdb=" C LEU D 28 " pdb=" CB LEU D 28 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" C51 Q7G C 602 " pdb=" C41 Q7G C 602 " pdb=" C61 Q7G C 602 " pdb=" O51 Q7G C 602 " both_signs ideal model delta sigma weight residual False -2.21 -2.49 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C5 Q7G C 602 " pdb=" C4 Q7G C 602 " pdb=" C6 Q7G C 602 " pdb=" O5 Q7G C 602 " both_signs ideal model delta sigma weight residual False -2.23 -2.50 0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 1737 not shown) Planarity restraints: 1904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C20 ERG A 301 " -0.097 2.00e-02 2.50e+03 9.78e-02 9.56e+01 pdb=" C22 ERG A 301 " 0.096 2.00e-02 2.50e+03 pdb=" C23 ERG A 301 " 0.099 2.00e-02 2.50e+03 pdb=" C24 ERG A 301 " -0.098 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 Q7G C 602 " 0.018 2.00e-02 2.50e+03 6.86e-02 5.88e+01 pdb=" C13 Q7G C 602 " 0.011 2.00e-02 2.50e+03 pdb=" C14 Q7G C 602 " 0.113 2.00e-02 2.50e+03 pdb=" C15 Q7G C 602 " -0.083 2.00e-02 2.50e+03 pdb=" C16 Q7G C 602 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C20 ERG A 303 " -0.052 2.00e-02 2.50e+03 5.20e-02 2.71e+01 pdb=" C22 ERG A 303 " 0.052 2.00e-02 2.50e+03 pdb=" C23 ERG A 303 " 0.052 2.00e-02 2.50e+03 pdb=" C24 ERG A 303 " -0.052 2.00e-02 2.50e+03 ... (remaining 1901 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 46 2.56 - 3.15: 8599 3.15 - 3.73: 15034 3.73 - 4.32: 20395 4.32 - 4.90: 35273 Nonbonded interactions: 79347 Sorted by model distance: nonbonded pdb=" CD1 PHE B 185 " pdb=" CD1 TYR B 186 " model vdw 1.975 3.640 nonbonded pdb=" CD1 PHE B 185 " pdb=" N TYR B 186 " model vdw 2.182 3.420 nonbonded pdb=" OH TYR B 460 " pdb=" OE1 GLU B 488 " model vdw 2.215 2.440 nonbonded pdb=" O ALA B 183 " pdb=" ND2 ASN B 188 " model vdw 2.262 2.520 nonbonded pdb=" O ASN A 74 " pdb=" OG1 THR A 78 " model vdw 2.273 2.440 ... (remaining 79342 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: 3.040 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: 16.920 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 31.830 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 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:2.810 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 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 : 0.006 0.123 11238 Z= 0.390 Angle : 0.841 12.756 15273 Z= 0.487 Chirality : 0.053 0.358 1740 Planarity : 0.006 0.098 1904 Dihedral : 15.396 137.534 4488 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.75 % Allowed : 5.02 % Favored : 94.23 % Cbeta Deviations : 0.08 % 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: -1.48 (0.20), residues: 1342 helix: -0.34 (0.19), residues: 595 sheet: 0.32 (0.51), residues: 113 loop : -1.86 (0.21), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 102 HIS 0.010 0.001 HIS A 206 PHE 0.013 0.001 PHE C 109 TYR 0.028 0.002 TYR B 186 ARG 0.004 0.001 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 233 time to evaluate : 1.222 Fit side-chains REVERT: A 82 GLN cc_start: 0.8846 (mm110) cc_final: 0.8629 (mm-40) REVERT: B 274 GLN cc_start: 0.8092 (tp-100) cc_final: 0.7826 (tp-100) REVERT: B 373 LEU cc_start: 0.9189 (tp) cc_final: 0.8924 (tt) REVERT: B 547 GLN cc_start: 0.7334 (tp40) cc_final: 0.7081 (tm-30) REVERT: C 23 GLN cc_start: 0.8608 (tp40) cc_final: 0.8380 (tp40) REVERT: D 7 SER cc_start: 0.8750 (t) cc_final: 0.8382 (p) outliers start: 9 outliers final: 2 residues processed: 240 average time/residue: 0.2623 time to fit residues: 86.2062 Evaluate side-chains 114 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 112 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 42 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 34 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A 180 HIS A 220 GLN B 50 HIS C 90 HIS C 142 HIS C 145 ASN C 229 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11238 Z= 0.264 Angle : 0.672 11.456 