Starting phenix.real_space_refine on Sat Aug 23 02:00:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qsk_18634/08_2025/8qsk_18634.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qsk_18634/08_2025/8qsk_18634.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qsk_18634/08_2025/8qsk_18634.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qsk_18634/08_2025/8qsk_18634.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qsk_18634/08_2025/8qsk_18634.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qsk_18634/08_2025/8qsk_18634.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.016 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 2 5.49 5 S 48 5.16 5 C 5702 2.51 5 N 1310 2.21 5 O 1444 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8506 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3978 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 23, 'TRANS': 499} Chain breaks: 1 Chain: "C" Number of atoms: 3978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3978 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 23, 'TRANS': 499} Chain breaks: 1 Chain: "A" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 275 Unusual residues: {'NAG': 1, 'PGT': 1, 'Y01': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 275 Unusual residues: {'NAG': 1, 'PGT': 1, 'Y01': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.30, per 1000 atoms: 0.27 Number of scatterers: 8506 At special positions: 0 Unit cell: (126.445, 76.285, 87.78, 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 48 16.00 P 2 15.00 O 1444 8.00 N 1310 7.00 C 5702 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS C 68 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 153 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 603 " - " ASN A 140 " " NAG C 604 " - " ASN C 140 " Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 325.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1916 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 2 sheets defined 81.6% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 16 through 28 removed outlier: 3.541A pdb=" N ALA A 20 " --> pdb=" O GLY A 16 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 57 removed outlier: 3.639A pdb=" N CYS A 37 " --> pdb=" O ARG A 33 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ASN A 57 " --> pdb=" O GLY A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 65 Processing helix chain 'A' and resid 70 through 98 removed outlier: 3.943A pdb=" N SER A 89 " --> pdb=" O THR A 85 " (cutoff:3.500A) Proline residue: A 90 - end of helix Processing helix chain 'A' and resid 101 through 118 Processing helix chain 'A' and resid 118 through 125 removed outlier: 3.846A pdb=" N LEU A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 132 Processing helix chain 'A' and resid 153 through 183 removed outlier: 4.480A pdb=" N THR A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) Proline residue: A 177 - end of helix removed outlier: 3.660A pdb=" N VAL A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 220 removed outlier: 3.531A pdb=" N THR A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 248 removed outlier: 3.686A pdb=" N ALA A 227 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ILE A 228 " --> pdb=" O THR A 224 " (cutoff:3.500A) Proline residue: A 229 - end of helix removed outlier: 4.155A pdb=" N SER A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL A 246 " --> pdb=" O CYS A 242 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE A 248 " --> pdb=" O GLN A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 273 removed outlier: 3.681A pdb=" N MET A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN A 271 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 305 removed outlier: 4.236A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 348 Proline residue: A 323 - end of helix Proline residue: A 330 - end of helix removed outlier: 3.874A pdb=" N VAL A 343 " --> pdb=" O GLN A 339 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A 