Starting phenix.real_space_refine on Thu Feb 13 14:35:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qsk_18634/02_2025/8qsk_18634.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qsk_18634/02_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_18634/02_2025/8qsk_18634.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qsk_18634/02_2025/8qsk_18634.map" model { file = "/net/cci-nas-00/data/ceres_data/8qsk_18634/02_2025/8qsk_18634.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qsk_18634/02_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.47, per 1000 atoms: 0.64 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: 2.26 Conformation dependent library (CDL) restraints added in 925.1 milliseconds 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: 0.75 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: 3.02 Time building geometry restraints manager: 2.63 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: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.360 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 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 : 0.909 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: 0.1738 time to fit residues: 56.6115 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 : 0.909 ------------------------------------------------------------------------------- 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 = 0.126262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.101932 restraints weight = 18533.593| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 3.23 r_work: 0.3461 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 8742 Z= 0.246 Angle : 0.685 14.738 11932 Z= 0.329 Chirality : 0.042 0.193 1398 Planarity : 0.005 0.035 1410 Dihedral : 11.156 153.781 2118 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.97 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 : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8394 (mm) REVERT: A 266 TYR cc_start: 0.9013 (m-80) cc_final: 0.8669 (m-80) REVERT: A 343 VAL cc_start: 0.8996 (t) cc_final: 0.8744 (m) REVERT: C 33 ARG cc_start: 0.7194 (OUTLIER) cc_final: 0.6747 (ptp90) REVERT: C 91 PHE cc_start: 0.7700 (m-10) cc_final: 0.7489 (m-10) REVERT: C 208 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8421 (mm) REVERT: C 266 TYR cc_start: 0.8989 (m-80) cc_final: 0.8719 (m-80) REVERT: C 269 CYS cc_start: 0.9204 (m) cc_final: 0.8981 (t) REVERT: C 307 PHE cc_start: 0.8355 (m-80) cc_final: 0.7973 (m-10) outliers start: 43 outliers final: 22 residues processed: 128 average time/residue: 0.1577 time to fit residues: 30.7909 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 : 0.930 ------------------------------------------------------------------------------- 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: 0.9990 chunk 26 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 chunk 92 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 1 optimal weight: 0.2980 chunk 13 optimal weight: 8.9990 chunk 7 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3965 r_free = 0.3965 target = 0.123934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.099439 restraints weight = 18616.294| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 3.23 r_work: 0.3422 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8742 Z= 0.179 Angle : 0.601 8.867 11932 Z= 0.291 Chirality : 0.039 0.171 1398 Planarity : 0.004 0.032 1410 Dihedral : 10.841 151.499 2110 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 4.39 % Allowed : 16.22 % 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 (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: 2.20 (0.18), residues: 782 sheet: None (None), residues: 0 loop : -1.96 (0.45), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 200 HIS 0.001 0.000 HIS A 395 PHE 0.014 0.001 PHE A 198 TYR 0.009 0.001 TYR A 266 ARG 0.004 0.000 ARG A 186 *********************** 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 128 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 92 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8461 (mm) REVERT: A 266 TYR cc_start: 0.8895 (m-80) cc_final: 0.8396 (m-80) REVERT: A 307 PHE cc_start: 0.8405 (m-80) cc_final: 0.7800 (m-10) REVERT: A 343 VAL cc_start: 0.9097 (t) cc_final: 0.8807 (m) REVERT: C 91 PHE cc_start: 0.7812 (m-10) cc_final: 0.7597 (m-10) REVERT: C 204 LEU cc_start: 0.8681 (tp) cc_final: 0.8475 (tp) REVERT: C 208 LEU cc_start: 0.8896 (mm) cc_final: 0.8414 (mm) REVERT: C 266 TYR cc_start: 0.8921 (m-80) cc_final: 0.8572 (m-80) REVERT: C 269 CYS cc_start: 0.9208 (m) cc_final: 0.8895 (t) REVERT: C 307 PHE cc_start: 0.8284 (m-80) cc_final: 0.7947 (m-10) outliers start: 36 outliers final: 25 residues processed: 119 average time/residue: 0.1397 time to fit residues: 26.2173 Evaluate side-chains 105 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 79 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 56 SER 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 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 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 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: 1.9990 chunk 13 optimal weight: 20.0000 chunk 33 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 52 optimal weight: 50.0000 chunk 24 optimal weight: 0.6980 chunk 71 optimal weight: 5.