15273 Z= 0.331 Chirality : 0.046 0.247 1740 Planarity : 0.004 0.043 1904 Dihedral : 11.522 122.964 1913 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.76 % Allowed : 11.21 % Favored : 86.03 % 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: -0.35 (0.22), residues: 1342 helix: 0.98 (0.21), residues: 603 sheet: 0.81 (0.47), residues: 118 loop : -1.73 (0.22), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 110 HIS 0.008 0.001 HIS C 90 PHE 0.026 0.002 PHE C 106 TYR 0.024 0.002 TYR B 186 ARG 0.004 0.001 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 122 time to evaluate : 1.257 Fit side-chains REVERT: A 82 GLN cc_start: 0.8808 (mm110) cc_final: 0.8607 (mm-40) REVERT: B 274 GLN cc_start: 0.7992 (tp-100) cc_final: 0.7728 (tp-100) REVERT: C 292 ARG cc_start: 0.7551 (mtp85) cc_final: 0.7068 (mtp85) REVERT: D 7 SER cc_start: 0.8736 (t) cc_final: 0.8426 (p) REVERT: D 37 LYS cc_start: 0.7345 (tttm) cc_final: 0.6934 (tppt) outliers start: 33 outliers final: 23 residues processed: 146 average time/residue: 0.2677 time to fit residues: 54.9808 Evaluate side-chains 125 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 102 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 172 LYS Chi-restraints excluded: chain C residue 229 ASN Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 56 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 67 optimal weight: 0.0980 chunk 37 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 82 optimal weight: 0.0010 chunk 33 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 90 HIS C 291 ASN D 60 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11238 Z= 0.158 Angle : 0.556 8.666 15273 Z= 0.270 Chirality : 0.042 0.277 1740 Planarity : 0.004 0.041 1904 Dihedral : 9.931 116.749 1910 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.43 % Allowed : 12.80 % Favored : 84.77 % 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: 0.12 (0.23), residues: 1342 helix: 1.48 (0.22), residues: 606 sheet: 0.53 (0.47), residues: 132 loop : -1.56 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 188 HIS 0.008 0.001 HIS C 90 PHE 0.017 0.001 PHE D 62 TYR 0.016 0.001 TYR B 66 ARG 0.003 0.000 ARG C 9 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 114 time to evaluate : 1.291 Fit side-chains REVERT: A 82 GLN cc_start: 0.8756 (mm110) cc_final: 0.8544 (mm-40) REVERT: B 91 GLN cc_start: 0.8360 (mm110) cc_final: 0.7767 (mp10) REVERT: B 274 GLN cc_start: 0.8014 (tp-100) cc_final: 0.7726 (tp-100) REVERT: C 292 ARG cc_start: 0.7584 (mtp85) cc_final: 0.7097 (mtp85) REVERT: C 405 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7982 (tt0) REVERT: C 424 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7817 (tm-30) REVERT: D 7 SER cc_start: 0.8702 (t) cc_final: 0.8441 (p) outliers start: 29 outliers final: 20 residues processed: 135 average time/residue: 0.2170 time to fit residues: 43.2027 Evaluate side-chains 125 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 103 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 552 CYS Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 172 LYS Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 405 GLN Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 424 GLU Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 56 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 128 optimal weight: 9.9990 chunk 63 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 chunk 34 optimal weight: 0.0270 overall best weight: 1.