344 " --> pdb=" O THR A 340 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N HIS A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 356 Processing helix chain 'A' and resid 367 through 395 removed outlier: 4.525A pdb=" N ASP A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA A 374 " --> pdb=" O THR A 370 " (cutoff:3.500A) Proline residue: A 382 - end of helix removed outlier: 4.612A pdb=" N ASP A 389 " --> pdb=" O ASP A 385 " (cutoff:3.500A) Proline residue: A 390 - end of helix removed outlier: 4.114A pdb=" N HIS A 395 " --> pdb=" O ILE A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 430 removed outlier: 3.912A pdb=" N ARG A 404 " --> pdb=" O SER A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 453 removed outlier: 3.512A pdb=" N TRP A 453 " --> pdb=" O SER A 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 450 through 453' Processing helix chain 'A' and resid 454 through 479 removed outlier: 3.516A pdb=" N TYR A 458 " --> pdb=" O GLN A 454 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ILE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA A 471 " --> pdb=" O PHE A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 511 Processing helix chain 'A' and resid 526 through 530 Processing helix chain 'A' and resid 531 through 560 removed outlier: 4.009A pdb=" N TYR A 535 " --> pdb=" O TYR A 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 28 removed outlier: 3.670A pdb=" N ALA C 24 " --> pdb=" O ALA C 20 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 57 removed outlier: 3.649A pdb=" N CYS C 37 " --> pdb=" O ARG C 33 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ASN C 57 " --> pdb=" O GLY C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 65 Processing helix chain 'C' and resid 70 through 98 removed outlier: 3.930A pdb=" N SER C 89 " --> pdb=" O THR C 85 " (cutoff:3.500A) Proline residue: C 90 - end of helix Processing helix chain 'C' and resid 101 through 118 Processing helix chain 'C' and resid 118 through 125 removed outlier: 3.869A pdb=" N LEU C 122 " --> pdb=" O LEU C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 132 Processing helix chain 'C' and resid 153 through 183 removed outlier: 4.510A pdb=" N THR C 176 " --> pdb=" O LYS C 172 " (cutoff:3.500A) Proline residue: C 177 - end of helix removed outlier: 3.701A pdb=" N VAL C 183 " --> pdb=" O GLY C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 220 removed outlier: 3.517A pdb=" N THR C 191 " --> pdb=" O GLY C 187 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA C 214 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 248 removed outlier: 3.697A pdb=" N ALA C 227 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE C 228 " --> pdb=" O THR C 224 " (cutoff:3.500A) Proline residue: C 229 - end of helix removed outlier: 4.153A pdb=" N SER C 245 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N VAL C 246 " --> pdb=" O CYS C 242 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ILE C 248 " --> pdb=" O GLN C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 273 removed outlier: 3.892A pdb=" N MET C 260 " --> pdb=" O ALA C 256 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE C 261 " --> pdb=" O PHE C 257 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS C 262 " --> pdb=" O THR C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 303 Processing helix chain 'C' and resid 308 through 348 Proline residue: C 323 - end of helix Proline residue: C 330 - end of helix removed outlier: 3.848A pdb=" N VAL C 343 " --> pdb=" O GLN C 339 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU C 344 " --> pdb=" O THR C 340 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N HIS C 348 " --> pdb=" O LEU C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 356 Processing helix chain 'C' and resid 367 through 395 removed outlier: 4.512A pdb=" N ASP C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA C 374 " --> pdb=" O THR C 370 " (cutoff:3.500A) Proline