Starting phenix.real_space_refine on Thu Mar 13 17:21:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qsk_18634/03_2025/8qsk_18634.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qsk_18634/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8qsk_18634/03_2025/8qsk_18634.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qsk_18634/03_2025/8qsk_18634.map" model { file = "/net/cci-nas-00/data/ceres_data/8qsk_18634/03_2025/8qsk_18634.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qsk_18634/03_2025/8qsk_18634.cif" } resolution = 3.3 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= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.70, per 1000 atoms: 0.67 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: 2.72 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.79 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: 2.34 Time building geometry restraints manager: 3.12 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: 0.04 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 16 through 560 or resid 601 through 602 or resid 605 throu \ gh 606)) selection = (chain 'C' and (resid 16 through 560 or resid 601 through 602 or resid 605 throu \ gh 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: 0.810 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.520 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.040 ------------------------------------------------------------------------------- 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 8742 Z= 0.210 Angle : 0.630 6.757 11932 Z= 0.367 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 (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: 1.79 (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 TRP 0.005 0.001 TRP A 197 HIS 0.001 0.000 HIS A 348 PHE 0.010 0.001 PHE A 67 TYR 0.008 0.001 TYR A 458 ARG 0.005 0.000 ARG A 426 *********************** 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 : 0.817 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: 0.2052 time to fit residues: 67.7803 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 : 0.996 ------------------------------------------------------------------------------- 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 87 optimal weight: 3.9990 chunk 78 optimal weight: 0.1980 chunk 43 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- 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 ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.126252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.101926 restraints weight = 18536.588| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 3.23 r_work: 0.3460 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 8742 Z= 0.247 Angle : 0.685 14.769 11932 Z= 0.329 Chirality : 0.042 0.193 1398 Planarity : 0.005 0.035 1410 Dihedral : 11.156 153.786 2118 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 5.24 % Allowed : 13.54 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.28), residues: 1038 helix: 2.26 (0.19), residues: 776 sheet: None (None), residues: 0 loop : -2.13 (0.43), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 69 HIS 0.002 0.001 HIS C 445 PHE 0.021 0.001 PHE C 198 TYR 0.013 0.001 TYR A 266 ARG 0.003 0.000 ARG A 426 *********************** 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 142 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 99 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8395 (mm) REVERT: A 266 TYR cc_start: 0.9019 (m-80) cc_final: 0.8673 (m-80) REVERT: A 343 VAL cc_start: 0.8998 (t) cc_final: 0.8746 (m) REVERT: C 33 ARG cc_start: 0.7196 (OUTLIER) cc_final: 0.6749 (ptp90) REVERT: C 91 PHE cc_start: 0.7702 (m-10) cc_final: 0.7489 (m-10) REVERT: C 208 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8419 (mm) REVERT: C 266 TYR cc_start: 0.8993 (m-80) cc_final: 0.8722 (m-80) REVERT: C 269 CYS cc_start: 0.9208 (m) cc_final: 0.8985 (t) REVERT: C 307 PHE cc_start: 0.8360 (m-80) cc_final: 0.7977 (m-10) outliers start: 43 outliers final: 22 residues processed: 128 average time/residue: 0.1570 time to fit residues: 30.5172 Evaluate side-chains 104 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU 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 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 33 ARG Chi-restraints excluded: chain C residue 110 LEU 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 47 optimal weight: 0.0770 chunk 26 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 34 optimal weight: 0.3980 chunk 92 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 1 optimal weight: 0.0570 chunk 13 optimal weight: 8.9990 chunk 7 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 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 = 0.3988 r_free = 0.3988 target = 0.125604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.101180 restraints weight = 18562.945| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 3.24 r_work: 0.3452 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8742 Z= 0.171 Angle : 0.599 9.071 11932 Z= 0.289 Chirality : 0.038 