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN B 258 HIS C 142 HIS C 379 GLN D 60 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 11238 Z= 0.252 Angle : 0.593 9.245 15273 Z= 0.298 Chirality : 0.044 0.216 1740 Planarity : 0.004 0.044 1904 Dihedral : 9.147 124.288 1910 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.43 % Allowed : 12.97 % Favored : 83.60 % 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: 0.09 (0.23), residues: 1342 helix: 1.62 (0.22), residues: 581 sheet: 0.39 (0.48), residues: 126 loop : -1.58 (0.22), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 188 HIS 0.004 0.001 HIS B 50 PHE 0.016 0.001 PHE B 318 TYR 0.019 0.001 TYR C 510 ARG 0.003 0.000 ARG C 9 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 116 time to evaluate : 1.269 Fit side-chains revert: symmetry clash REVERT: A 178 TYR cc_start: 0.6014 (t80) cc_final: 0.5750 (t80) REVERT: C 85 PHE cc_start: 0.7869 (m-10) cc_final: 0.7666 (m-10) REVERT: C 292 ARG cc_start: 0.7689 (mtp85) cc_final: 0.7205 (mtp85) REVERT: C 405 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.8071 (tt0) REVERT: C 424 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8243 (tt0) outliers start: 41 outliers final: 34 residues processed: 146 average time/residue: 0.2446 time to fit residues: 50.8856 Evaluate side-chains 146 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 110 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 172 LYS Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 405 GLN Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 424 GLU Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 56 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 109 optimal weight: 0.4980 chunk 88 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A 138 ASN C 23 GLN D 60 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11238 Z= 0.217 Angle : 0.547 9.301 15273 Z= 0.275 Chirality : 0.043 0.213 1740 Planarity : 0.004 0.042 1904 Dihedral : 8.956 123.706 1910 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.85 % Allowed : 13.72 % Favored : 82.43 % 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: 0.15 (0.23), residues: 1342 helix: 1.75 (0.22), residues: 576 sheet: 0.29 (0.48), residues: 126 loop : -1.57 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 188 HIS 0.005 0.001 HIS D 60 PHE 0.014 0.001 PHE C 329 TYR 0.017 0.001 TYR C 510 ARG 0.004 0.000 ARG C 43 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 109 time to evaluate : 1.368 Fit side-chains revert: symmetry clash REVERT: A 178 TYR cc_start: 0.6048 (t80) cc_final: 0.5756 (t80) REVERT: B 280 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8574 (tt) REVERT: C 292 ARG cc_start: 0.7690 (mtp85) cc_final: 0.7215 (mtp85) REVERT: C 405 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.8019 (tt0) REVERT: C 424 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8287 (tt0) outliers start: 46 outliers final: 32 residues processed: 142 average time/residue: 0.2361 time to fit residues: 48.6794 Evaluate side-chains 143 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 108 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 172 LYS Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 405 GLN Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 424 GLU Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 56 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 0.5980 chunk 115 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN D 60 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.5045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11238 Z= 0.195 Angle : 0.526 8.975 15273 Z= 0.264 Chirality : 0.042 0.207 1740 Planarity : 0.004 0.041 1904 Dihedral : 8.763 121.143 1910 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.18 % Allowed : 14.64 % Favored : 82.18 % 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: 0.27 (0.23), residues: 1342 helix: 1.92 (0.22), residues: 571 sheet: 0.29 (0.48), residues: 132 loop : -1.57 (0.22), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 110 HIS 0.004 0.001 HIS D 60 PHE 0.014 0.001 PHE C 329 TYR 0.017 0.001 TYR C 510 ARG 0.002 0.000 ARG C 9 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 111 time to evaluate : 1.370 Fit side-chains revert: symmetry clash REVERT: A 178 TYR cc_start: 0.6039 (t80) cc_final: 0.5731 (t80) REVERT: B 