residue: C 382 - end of helix removed outlier: 4.615A pdb=" N ASP C 389 " --> pdb=" O ASP C 385 " (cutoff:3.500A) Proline residue: C 390 - end of helix removed outlier: 4.112A pdb=" N HIS C 395 " --> pdb=" O ILE C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 430 removed outlier: 3.947A pdb=" N ARG C 404 " --> pdb=" O SER C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 453 removed outlier: 3.518A pdb=" N TRP C 453 " --> pdb=" O SER C 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 450 through 453' Processing helix chain 'C' and resid 454 through 479 removed outlier: 3.503A pdb=" N TYR C 458 " --> pdb=" O GLN C 454 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ILE C 470 " --> pdb=" O ILE C 466 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA C 471 " --> pdb=" O PHE C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 511 Processing helix chain 'C' and resid 526 through 530 Processing helix chain 'C' and resid 532 through 560 Processing sheet with id=AA1, first strand: chain 'A' and resid 435 through 436 Processing sheet with id=AA2, first strand: chain 'C' and resid 435 through 436 592 hydrogen bonds defined for protein. 1746 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: 1.37 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1253 1.32 - 1.44: 2341 1.44 - 1.56: 5074 1.56 - 1.69: 4 1.69 - 1.81: 70 Bond restraints: 8742 Sorted by residual: bond pdb=" N HIS C 303 " pdb=" CA HIS C 303 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.29e-02 6.01e+03 7.51e+00 bond pdb=" N THR C 308 " pdb=" CA THR C 308 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.31e-02 5.83e+03 6.90e+00 bond pdb=" N THR A 308 " pdb=" CA THR A 308 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.31e-02 5.83e+03 6.88e+00 bond pdb=" N ILE A 421 " pdb=" CA ILE A 421 " ideal model delta sigma weight residual 1.461 1.492 -0.030 1.17e-02 7.31e+03 6.75e+00 bond pdb=" N ILE C 421 " pdb=" CA ILE C 421 " ideal model delta sigma weight residual 1.461 1.492 -0.030 1.17e-02 7.31e+03 6.75e+00 ... (remaining 8737 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 11427 1.35 - 2.70: 376 2.70 - 4.05: 94 4.05 - 5.41: 31 5.41 - 6.76: 4 Bond angle restraints: 11932 Sorted by residual: angle pdb=" N LEU C 429 " pdb=" CA LEU C 429 " pdb=" C LEU C 429 " ideal model delta sigma weight residual 113.18 108.36 4.82 1.21e+00 6.83e-01 1.59e+01 angle pdb=" N LEU A 429 " pdb=" CA LEU A 429 " pdb=" C LEU A 429 " ideal model delta sigma weight residual 113.18 108.42 4.76 1.21e+00 6.83e-01 1.55e+01 angle pdb=" N ASN A 428 " pdb=" CA ASN A 428 " pdb=" C ASN A 428 " ideal model delta sigma weight residual 113.88 109.04 4.84 1.23e+00 6.61e-01 1.55e+01 angle pdb=" N ASN C 428 " pdb=" CA ASN C 428 " pdb=" C ASN C 428 " ideal model delta sigma weight residual 113.88 109.07 4.81 1.23e+00 6.61e-01 1.53e+01 angle pdb=" CA GLY A 305 " pdb=" C GLY A 305 " pdb=" O GLY A 305 " ideal model delta sigma weight residual 122.46 118.70 3.76 9.70e-01 1.06e+00 1.50e+01 ... (remaining 11927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.88: 5593 31.88 - 63.76: 136 63.76 - 95.65: 3 95.65 - 127.53: 0 127.53 - 159.41: 2 Dihedral angle restraints: 5734 sinusoidal: 2742 harmonic: 2992 Sorted by residual: dihedral pdb=" C3 PGT A 607 " pdb=" C1 PGT A 607 " pdb=" C2 PGT A 607 " pdb=" O3P PGT A 607 " ideal model delta sinusoidal sigma weight residual -66.13 93.28 -159.41 1 3.00e+01 1.11e-03 2.07e+01 dihedral pdb=" C3 PGT C 608 " pdb=" C1 PGT C 608 " pdb=" C2 PGT C 608 " pdb=" O3P PGT C 608 " ideal model delta sinusoidal sigma weight residual -66.13 92.55 -158.68 1 3.00e+01 1.11e-03 2.06e+01 dihedral pdb=" CA LEU C 397 " pdb=" C LEU C 397 " pdb=" N LEU C 398 " pdb=" CA LEU C 398 " ideal model delta harmonic sigma weight residual -180.00 -161.36 -18.64 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 5731 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1042 0.037 - 0.073: 245 0.073 - 0.109: 86 0.109 - 0.146: 13 0.146 - 0.182: 