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 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 = 0.3818 r_free = 0.3818 target = 0.113681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.089211 restraints weight = 18842.703| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 3.12 r_work: 0.3243 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8742 Z= 0.308 Angle : 0.696 10.150 11932 Z= 0.337 Chirality : 0.042 0.213 1398 Planarity : 0.005 0.043 1410 Dihedral : 10.709 150.640 2110 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 5.49 % Allowed : 18.05 % Favored : 76.46 % 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: 1.46 (0.27), residues: 1038 helix: 1.89 (0.18), residues: 770 sheet: -1.98 (0.99), residues: 20 loop : -1.78 (0.46), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 368 HIS 0.004 0.001 HIS A 395 PHE 0.018 0.002 PHE A 67 TYR 0.015 0.002 TYR A 52 ARG 0.005 0.001 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 122 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 77 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8671 (mm) REVERT: A 266 TYR cc_start: 0.9037 (m-10) cc_final: 0.8567 (m-80) REVERT: A 307 PHE cc_start: 0.8554 (m-80) cc_final: 0.7692 (m-10) REVERT: C 208 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8559 (mm) REVERT: C 266 TYR cc_start: 0.8869 (m-10) cc_final: 0.8442 (m-80) REVERT: C 307 PHE cc_start: 0.8372 (m-80) cc_final: 0.8044 (m-10) outliers start: 45 outliers final: 29 residues processed: 112 average time/residue: 0.1436 time to fit residues: 25.3323 Evaluate side-chains 103 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 72 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 110 LEU 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 269 CYS 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 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 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: 0.0980 chunk 49 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 52 optimal weight: 60.0000 chunk 74 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.114487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.090222 restraints weight = 18642.709| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 3.12 r_work: 0.3267 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8742 Z= 0.211 Angle : 0.606 8.029 11932 Z= 0.292 Chirality : 0.039 0.178 1398 Planarity : 0.004 0.033 1410 Dihedral : 10.610 150.211 2110 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 4.39 % Allowed : 19.51 % 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: 1.64 (0.27), residues: 1038 helix: 1.99 (0.18), residues: 774 sheet: None (None), residues: 0 loop : -1.78 (0.43), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 452 HIS 0.001 0.000 HIS A 445 PHE 0.013 0.001 PHE C 198 TYR 0.011 0.001 TYR C 444 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 122 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 86 time to evaluate : 0.842 Fit side-chains REVERT: A 208 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8615 (mm) REVERT: A 266 TYR cc_start: 0.9027 (m-10) cc_final: 0.8502 (m-80) REVERT: A 307 PHE cc_start: 0.8507 (m-80) cc_final: 0.7859 (m-10) REVERT: A 318 LEU cc_start: 0.8867 (mp) cc_final: 0.8588 (mp) REVERT: C 208 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8502 (mm) REVERT: C 266 TYR cc_start: 0.8877 (m-10) cc_final: 0.8431 (m-80) REVERT: C 307 PHE cc_start: 0.8324 (m-80) cc_final: 0.8000 (m-10) outliers start: 36 outliers final: 26 residues processed: 116 average time/residue: 0.1401 time to fit residues: 25.4764 Evaluate side-chains 100 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 72 time to evaluate : 0.910 ------------------------------------------------------------------------------- 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 142 THR Chi-restraints excluded: chain A residue 154 SER 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 298 SER Chi-restraints excluded: chain A residue 357 ILE 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 112 LEU Chi-restraints excluded: chain C residue 154 SER 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 357 ILE Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 383 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 32 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3830 r_free = 0.3830 target = 0.114893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.090603 restraints weight = 18414.615| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 3.12 r_work: 0.3260 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.4814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8742 Z= 0.180 Angle : 0.601 9.676 11932 Z= 0.284 Chirality : 0.038 0.164 1398 Planarity : 0.004 0.041 1410 Dihedral : 10.213 148.781 2106 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 4.02 % Allowed : 20.61 % Favored : 75.37 % 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: 1.74 (0.28), residues: 1038 helix: 2.04 (0.18), residues: 776 sheet: -0.66 (1.12), residues: 20 loop : -1.72 (0.47), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 452 HIS 0.001 0.000 HIS A 395 PHE 0.012 0.001 PHE C 198 TYR 0.007 0.001 TYR C 52 ARG 0.003 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 113 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 80 time to evaluate : 0.912 Fit side-chains revert: symmetry clash REVERT: A 208 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8552 (mm) REVERT: A 266 TYR cc_start: 0.9102 (m-10) cc_final: 0.8609 (m-80) REVERT: A 307 PHE cc_start: 0.8441 (m-80) cc_final: 0.7795 (m-10) REVERT: A 318 LEU cc_start: 0.8898 (mp) cc_final: 0.8592 (mp) REVERT: C 208 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8437 (mm) REVERT: C 266 TYR cc_start: 0.8975 (m-10) cc_final: 