280 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8557 (tt) REVERT: B 424 PHE cc_start: 0.7393 (OUTLIER) cc_final: 0.6815 (t80) REVERT: C 292 ARG cc_start: 0.7600 (mtp85) cc_final: 0.7155 (mtp85) REVERT: D 5 LYS cc_start: 0.7661 (mmmt) cc_final: 0.7089 (mmtp) outliers start: 38 outliers final: 30 residues processed: 138 average time/residue: 0.2368 time to fit residues: 47.4210 Evaluate side-chains 138 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 106 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 172 LYS Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 56 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 128 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 405 GLN D 60 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.5230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11238 Z= 0.328 Angle : 0.622 9.773 15273 Z= 0.317 Chirality : 0.045 0.272 1740 Planarity : 0.004 0.042 1904 Dihedral : 8.975 120.530 1910 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.43 % Allowed : 14.81 % Favored : 81.76 % 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: -0.03 (0.23), residues: 1342 helix: 1.62 (0.22), residues: 578 sheet: 0.20 (0.45), residues: 133 loop : -1.73 (0.22), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 110 HIS 0.004 0.001 HIS D 60 PHE 0.031 0.002 PHE B 29 TYR 0.019 0.002 TYR C 510 ARG 0.002 0.000 ARG B 228 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 102 time to evaluate : 1.181 Fit side-chains REVERT: A 178 TYR cc_start: 0.6134 (t80) cc_final: 0.5784 (t80) REVERT: B 25 LEU cc_start: 0.6932 (mt) cc_final: 0.6642 (tp) REVERT: B 280 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8606 (tt) REVERT: B 424 PHE cc_start: 0.7803 (OUTLIER) cc_final: 0.7017 (t80) REVERT: C 117 ARG cc_start: 0.8235 (mmt90) cc_final: 0.7501 (mmm160) REVERT: C 146 GLU cc_start: 0.8540 (tp30) cc_final: 0.8245 (mt-10) REVERT: C 239 LYS cc_start: 0.8385 (ttmt) cc_final: 0.7944 (ttpp) REVERT: C 247 GLU cc_start: 0.7603 (pt0) cc_final: 0.7362 (pt0) REVERT: C 292 ARG cc_start: 0.7692 (mtp85) cc_final: 0.7175 (mtp85) REVERT: C 424 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8419 (tt0) REVERT: D 5 LYS cc_start: 0.7608 (mmmt) cc_final: 0.7065 (mmtp) outliers start: 41 outliers final: 31 residues processed: 134 average time/residue: 0.2284 time to fit residues: 44.3322 Evaluate side-chains 132 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 98 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 172 LYS Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 424 GLU Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 56 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 0.3980 chunk 51 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 192 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.5330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11238 Z= 0.175 Angle : 0.533 9.307 15273 Z= 0.267 Chirality : 0.042 0.285 1740 Planarity : 0.004 0.038 1904 Dihedral : 8.718 119.191 1910 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.85 % Allowed : 15.48 % Favored : 81.67 % 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: 0.18 (0.23), residues: 1342 helix: 1.88 (0.22), residues: 575 sheet: 0.05 (0.48), residues: 132 loop : -1.61 (0.22), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 110 HIS 0.003 0.001 HIS C 203 PHE 0.039 0.001 PHE B 29 TYR 0.017 0.001 TYR C 510 ARG 0.002 0.000 ARG C 9 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 102 time to evaluate : 1.316 Fit side-chains REVERT: A 178 TYR cc_start: 0.6097 (t80) cc_final: 0.5755 (t80) REVERT: B 25 LEU cc_start: 0.6956 (mt) cc_final: 0.6714 (tp) REVERT: B 280 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8584 (tt) REVERT: B 424 PHE cc_start: 0.7395 (OUTLIER) cc_final: 0.6826 (t80) REVERT: C 117 ARG cc_start: 0.8240 (mmt90) cc_final: 0.7557 (mmm-85) REVERT: C 146 GLU cc_start: 0.8518 (tp30) cc_final: 