12 Chirality restraints: 1398 Sorted by residual: chirality pdb=" CB VAL A 430 " pdb=" CA VAL A 430 " pdb=" CG1 VAL A 430 " pdb=" CG2 VAL A 430 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.33e-01 chirality pdb=" CA ILE C 421 " pdb=" N ILE C 421 " pdb=" C ILE C 421 " pdb=" CB ILE C 421 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.09e-01 chirality pdb=" CB VAL C 430 " pdb=" CA VAL C 430 " pdb=" CG1 VAL C 430 " pdb=" CG2 VAL C 430 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.75e-01 ... (remaining 1395 not shown) Planarity restraints: 1412 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 426 " -0.401 9.50e-02 1.11e+02 1.80e-01 1.99e+01 pdb=" NE ARG C 426 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG C 426 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG C 426 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 426 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 426 " 0.344 9.50e-02 1.11e+02 1.54e-01 1.47e+01 pdb=" NE ARG A 426 " -0.022 2.00e-02 2.50e+03 pdb=" CZ ARG A 426 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 426 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 426 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 462 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.61e+00 pdb=" C GLY C 462 " -0.028 2.00e-02 2.50e+03 pdb=" O GLY C 462 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE C 463 " 0.009 2.00e-02 2.50e+03 ... (remaining 1409 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1490 2.77 - 3.30: 9050 3.30 - 3.83: 14177 3.83 - 4.37: 16095 4.37 - 4.90: 27384 Nonbonded interactions: 68196 Sorted by model distance: nonbonded pdb=" O LEU A 264 " pdb=" OG SER A 267 " model vdw 2.235 3.040 nonbonded pdb=" O LEU A 122 " pdb=" OG1 THR A 128 " model vdw 2.254 3.040 nonbonded pdb=" O LEU C 122 " pdb=" OG1 THR C 128 " model vdw 2.257 3.040 nonbonded pdb=" O ILE A 461 " pdb=" OG SER A 464 " model vdw 2.261 3.040 nonbonded pdb=" O LYS A 262 " pdb=" OG1 THR A 265 " model vdw 2.265 3.040 ... (remaining 68191 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 16 through 602 or resid 605 through 606)) selection = (chain 'C' and (resid 16 through 602 or resid 605 through 606)) } 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: 0.870 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.860 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 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:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8748 Z= 0.209 Angle : 0.631 6.757 11946 Z= 0.368 Chirality : 0.040 0.182 1398 Planarity : 0.008 0.180 1410 Dihedral : 12.956 159.410 3806 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.94 % Favored : 92.87 % Rotamer: Outliers : 1.59 % Allowed : 8.90 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.28), residues: 1038 helix: 2.22 (0.19), residues: 766 sheet: None (None), residues: 0 loop : -2.00 (0.42), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 426 TYR 0.008 0.001 TYR A 458 PHE 0.010 0.001 PHE A 67 TRP 0.005 0.001 TRP A 197 HIS 0.001 0.000 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 8742) covalent geometry : angle 0.62998 (11932) SS BOND : bond 0.00055 ( 4) SS BOND : angle 0.33645 ( 8) hydrogen bonds : bond 0.10809 ( 592) hydrogen bonds : angle 5.09535 ( 1746) link_NAG-ASN : bond 0.00362 ( 2) link_NAG-ASN : angle 2.06753 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 221 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ILE cc_start: 0.8484 (mm) cc_final: 0.7688 (mm) REVERT: A 185 ASP cc_start: 0.8443 (m-30) cc_final: 0.8090 (m-30) REVERT: A 343 VAL cc_start: 0.8969 (t) cc_final: 0.8755 (m) REVERT: C 269 CYS cc_start: 0.9218 (m) cc_final: 0.8959 (t) outliers start: 13 outliers final: 6 residues processed: 229 average time/residue: 0.0825 time to fit residues: 27.2246 Evaluate side-chains 108 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 102 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 247 PHE Chi-restraints excluded: chain C