0.171 1398 Planarity : 0.004 0.036 1410 Dihedral : 10.877 151.786 2110 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 4.27 % Allowed : 16.22 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.89 (0.28), residues: 1038 helix: 2.22 (0.18), residues: 782 sheet: None (None), residues: 0 loop : -1.97 (0.45), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 200 HIS 0.001 0.000 HIS A 348 PHE 0.015 0.001 PHE A 198 TYR 0.007 0.001 TYR C 52 ARG 0.002 0.000 ARG A 426 *********************** 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 125 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 90 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8387 (mm) REVERT: A 266 TYR cc_start: 0.8955 (m-80) cc_final: 0.8443 (m-80) REVERT: A 307 PHE cc_start: 0.8402 (m-80) cc_final: 0.8056 (m-10) REVERT: A 343 VAL cc_start: 0.9070 (t) cc_final: 0.8786 (m) REVERT: C 33 ARG cc_start: 0.7191 (OUTLIER) cc_final: 0.6933 (ptp90) REVERT: C 91 PHE cc_start: 0.7754 (m-10) cc_final: 0.7508 (m-10) REVERT: C 208 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8382 (mm) REVERT: C 266 TYR cc_start: 0.8885 (m-80) cc_final: 0.8510 (m-80) REVERT: C 269 CYS cc_start: 0.9209 (m) cc_final: 0.8900 (t) outliers start: 35 outliers final: 23 residues processed: 116 average time/residue: 0.1477 time to fit residues: 26.4442 Evaluate side-chains 108 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 82 time to evaluate : 0.883 ------------------------------------------------------------------------------- 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 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 443 VAL Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 158 PHE 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 443 VAL 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 43 optimal weight: 2.9990 chunk 13 optimal weight: 20.0000 chunk 33 optimal weight: 4.9990 chunk 23 optimal weight: 0.0370 chunk 30 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 chunk 52 optimal weight: 60.0000 chunk 24 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 overall best weight: 0.8460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 ASN ** 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 = 0.3938 r_free = 0.3938 target = 0.122051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.097304 restraints weight = 18664.237| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 3.23 r_work: 0.3391 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8742 Z= 0.189 Angle : 0.592 7.784 11932 Z= 0.285 Chirality : 0.038 0.161 1398 Planarity : 0.004 0.036 1410 Dihedral : 10.673 150.353 2110 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 4.76 % Allowed : 16.71 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.28), residues: 1038 helix: 2.22 (0.18), residues: 774 sheet: None (None), residues: 0 loop : -1.86 (0.44), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 200 HIS 0.001 0.000 HIS C 395 PHE 0.014 0.001 PHE C 198 TYR 0.008 0.001 TYR C 52 ARG 0.004 0.000 ARG C 186 *********************** 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 120 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 81 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 PHE cc_start: 0.7957 (m-10) cc_final: 0.7710 (m-10) REVERT: A 185 ASP cc_start: 0.8478 (m-30) cc_final: 0.8150 (t70) REVERT: A 208 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8501 (mm) REVERT: A 258 THR cc_start: 0.8008 (OUTLIER) cc_final: 0.7802 (t) REVERT: A 266 TYR cc_start: 0.8890 (m-10) cc_final: 0.8425 (m-80) REVERT: A 307 PHE cc_start: 0.8546 (m-80) cc_final: 0.7685 (m-10) REVERT: C 208 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8515 (mm) REVERT: C 266 TYR cc_start: 0.8926 (m-10) cc_final: 0.8546 (m-80) REVERT: C 307 PHE cc_start: 0.8306 (m-80) cc_final: 0.8011 (m-10) outliers start: 39 outliers final: 31 residues processed: 113 average time/residue: 0.1396 time to fit residues: 24.8490 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 : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 158 PHE 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 258 THR 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 140 ASN Chi-restraints excluded: chain C residue 158 PHE 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 84 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 52 optimal weight: 50.0000 chunk 74 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 521 HIS C 543 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.114041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.089490 restraints weight = 18827.823| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 3.15 r_work: 0.3257 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8742 Z= 0.251 Angle : 0.635 5.781 11932 Z= 0.311 Chirality : 0.041 0.201 1398 Planarity : 0.004 0.038 1410 Dihedral : 10.533 149.505 2110 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 5.37 % Allowed : 18.54 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.27), residues: 1038 helix: 1.99 (0.18), residues: 774 sheet: -1.85 (1.00), residues: 20 loop : -1.66 (0.47), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 368 HIS 0.002 0.001 HIS C 445 PHE 0.016 0.002 PHE A 67 TYR 0.015 0.002 TYR C 52 ARG 0.004 0.000 ARG C 186 *********************** 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 127 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 83 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: A 208 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8583 (mm) REVERT: A 266 TYR cc_start: 0.9068 (m-10) cc_final: 0.8564 (m-80) REVERT: A 307 PHE cc_start: 0.8469 (m-80) cc_final: 0.7884 (m-10) REVERT: C 208 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8600 (mm) REVERT: C 266 TYR cc_start: 0.8910 (m-10) cc_final: 0.8464 (m-80) REVERT: C 307 PHE cc_start: 0.8336 (m-80) cc_final: 0.7708 (m-10) outliers start: 44 outliers final: 29 residues processed: 117 average time/residue: 0.1467 time to fit residues: 26.6045 Evaluate side-chains 101 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 70 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 112 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 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 357 ILE Chi-restraints excluded: chain A residue 370 THR 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 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 231 VAL 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 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 32 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 28 optimal weight: 0.0980 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 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 = 0.3825 r_free = 0.3825 target = 0.113763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.089150 restraints weight = 18586.495| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 3.08 r_work: 0.3255 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8742 Z= 0.228 Angle : 0.611 7.684 11932 Z= 0.293 Chirality : 0.039 0.176 1398 Planarity : 0.004 0.034 1410 Dihedral : 10.318 148.986 2108 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 4.02 % Allowed : 20.12 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.27), residues: 1038 helix: 2.01 (0.18), residues: 778 sheet: -0.97 (1.07), residues: 20 loop : -1.63 (0.47), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 368 HIS 0.001 0.000 HIS A 395 PHE 0.013 0.001 PHE A 67 TYR 0.010 0.001 TYR C 444 ARG 0.004 0.000 ARG C 186 *********************** 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 110 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 77 time to evaluate : 0.910 Fit side-chains REVERT: A 208 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8545 (mm) REVERT: A 266 TYR cc_start: 0.9105 (m-10) cc_final: 0.8604 (m-80) REVERT: A 307 PHE cc_start: 0.8413 (m-80) cc_final: 0.7812 (m-10) REVERT: A 318 LEU cc_start: 0.8880 (mp) cc_final: 0.8601 (mp) REVERT: C 208 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8616 (mm) REVERT: C 266 TYR cc_start: 0.8979 (m-10) cc_final: 0.8572 (m-80) REVERT: C 307 PHE cc_start: 0.8387 (m-80) cc_final: 0.7754 (m-10) REVERT: C 318 LEU cc_start: 0.8927 (mp) cc_final: 0.8640 (mp) outliers start: 33 outliers final: 25 residues processed: 109 average time/residue: 0.1336 time to fit residues: 23.4239 Evaluate side-chains 100 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 73 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 112 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 298 SER Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 370 THR 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 298 SER Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 370 THR 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 36 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 52 optimal weight: 50.0000 chunk 83 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 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 = 0.3819 r_free = 0.3819 target = 0.113779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.089537 restraints weight = 18690.758| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 3.09 r_work: 0.3257 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.4961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8742 Z= 0.190 Angle : 0.601 7.537 11932 Z= 0.285 Chirality : 0.038 0.169 1398 Planarity : 0.004 0.036 1410 Dihedral : 10.077 147.971 2106 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 4.15 % Allowed : 21.10 % Favored : 74.76 % 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: 1.83 (0.28), residues: 1038 helix: 2.07 (0.18), residues: 776 sheet: -0.53 (1.13), residues: 20 loop : -1.58 (0.47), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 452 HIS 0.001 0.000 HIS A 395 PHE 0.012 0.001 PHE A 67 TYR 0.007 0.001 TYR C 52 ARG 0.004 0.000 ARG C 186 *********************** 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 111 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 77 time to evaluate : 0.934 Fit side-chains REVERT: A 208 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8538 (mm) REVERT: A 266 TYR cc_start: 0.9083 (m-10) cc_final: 0.8606 (m-80) REVERT: A 307 PHE cc_start: 0.8369 (m-80) cc_final: 0.7760 (m-10) REVERT: A 318 LEU cc_start: 0.8926 (mp) cc_final: 0.8648 (mp) REVERT: C 208 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8599 (mm) REVERT: C 266 TYR cc_start: 0.9017 (m-10) cc_final: 0.8600 (m-80) REVERT: C 307 PHE cc_start: 0.8330 (m-80) cc_final: 0.7643 (m-10) REVERT: C 318 LEU cc_start: 0.8940 (mp) cc_final: 0.8655 (mp) REVERT: C 339 GLN cc_start: 0.8752 (tt0) cc_final: 0.8483 (mt0) outliers start: 34 outliers final: 26 residues processed: 109 average time/residue: 0.1357 time to fit residues: 23.7510 Evaluate side-chains 101 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 73 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 112 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 370 THR Chi-restraints excluded: chain A residue 383 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 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 298 SER Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 370 THR 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 ************** Weight determination summary: number of chunks: 104 random chunks: chunk 0 optimal weight: 50.0000 chunk 71 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 25 optimal weight: 9.9990 chunk 95 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 92 optimal weight: 0.0470 chunk 100 optimal weight: 4.9990 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 485 GLN ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 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 = 0.3834 r_free = 0.3834 target = 0.114613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.090312 restraints weight = 18765.833| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 3.12 r_work: 0.3263 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.5100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8742 Z= 0.164 Angle : 0.591 7.534 11932 Z= 0.279 Chirality : 0.038 0.187 1398 Planarity : 0.004 0.035 1410 Dihedral : 9.920 146.781 2106 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 4.02 % Allowed : 21.10 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.28), residues: 1038 helix: 2.10 (0.18), residues: 784 sheet: -0.29 (1.14), residues: 20 loop : -1.44 (0.48), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 452 HIS 0.001 0.000 HIS A 521 PHE 0.011 0.001 PHE C 198 TYR 0.006 0.001 TYR A 113 ARG 0.003 0.000 ARG C 186 *********************** REFINEMENT MACRO_CYCLE 8 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 111 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 78 time to evaluate : 0.837 Fit side-chains REVERT: A 208 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8502 (mm) REVERT: A 266 TYR cc_start: 0.9100 (m-10) cc_final: 0.8633 (m-80) REVERT: A 307 PHE cc_start: 0.8380 (m-80) cc_final: 0.7775 (m-10) REVERT: A 318 LEU cc_start: 0.8927 (mp) cc_final: 0.8679 (mp) REVERT: A 441 ASN cc_start: 0.7040 (m-40) cc_final: 0.6571 (p0) REVERT: C 208 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8564 (mm) REVERT: C 266 TYR cc_start: 0.9037 (m-10) cc_final: 0.8564 (m-80) REVERT: C 307 PHE cc_start: 0.8378 (m-80) cc_final: 0.7695 (m-10) REVERT: C 318 LEU cc_start: 0.8934 (mp) cc_final: 0.8653 (mp) REVERT: C 339 GLN cc_start: 0.8672 (tt0) cc_final: 0.8421 (mt0) outliers start: 33 outliers final: 23 residues processed: 107 average time/residue: 0.1327 time to fit residues: 22.7058 Evaluate side-chains 99 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE 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 370 THR 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 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 395 HIS Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 554 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 86 optimal weight: 0.2980 chunk 26 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 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 = 0.3802 r_free = 0.3802 target = 0.112466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.088311 restraints weight = 19004.714| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 3.12 r_work: 0.3233 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.5380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8742 Z= 0.223 Angle : 0.621 7.705 11932 Z= 0.296 Chirality : 0.039 0.176 1398 Planarity : 0.004 0.038 1410 Dihedral : 9.833 146.643 2106 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 3.90 % Allowed : 21.46 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.28), residues: 1038 helix: 2.03 (0.18), residues: 784 sheet: -0.11 (1.17), residues: 20 loop : -1.46 (0.48), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 368 HIS 0.002 0.001 HIS A 395 PHE 0.014 0.001 PHE A 67 TYR 0.010 0.001 TYR C 52 ARG 0.003 0.000 ARG C 186 *********************** REFINEMENT MACRO_CYCLE 9 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 108 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 76 time to evaluate : 0.874 Fit side-chains REVERT: A 208 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8514 (mm) REVERT: A 266 TYR cc_start: 0.9128 (m-10) cc_final: 0.8654 (m-80) REVERT: A 307 PHE cc_start: 0.8376 (m-80) cc_final: 0.7759 (m-10) REVERT: A 318 LEU cc_start: 0.8994 (mp) cc_final: 0.8700 (mp) REVERT: A 441 ASN cc_start: 0.7226 (m-40) cc_final: 0.6841 (p0) REVERT: C 113 TYR cc_start: 0.8654 (t80) cc_final: 0.8279 (t80) REVERT: C 208 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8512 (mm) REVERT: C 266 TYR cc_start: 0.9009 (m-10) cc_final: 0.8561 (m-80) REVERT: C 307 PHE cc_start: 0.8344 (m-80) cc_final: 0.7636 (m-10) REVERT: C 318 LEU cc_start: 0.8977 (mp) cc_final: 0.8688 (mp) REVERT: C 339 GLN cc_start: 0.8780 (tt0) cc_final: 0.8536 (mt0) outliers start: 32 outliers final: 24 residues processed: 104 average time/residue: 0.1722 time to fit residues: 28.5446 Evaluate side-chains 99 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 73 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 112 LEU 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 370 THR 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 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 338 MET Chi-restraints excluded: chain C residue 370 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 8 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 23 optimal weight: 0.3980 chunk 85 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 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 = 0.3819 r_free = 0.3819 target = 0.113469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.089603 restraints weight = 18731.301| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 3.09 r_work: 0.3257 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.5505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8742 Z= 0.178 Angle : 0.602 8.510 11932 Z= 0.283 Chirality : 0.039 0.219 1398 Planarity : 0.004 0.037 1410 Dihedral : 9.784 146.341 2106 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.29 % Allowed : 21.83 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.28), residues: 1038 helix: 2.08 (0.18), residues: 786 sheet: 0.06 (1.16), residues: 20 loop : -1.51 (0.48), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 452 HIS 0.001 0.000 HIS A 521 PHE 0.016 0.001 PHE C 67 TYR 0.010 0.001 TYR C 113 ARG 0.003 0.000 ARG C 186 ********************** REFINEMENT MACRO_CYCLE 10 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 104 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 77 time to evaluate : 1.659 Fit side-chains REVERT: A 208 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8531 (mm) REVERT: A 266 TYR cc_start: 0.9099 (m-10) cc_final: 0.8591 (m-80) REVERT: A 307 PHE cc_start: 0.8347 (m-80) cc_final: 0.7717 (m-10) REVERT: A 318 LEU cc_start: 0.8975 (mp) cc_final: 0.8701 (mp) REVERT: A 441 ASN cc_start: 0.6986 (m-40) cc_final: 0.6714 (p0) REVERT: C 113 TYR cc_start: 0.8627 (t80) cc_final: 0.8256 (t80) REVERT: C 208 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8509 (mm) REVERT: C 266 TYR cc_start: 0.9011 (m-10) cc_final: 0.8588 (m-80) REVERT: C 307 PHE cc_start: 0.8325 (m-80) cc_final: 0.7608 (m-10) REVERT: C 318 LEU cc_start: 0.8963 (mp) cc_final: 0.8691 (mp) REVERT: C 339 GLN cc_start: 0.8803 (tt0) cc_final: 0.8562 (mt0) outliers start: 27 outliers final: 22 residues processed: 101 average time/residue: 0.1681 time to fit residues: 27.2021 Evaluate side-chains 98 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE 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 370 THR 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 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 370 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 9 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 71 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 0 optimal weight: 50.0000 chunk 70 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 ASN ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 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 = 0.3817 r_free = 0.3817 target = 0.113099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.089186 restraints weight = 18958.786| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 3.10 r_work: 0.3251 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.5634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8742 Z= 0.176 Angle : 0.601 8.524 11932 Z= 0.283 Chirality : 0.039 0.189 1398 Planarity : 0.004 0.037 1410 Dihedral : 9.671 145.992 2106 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 3.29 % Allowed : 21.95 % Favored : 74.76 % 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: 2.00 (0.28), residues: 1038 helix: 2.12 (0.18), residues: 786 sheet: 0.23 (1.22), residues: 20 loop : -1.45 (0.48), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 368 HIS 0.002 0.000 HIS C 395 PHE 0.017 0.001 PHE A 67 TYR 0.010 0.001 TYR C 113 ARG 0.003 0.000 ARG C 186 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3517.72 seconds wall clock time: 62 minutes 16.10 seconds (3736.10 seconds total)