0.8556 (m-80) REVERT: C 307 PHE cc_start: 0.8384 (m-80) cc_final: 0.8031 (m-10) outliers start: 33 outliers final: 25 residues processed: 111 average time/residue: 0.1377 time to fit residues: 24.3659 Evaluate side-chains 103 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 76 time to evaluate : 0.974 ------------------------------------------------------------------------------- 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 154 SER 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 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 154 SER 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 357 ILE Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 395 HIS Chi-restraints excluded: chain C residue 428 ASN Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 461 ILE 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: 0.8980 chunk 52 optimal weight: 50.0000 chunk 83 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3831 r_free = 0.3831 target = 0.114365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.090049 restraints weight = 18568.147| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 3.08 r_work: 0.3263 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.4986 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= 0.192 Angle : 0.612 11.958 11932 Z= 0.288 Chirality : 0.038 0.173 1398 Planarity : 0.004 0.038 1410 Dihedral : 10.092 148.028 2106 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 3.78 % Allowed : 21.22 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.28), residues: 1038 helix: 2.04 (0.18), residues: 780 sheet: -0.53 (1.12), residues: 20 loop : -1.63 (0.48), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 368 HIS 0.001 0.000 HIS A 395 PHE 0.012 0.001 PHE A 67 TYR 0.008 0.001 TYR C 52 ARG 0.003 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 110 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 79 time to evaluate : 0.727 Fit side-chains revert: symmetry clash REVERT: A 208 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8543 (mm) REVERT: A 266 TYR cc_start: 0.9109 (m-10) cc_final: 0.8643 (m-80) REVERT: A 307 PHE cc_start: 0.8470 (m-80) cc_final: 0.7834 (m-10) REVERT: A 318 LEU cc_start: 0.8928 (mp) cc_final: 0.8627 (mp) REVERT: C 208 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8438 (mm) REVERT: C 266 TYR cc_start: 0.8998 (m-10) cc_final: 0.8564 (m-80) REVERT: C 307 PHE cc_start: 0.8357 (m-80) cc_final: 0.8023 (m-10) outliers start: 31 outliers final: 26 residues processed: 106 average time/residue: 0.1400 time to fit residues: 23.4140 Evaluate side-chains 102 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 74 time to evaluate : 0.863 ------------------------------------------------------------------------------- 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 142 THR Chi-restraints excluded: chain A residue 154 SER 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 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 140 ASN Chi-restraints excluded: chain C residue 154 SER 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 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 461 ILE 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: 4.9990 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 chunk 95 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 GLN A 457 GLN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.113761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.089449 restraints weight = 18748.357| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 3.12 r_work: 0.3265 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.5187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8742 Z= 0.193 Angle : 0.616 11.723 11932 Z= 0.290 Chirality : 0.038 0.181 1398 Planarity : 0.004 0.042 1410 Dihedral : 9.977 147.311 2106 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 3.90 % Allowed : 21.10 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.28), residues: 1038 helix: 2.04 (0.18), residues: 778 sheet: -0.36 (1.16), residues: 20 loop : -1.66 (0.48), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 368 HIS 0.001 0.000 HIS A 395 PHE 0.012 0.001 PHE C 67 TYR 0.007 0.001 TYR C 52 ARG 0.004 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 107 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 75 time to evaluate : 0.881 Fit side-chains REVERT: A 208 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8521 (mm) REVERT: A 266 TYR cc_start: 0.9108 (m-10) cc_final: 0.8670 (m-80) REVERT: A 307 PHE cc_start: 0.8410 (m-80) cc_final: 0.7792 (m-10) REVERT: A 318 LEU cc_start: 0.8944 (mp) cc_final: 0.8654 (mp) REVERT: C 208 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8447 (mm) REVERT: C 266 TYR cc_start: 0.9000 (m-10) cc_final: 0.8540 (m-80) REVERT: C 307 PHE cc_start: 0.8319 (m-80) cc_final: 0.7972 (m-10) outliers start: 32 outliers final: 24 residues processed: 104 average time/residue: 0.1394 time to fit residues: 23.0002 Evaluate side-chains 100 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 74 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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 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 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 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 415 SER Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 461 ILE 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: 0.0670 chunk 26 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 102 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 13 