residue 395 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.0970 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.0470 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 GLN ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.129326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.105072 restraints weight = 18596.704| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 3.28 r_work: 0.3515 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 8748 Z= 0.144 Angle : 0.669 14.969 11946 Z= 0.319 Chirality : 0.041 0.182 1398 Planarity : 0.005 0.033 1410 Dihedral : 11.150 153.704 2118 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 4.88 % Allowed : 14.27 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.97 (0.28), residues: 1038 helix: 2.32 (0.19), residues: 774 sheet: None (None), residues: 0 loop : -1.96 (0.44), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 19 TYR 0.009 0.001 TYR A 534 PHE 0.021 0.001 PHE C 198 TRP 0.010 0.001 TRP A 69 HIS 0.003 0.001 HIS A 521 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 8742) covalent geometry : angle 0.66705 (11932) SS BOND : bond 0.00084 ( 4) SS BOND : angle 0.43597 ( 8) hydrogen bonds : bond 0.04186 ( 592) hydrogen bonds : angle 4.08639 ( 1746) link_NAG-ASN : bond 0.00168 ( 2) link_NAG-ASN : angle 2.46780 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 109 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8418 (mm) REVERT: A 266 TYR cc_start: 0.8968 (m-80) cc_final: 0.8642 (m-80) REVERT: A 343 VAL cc_start: 0.8971 (t) cc_final: 0.8741 (m) REVERT: A 546 THR cc_start: 0.8964 (m) cc_final: 0.8758 (p) REVERT: C 33 ARG cc_start: 0.7200 (OUTLIER) cc_final: 0.6796 (ptp90) REVERT: C 91 PHE cc_start: 0.7605 (m-10) cc_final: 0.7394 (m-10) REVERT: C 208 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8450 (mm) REVERT: C 266 TYR cc_start: 0.8957 (m-80) cc_final: 0.8749 (m-80) REVERT: C 269 CYS cc_start: 0.9142 (m) cc_final: 0.8928 (t) REVERT: C 307 PHE cc_start: 0.8358 (m-80) cc_final: 0.7958 (m-10) outliers start: 40 outliers final: 19 residues processed: 134 average time/residue: 0.0712 time to fit residues: 14.6998 Evaluate side-chains 109 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 554 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 28 optimal weight: 0.3980 chunk 5 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 88 optimal weight: 0.3980 chunk 18 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.125947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.101604 restraints weight = 18382.249| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 3.24 r_work: 0.3465 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8748 Z= 0.129 Angle : 0.602 6.787 11946 Z= 0.292 Chirality : 0.039 0.172 1398 Planarity : 0.004 0.032 1410 Dihedral : 10.812 151.123 2110 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 4.15 % Allowed : 16.46 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.96 (0.28), residues: 1038 helix: 2.25 (0.18), residues: 780 sheet: None (None), residues: 0 loop : -1.83 (0.46), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 186 TYR 0.010 0.001 TYR A 266 PHE 0.014 0.001 PHE A 198 TRP 0.007 0.001 TRP A 200 HIS 0.002 0.000 HIS A 445 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 8742) covalent geometry : angle 0.60047 (11932) SS BOND : bond 0.00048 ( 4) SS BOND : angle 0.21386 ( 8) hydrogen bonds : bond 0.03869 ( 592) hydrogen bonds : angle 3.94601 ( 1746) link_NAG-ASN : bond 0.00248 ( 2) link_NAG-ASN : angle 2.34833 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 87 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 PHE cc_start: 0.7835 (m-10) cc_final: 0.7567 (m-10) REVERT: A 185 ASP cc_start: 0.8452 (m-30) cc_final: 0.8082 (t70) REVERT: A 208 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8421 (mm) REVERT: A 266 TYR cc_start: 0.8959 (m-80) cc_final: 0.8519 (m-80) REVERT: A 307 PHE cc_start: 0.8446 (m-80) cc_final: 0.7883 (m-10) REVERT: C 91 PHE cc_start: 0.7733 (m-10) cc_final: 0.7472 (m-10) REVERT: C 208 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8394 (mm) REVERT: C 266 TYR cc_start: 0.8900 (m-80) cc_final: 0.8559 (m-80) REVERT: C 269 CYS cc_start: 0.9218 (m) cc_final: 0.8913 (t) outliers start: 34 outliers final: 18 residues processed: 112 average time/residue: 0.0636 time to fit residues: 11.5109 Evaluate side-chains 93 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 554 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 31 optimal weight: 0.0370 chunk 84 optimal weight: 0.0370 chunk 39 optimal weight: 0.0470 chunk 94 optimal weight: 0.5980 chunk 102 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 ASN ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.126088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.101182 restraints weight = 18875.889| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 3.31 r_work: 0.3454 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8748 Z= 0.110 Angle : 0.574 7.498 11946 Z= 0.275 Chirality : 0.038 0.156 1398 Planarity : 0.004 0.034 1410 Dihedral : 10.618 149.628 2110 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 4.27 % Allowed : 17.93 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.01 (0.28), residues: 1038 helix: 2.28 (0.18), residues: 772 sheet: None (None), residues: 0 loop : -1.66 (0.46), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 186 TYR 0.007 0.001 TYR A 113 PHE 0.013 0.001 PHE C 198 TRP 0.003 0.001 TRP C 94 HIS 0.001 0.000 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 8742) covalent geometry : angle 0.57171 (11932) SS BOND : bond 0.00004 ( 4) SS BOND : angle 0.15296 ( 8) hydrogen bonds : bond 0.03610 ( 592) hydrogen bonds : angle 3.88324 ( 1746) link_NAG-ASN : bond 0.00269 ( 2) link_NAG-ASN : angle 2.26173 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 80 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 PHE cc_start: 0.7783 (m-10) cc_final: 0.7434 (m-10) REVERT: A 185 ASP cc_start: 0.8412 (m-30) cc_final: 0.8200 (t70) REVERT: A 208 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8412 (mm) REVERT: A 263 ILE cc_start: 0.9520 (mt) cc_final: 0.9175 (mt) REVERT: A 266 TYR cc_start: 0.8860 (m-10) cc_final: 0.8453 (m-80) REVERT: A 307 PHE cc_start: 0.8500 (m-80) cc_final: 0.7810 (m-10) REVERT: C 91 PHE cc_start: 0.7760 (m-10) cc_final: 0.7476 (m-10) REVERT: C 208 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8410 (mm) REVERT: C 266 TYR cc_start: 0.8897 (m-10) cc_final: 0.8504 (m-80) REVERT: C 307 PHE cc_start: 0.8218 (m-80) cc_final: 0.7909 (m-10) outliers start: 35 outliers final: 26 residues processed: 107 average time/residue: 0.0591 time to fit residues: 10.4155 Evaluate side-chains 104 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 76 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 395 HIS Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 554 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 40 optimal weight: 0.0040 chunk 76 optimal weight: 0.1980 chunk 43 optimal weight: 2.9990 chunk 65 optimal weight: 20.0000 chunk 4 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 53 optimal weight: 0.0970 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.124366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.099897 restraints weight = 18578.661| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 3.25 r_work: 0.3436 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8748 Z= 0.108 Angle : 0.558 9.081 11946 Z= 0.267 Chirality : 0.037 0.160 1398 Planarity : 0.004 0.033 1410 Dihedral : 10.424 148.125 2110 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 4.15 % Allowed : 18.66 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.11 (0.28), residues: 1038 helix: 2.32 (0.18), residues: 772 sheet: None (None), residues: 0 loop : -1.53 (0.46), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 186 TYR 0.006 0.001 TYR C 52 PHE 0.012 0.001 PHE C 198 TRP 0.004 0.001 TRP C 452 HIS 0.001 0.000 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 