0.8261 (mt-10) REVERT: C 239 LYS cc_start: 0.8335 (ttmt) cc_final: 0.7879 (ttpp) REVERT: C 292 ARG cc_start: 0.7615 (mtp85) cc_final: 0.7145 (mtp85) REVERT: C 424 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8369 (tt0) REVERT: D 5 LYS cc_start: 0.7618 (mmmt) cc_final: 0.7064 (mmtp) outliers start: 34 outliers final: 27 residues processed: 129 average time/residue: 0.2362 time to fit residues: 44.3613 Evaluate side-chains 126 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 96 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 172 LYS Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 424 GLU Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 56 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 0.6980 chunk 122 optimal weight: 0.0970 chunk 112 optimal weight: 0.2980 chunk 119 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.5397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11238 Z= 0.186 Angle : 0.528 9.065 15273 Z= 0.264 Chirality : 0.042 0.279 1740 Planarity : 0.004 0.039 1904 Dihedral : 8.596 117.186 1910 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.76 % Allowed : 16.23 % Favored : 81.00 % 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: 0.21 (0.23), residues: 1342 helix: 1.86 (0.22), residues: 583 sheet: 0.13 (0.48), residues: 134 loop : -1.62 (0.22), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 110 HIS 0.005 0.001 HIS D 60 PHE 0.034 0.001 PHE B 29 TYR 0.017 0.001 TYR B 66 ARG 0.002 0.000 ARG C 9 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 99 time to evaluate : 1.353 Fit side-chains REVERT: A 178 TYR cc_start: 0.6120 (t80) cc_final: 0.5786 (t80) REVERT: B 25 LEU cc_start: 0.6918 (mt) cc_final: 0.6687 (tp) REVERT: B 280 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8584 (tt) REVERT: B 424 PHE cc_start: 0.7501 (OUTLIER) cc_final: 0.6936 (t80) REVERT: C 117 ARG cc_start: 0.8269 (mmt90) cc_final: 0.7613 (mmm-85) REVERT: C 146 GLU cc_start: 0.8508 (tp30) cc_final: 0.8221 (mt-10) REVERT: C 292 ARG cc_start: 0.7611 (mtp85) cc_final: 0.7136 (mtp85) REVERT: D 5 LYS cc_start: 0.7620 (mmmt) cc_final: 0.7097 (mmtp) outliers start: 33 outliers final: 24 residues processed: 125 average time/residue: 0.2245 time to fit residues: 40.5762 Evaluate side-chains 123 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 97 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 172 LYS Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 56 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 105 optimal weight: 0.4980 chunk 10 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 554 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.5451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11238 Z= 0.173 Angle : 0.522 8.938 15273 Z= 0.260 Chirality : 0.041 0.281 1740 Planarity : 0.004 0.038 1904 Dihedral : 8.474 115.494 1910 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.43 % Allowed : 16.40 % Favored : 81.17 % 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: 0.29 (0.23), residues: 1342 helix: 1.85 (0.22), residues: 595 sheet: 0.21 (0.49), residues: 134 loop : -1.56 (0.22), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 110 HIS 0.002 0.001 HIS C 514 PHE 0.031 0.001 PHE B 29 TYR 0.016 0.001 TYR B 66 ARG 0.002 0.000 ARG C 9 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 103 time to evaluate : 1.166 Fit side-chains REVERT: A 178 TYR cc_start: 0.6137 (t80) cc_final: 0.5796 (t80) REVERT: B 25 LEU cc_start: 0.6997 (mt) cc_final: 0.6766 (tp) REVERT: B 280 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8591 (tt) REVERT: B 424 PHE cc_start: 0.7375 (OUTLIER) cc_final: 0.6836 (t80) REVERT: C 117 ARG cc_start: 0.8281 (mmt90) cc_final: 0.7678 (mmm-85) REVERT: C 146 GLU cc_start: 0.8476 (tp30) cc_final: 0.8170 (mt-10) REVERT: C 292 ARG cc_start: 0.7571 (mtp85) cc_final: 0.7106 (mtp85) REVERT: C 473 MET cc_start: 0.8501 (mmm) cc_final: 0.8022 (mmt) REVERT: D 5 LYS cc_start: 0.7632 (mmmt) cc_final: 0.7093 (mmtp) outliers start: 29 outliers final: 25 residues processed: 126 average time/residue: 0.2340 time to fit residues: 43.1248 Evaluate side-chains 128 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 101 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 172 LYS Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 291 ASN Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 56 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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-5322/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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-5322/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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-5322/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-5322/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-5322/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-5322/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-5322/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-5322/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-5322/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-5322/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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-5322/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-5322/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-5322/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-5322/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: 53.2006 > 50: distance: 24 - 136: 10.636 distance: 35 - 139: 20.364 distance: 43 - 63: 20.347 distance: 59 - 63: 20.550 distance: 63 - 64: 12.056 distance: 64 - 65: 13.523 distance: 64 - 67: 14.927 distance: 65 - 66: 22.503 distance: 65 - 72: 20.575 distance: 67 - 68: 19.111 distance: 68 - 69: 4.667 distance: 69 - 70: 11.197 distance: 72 - 73: 11.671 distance: 73 - 74: 13.387 distance: 73 - 76: 3.666 distance: 74 - 75: 25.372 distance: 74 - 81: 9.362 distance: 76 - 77: 14.399 distance: 77 - 78: 9.218 distance: 78 - 79: 17.337 distance: 79 - 80: 5.344 distance: 81 - 82: 12.032 distance: 82 - 83: 16.575 distance: 82 - 85: 26.190 distance: 83 - 84: 16.345 distance: 85 - 86: 19.575 distance: 86 - 87: 7.051 distance: 86 - 88: 3.355 distance: 89 - 90: 11.369 distance: 89 - 95: 7.417 distance: 90 - 91: 8.564 distance: 90 - 93: 9.020 distance: 91 - 92: 15.906 distance: 91 - 96: 11.847 distance: 93 - 94: 13.363 distance: 94 - 95: 12.222 distance: 96 - 97: 8.808 distance: 97 - 98: 13.069 distance: 97 - 100: 22.473 distance: 98 - 99: 11.212 distance: 98 - 101: 7.069 distance: 101 - 102: 11.848 distance: 102 - 103: 22.087 distance: 102 - 105: 6.957 distance: 103 - 104: 13.980 distance: 103 - 109: 35.537 distance: 105 - 106: 14.826 distance: 105 - 107: 28.959 distance: 106 - 108: 9.005 distance: 109 - 110: 8.474 distance: 109 - 115: 20.767 distance: 110 - 111: 21.653 distance: 110 - 113: 19.484 distance: 111 - 112: 16.072 distance: 111 - 116: 14.543 distance: 113 - 114: 11.744 distance: 114 - 115: 15.957 distance: 116 - 117: 7.915 distance: 117 - 118: 17.244 distance: 117 - 120: 16.647 distance: 118 - 119: 18.972 distance: 118 - 127: 7.132 distance: 120 - 121: 4.800 distance: 121 - 122: 22.852 distance: 122 - 123: 24.389 distance: 123 - 124: 11.714 distance: 124 - 125: 12.308 distance: 124 - 126: 13.257 distance: 127 - 128: 5.277 distance: 128 - 129: 5.281 distance: 128 - 131: 16.489 distance: 129 - 130: 11.148 distance: 129 - 136: 3.933 distance: 131 - 132: 22.777 distance: 132 - 133: 4.871 distance: 133 - 134: 16.725 distance: 134 - 135: 10.367 distance: 137 - 138: 11.051 distance: 137 - 140: 6.597 distance: 138 - 139: 20.464 distance: 138 - 147: 6.741 distance: 140 - 141: 3.574 distance: 141 - 142: 9.719 distance: 141 - 143: 9.815 distance: 142 - 144: 5.284 distance: 143 - 145: 8.875 distance: 144 - 146: 4.276 distance: 145 - 146: 8.617