optimal weight: 0.0000 overall best weight: 0.5322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3835 r_free = 0.3835 target = 0.114698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.090667 restraints weight = 18810.286| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 3.10 r_work: 0.3282 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.5281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8742 Z= 0.159 Angle : 0.614 13.564 11932 Z= 0.286 Chirality : 0.038 0.178 1398 Planarity : 0.004 0.035 1410 Dihedral : 9.892 146.542 2106 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 3.54 % Allowed : 20.98 % Favored : 75.49 % 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: 1.84 (0.28), residues: 1038 helix: 2.08 (0.18), residues: 778 sheet: -0.36 (1.18), residues: 20 loop : -1.60 (0.48), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 452 HIS 0.001 0.000 HIS A 362 PHE 0.012 0.001 PHE C 198 TYR 0.006 0.001 TYR C 113 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 112 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 83 time to evaluate : 0.885 Fit side-chains REVERT: A 208 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8480 (mm) REVERT: A 266 TYR cc_start: 0.9084 (m-10) cc_final: 0.8632 (m-80) REVERT: A 307 PHE cc_start: 0.8386 (m-80) cc_final: 0.7753 (m-10) REVERT: A 318 LEU cc_start: 0.8953 (mp) cc_final: 0.8652 (mp) REVERT: C 208 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8431 (mm) REVERT: C 266 TYR cc_start: 0.8937 (m-10) cc_final: 0.8480 (m-80) REVERT: C 307 PHE cc_start: 0.8311 (m-80) cc_final: 0.7969 (m-10) outliers start: 29 outliers final: 21 residues processed: 109 average time/residue: 0.1355 time to fit residues: 23.6816 Evaluate side-chains 99 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 158 PHE 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 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 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 415 SER Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 461 ILE 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: 0.9990 chunk 69 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 23 optimal weight: 0.1980 chunk 85 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3829 r_free = 0.3829 target = 0.114071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.090194 restraints weight = 18612.847| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 3.09 r_work: 0.3273 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.5400 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= 0.180 Angle : 0.632 13.807 11932 Z= 0.293 Chirality : 0.039 0.230 1398 Planarity : 0.004 0.038 1410 Dihedral : 9.800 146.164 2106 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 2.93 % Allowed : 22.20 % 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: 1.87 (0.28), residues: 1038 helix: 2.04 (0.18), residues: 786 sheet: -0.29 (1.21), residues: 20 loop : -1.49 (0.48), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 368 HIS 0.001 0.000 HIS A 395 PHE 0.015 0.001 PHE C 67 TYR 0.007 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 102 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 0.918 Fit side-chains revert: symmetry clash REVERT: A 208 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8510 (mm) REVERT: A 266 TYR cc_start: 0.9100 (m-10) cc_final: 0.8610 (m-80) REVERT: A 307 PHE cc_start: 0.8408 (m-80) cc_final: 0.8104 (m-10) REVERT: A 318 LEU cc_start: 0.8993 (mp) cc_final: 0.8683 (mp) REVERT: A 441 ASN cc_start: 0.6988 (m-40) cc_final: 0.6553 (p0) REVERT: C 113 TYR cc_start: 0.8560 (t80) cc_final: 0.8235 (t80) REVERT: C 208 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8635 (mm) REVERT: C 266 TYR cc_start: 0.8955 (m-10) cc_final: 0.8517 (m-80) REVERT: C 307 PHE cc_start: 0.8349 (m-80) cc_final: 0.8003 (m-10) outliers start: 24 outliers final: 22 residues processed: 99 average time/residue: 0.1439 time to fit residues: 22.9946 Evaluate side-chains 101 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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 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 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 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 415 SER Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 461 ILE 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: 3.9990 chunk 99 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 0 optimal weight: 50.0000 chunk 70 optimal weight: 0.6980 chunk 13 optimal weight: 0.3980 chunk 76 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3808 r_free = 0.3808 target = 0.112533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.088559 restraints weight = 18961.976| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 3.12 r_work: 0.3243 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.5645 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= 0.199 Angle : 0.646 14.344 11932 Z= 0.299 Chirality : 0.039 0.200 1398 Planarity : 0.004 0.030 1410 Dihedral : 9.737 146.238 2106 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.41 % Allowed : 21.46 % Favored : 75.12 % 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: 1.90 (0.28), residues: 1038 helix: 2.04 (0.18), residues: 786 sheet: -0.01 (1.19), residues: 20 loop : -1.44 (0.48), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 368 HIS 0.001 0.000 HIS A 395 PHE 0.016 0.001 PHE C 67 TYR 0.009 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: 3274.10 seconds wall clock time: 59 minutes 13.55 seconds (3553.55 seconds total)