8742) covalent geometry : angle 0.55664 (11932) SS BOND : bond 0.00026 ( 4) SS BOND : angle 0.15743 ( 8) hydrogen bonds : bond 0.03479 ( 592) hydrogen bonds : angle 3.81607 ( 1746) link_NAG-ASN : bond 0.00289 ( 2) link_NAG-ASN : angle 2.11663 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 86 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 PHE cc_start: 0.7753 (m-10) cc_final: 0.7364 (m-10) REVERT: A 208 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8473 (mm) REVERT: A 266 TYR cc_start: 0.8970 (m-10) cc_final: 0.8504 (m-80) REVERT: A 307 PHE cc_start: 0.8470 (m-80) cc_final: 0.7909 (m-10) REVERT: C 208 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8445 (mm) REVERT: C 266 TYR cc_start: 0.8797 (m-10) cc_final: 0.8482 (m-80) REVERT: C 307 PHE cc_start: 0.8266 (m-80) cc_final: 0.7703 (m-10) outliers start: 34 outliers final: 29 residues processed: 111 average time/residue: 0.0719 time to fit residues: 12.4565 Evaluate side-chains 111 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 80 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 395 HIS Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 554 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 18 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 80 optimal weight: 0.0010 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 GLN ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 521 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.121756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.097015 restraints weight = 18572.566| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 3.20 r_work: 0.3394 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8748 Z= 0.117 Angle : 0.568 8.516 11946 Z= 0.269 Chirality : 0.037 0.150 1398 Planarity : 0.004 0.036 1410 Dihedral : 10.236 146.889 2110 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 4.51 % Allowed : 19.76 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.06 (0.28), residues: 1038 helix: 2.31 (0.18), residues: 774 sheet: None (None), residues: 0 loop : -1.64 (0.45), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 186 TYR 0.007 0.001 TYR C 52 PHE 0.012 0.001 PHE A 198 TRP 0.004 0.001 TRP C 452 HIS 0.001 0.000 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 8742) covalent geometry : angle 0.56609 (11932) SS BOND : bond 0.00013 ( 4) SS BOND : angle 0.17899 ( 8) hydrogen bonds : bond 0.03594 ( 592) hydrogen bonds : angle 3.79293 ( 1746) link_NAG-ASN : bond 0.00299 ( 2) link_NAG-ASN : angle 2.02157 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 80 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 91 PHE cc_start: 0.7837 (m-10) cc_final: 0.7588 (m-10) REVERT: A 208 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8477 (mm) REVERT: A 266 TYR cc_start: 0.9052 (m-10) cc_final: 0.8541 (m-80) REVERT: A 307 PHE cc_start: 0.8450 (m-80) cc_final: 0.7891 (m-10) REVERT: A 428 ASN cc_start: 0.8718 (OUTLIER) cc_final: 0.8479 (t0) REVERT: C 208 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8500 (mm) REVERT: C 266 TYR cc_start: 0.8832 (m-10) cc_final: 0.8477 (m-80) REVERT: C 307 PHE cc_start: 0.8244 (m-80) cc_final: 0.7653 (m-10) outliers start: 37 outliers final: 31 residues processed: 109 average time/residue: 0.0527 time to fit residues: 9.3450 Evaluate side-chains 109 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 75 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 395 HIS Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 554 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 101 optimal weight: 0.0070 chunk 58 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 88 optimal weight: 0.1980 chunk 46 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 GLN ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.120844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.096330 restraints weight = 18686.813| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 3.20 r_work: 0.3380 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8748 Z= 0.114 Angle : 0.569 8.168 11946 Z= 0.272 Chirality : 0.037 0.166 1398 Planarity : 0.004 0.038 1410 Dihedral : 10.006 145.837 2108 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 4.39 % Allowed : 20.37 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.12 (0.28), residues: 1038 helix: 2.31 (0.18), residues: 776 sheet: None (None), residues: 0 loop : -1.51 (0.45), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 186 TYR 0.007 0.001 TYR C 52 PHE 0.012 0.001 PHE C 198 TRP 0.005 0.001 TRP A 453 HIS 0.001 0.000 HIS A 445 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 8742) covalent geometry : angle 0.56819 (11932) SS BOND : bond 0.00025 ( 4) SS BOND : angle 0.15684 ( 8) hydrogen bonds : bond 0.03566 ( 592) hydrogen bonds : angle 3.81812 ( 1746) link_NAG-ASN : bond 0.00484 ( 2) link_NAG-ASN : angle 1.78350 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 86 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 91 PHE cc_start: 0.7970 (m-10) cc_final: 0.7743 (m-10) REVERT: A 208 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8500 (mm) REVERT: A 266 TYR cc_start: 0.9005 (m-10) cc_final: 0.8526 (m-80) REVERT: A 307 PHE cc_start: 0.8409 (m-80) cc_final: 0.7858 (m-10) REVERT: C 208 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8488 (mm) REVERT: C 266 TYR cc_start: 0.8905 (m-10) cc_final: 0.8528 (m-80) REVERT: C 307 PHE cc_start: 0.8266 (m-80) cc_final: 0.7664 (m-10) outliers start: 36 outliers final: 31 residues processed: 112 average time/residue: 0.0587 time to fit residues: 10.5118 Evaluate side-chains 113 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 80 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 395 HIS Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 554 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.8109 > 50: distance: 47 - 67: 3.722 distance: 51 - 55: 7.462 distance: 52 - 74: 9.837 distance: 55 - 56: 12.240 distance: 55 - 61: 8.688 distance: 56 - 57: 11.377 distance: 56 - 59: 8.806 distance: 57 - 58: 21.575 distance: 57 - 62: 25.227 distance: 58 - 85: 7.502 distance: 59 - 60: 13.116 distance: 60 - 61: 17.724 distance: 62 - 63: 22.488 distance: 63 - 64: 24.473 distance: 63 - 66: 20.418 distance: 64 - 65: 7.268 distance: 64 - 67: 16.074 distance: 65 - 90: 30.244 distance: 67 - 68: 4.225 distance: 68 - 69: 7.104 distance: 68 - 71: 6.505 distance: 69 - 70: 10.725 distance: 69 - 74: 7.874 distance: 71 - 72: 18.117 distance: 71 - 73: 17.388 distance: 74 - 75: 3.166 distance: 75 - 76: 10.714 distance: 75 - 78: 5.988 distance: 76 - 77: 10.187 distance: 76 - 85: 7.227 distance: 77 - 102: 23.612 distance: 78 - 79: 10.203 distance: 79 - 80: 12.824 distance: 79 - 81: 3.408 distance: 80 - 82: 15.769 distance: 81 - 83: 11.249 distance: 82 - 84: 9.449 distance: 83 - 84: 6.270 distance: 85 - 86: 9.681 distance: 86 - 87: 17.011 distance: 86 - 89: 15.028 distance: 87 - 88: 5.552 distance: 87 - 90: 11.647 distance: 88 - 109: 4.468 distance: 90 - 91: 19.593 distance: 91 - 92: 16.895 distance: 92 - 93: 22.290 distance: 92 - 94: 9.239 distance: 93 - 117: 22.320 distance: 94 - 95: 9.887 distance: 95 - 96: 7.166 distance: 96 - 97: 23.740 distance: 96 - 102: 6.751 distance: 97 - 124: 29.368 distance: 98 - 99: 6.085 distance: 99 - 100: 10.979 distance: 99 - 101: 8.986 distance: 102 - 103: 4.204 distance: 103 - 104: 4.301 distance: 103 - 106: 6.114 distance: 104 - 105: 15.452 distance: 104 - 109: 7.017 distance: 105 - 128: 12.803 distance: 106 - 107: 9.092 distance: 106 - 108: 10.806 distance: 109 - 110: 7.401 distance: 110 - 111: 4.894 distance: 110 - 113: 3.097 distance: 111 - 112: 6.047 distance: 111 - 117: 3.638 distance: 112 - 136: 7.218 distance: 113 - 114: 10.121 distance: 114 - 115: 12.864 distance: 114 - 116: 24.693 distance: 117 - 118: 5.803 distance: 118 - 119: 8.825 distance: 118 - 121: 8.821 distance: 119 - 120: 7.349 distance: 119 - 124: 5.732 distance: 120 - 140: 7.629 distance: 121 - 122: 9.497 distance: 121 - 123: 8.999