Starting phenix.real_space_refine on Sat Aug 3 22:49:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsk_18634/08_2024/8qsk_18634.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsk_18634/08_2024/8qsk_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsk_18634/08_2024/8qsk_18634.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsk_18634/08_2024/8qsk_18634.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsk_18634/08_2024/8qsk_18634.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsk_18634/08_2024/8qsk_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 Residue "A PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 5.51, per 1000 atoms: 0.65 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 603 " - " ASN A 140 " " NAG C 604 " - " ASN C 140 " Time building additional restraints: 3.72 Conformation dependent library (CDL) restraints added in 1.6 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: 0.77 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: 2.23 Time building geometry restraints manager: 4.05 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: 92.92 - 101.13: 33 101.13 - 109.35: 619 109.35 - 117.56: 6101 117.56 - 125.77: 5040 125.77 - 133.99: 139 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: 0.00 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: 0.860 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: 0.100 Process input model: 26.650 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.800 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 13 poor density : 221 time to evaluate : 0.928 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: 0.1754 time to fit residues: 56.9448 Evaluate side-chains 108 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 102 time to evaluate : 0.886 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 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 fitting. rotamer outliers: 43 poor density : 99 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8405 (mm) REVERT: A 266 TYR cc_start: 0.8993 (m-80) cc_final: 0.8639 (m-80) REVERT: A 343 VAL cc_start: 0.8982 (t) cc_final: 0.8752 (m) REVERT: C 33 ARG cc_start: 0.7117 (OUTLIER) cc_final: 0.6690 (ptp90) REVERT: C 208 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8448 (mm) REVERT: C 266 TYR cc_start: 0.8957 (m-80) cc_final: 0.8698 (m-80) REVERT: C 269 CYS cc_start: 0.9112 (m) cc_final: 0.8898 (t) REVERT: C 307 PHE cc_start: 0.8222 (m-80) cc_final: 0.7876 (m-10) outliers start: 43 outliers final: 22 residues processed: 128 average time/residue: 0.1550 time to fit residues: 30.2365 Evaluate side-chains 104 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 79 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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 52 optimal weight: 60.0000 chunk 29 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 93 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8742 Z= 0.229 Angle : 0.627 9.012 11932 Z= 0.304 Chirality : 0.040 0.173 1398 Planarity : 0.004 0.038 1410 Dihedral : 10.857 151.856 2110 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 4.63 % Allowed : 16.10 % Favored : 79.27 % 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: 2.12 (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 0.002 0.001 HIS A 395 PHE 0.014 0.001 PHE A 198 TYR 0.012 0.001 TYR A 266 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 124 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 86 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 ASP cc_start: 0.8367 (m-30) cc_final: 0.8132 (t70) REVERT: A 208 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8558 (mm) REVERT: A 266 TYR cc_start: 0.8890 (m-80) cc_final: 0.8419 (m-80) REVERT: A 307 PHE cc_start: 0.8357 (m-80) cc_final: 0.7767 (m-10) REVERT: C 33 ARG cc_start: 0.7179 (OUTLIER) cc_final: 0.6940 (ptp90) REVERT: C 266 TYR cc_start: 0.8902 (m-80) cc_final: 0.8575 (m-80) REVERT: C 269 CYS cc_start: 0.9140 (m) cc_final: 0.8816 (t) REVERT: C 307 PHE cc_start: 0.8191 (m-80) cc_final: 0.7875 (m-10) outliers start: 38 outliers final: 25 residues processed: 116 average time/residue: 0.1418 time to fit residues: 25.8343 Evaluate side-chains 103 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 76 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 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 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 162 VAL 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 370 THR Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 501 PHE 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 93 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 63 optimal weight: 0.0570 chunk 94 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.9300 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8742 Z= 0.193 Angle : 0.604 8.685 11932 Z= 0.291 Chirality : 0.039 0.163 1398 Planarity : 0.004 0.039 1410 Dihedral : 10.665 150.298 2110 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 5.12 % Allowed : 17.80 % Favored : 77.07 % 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: 1.75 (0.28), residues: 1038 helix: 2.12 (0.18), residues: 772 sheet: None (None), residues: 0 loop : -1.87 (0.44), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 200 HIS 0.001 0.001 HIS A 395 PHE 0.013 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 121 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 79 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8574 (mm) REVERT: A 266 TYR cc_start: 0.8963 (m-10) cc_final: 0.8544 (m-80) REVERT: A 307 PHE cc_start: 0.8493 (m-80) cc_final: 0.7640 (m-10) REVERT: C 117 MET cc_start: 0.8429 (tpp) cc_final: 0.8088 (ttt) REVERT: C 208 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8533 (mm) REVERT: C 266 TYR cc_start: 0.8817 (m-10) cc_final: 0.8430 (m-80) REVERT: C 307 PHE cc_start: 0.8148 (m-80) cc_final: 0.7889 (m-10) outliers start: 42 outliers final: 25 residues processed: 112 average time/residue: 0.1424 time to fit residues: 25.1161 Evaluate side-chains 101 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 74 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 176 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 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 57 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 85 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 73 GLN ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 521 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8742 Z= 0.328 Angle : 0.677 7.213 11932 Z= 0.331 Chirality : 0.042 0.214 1398 Planarity : 0.004 0.032 1410 Dihedral : 10.618 150.428 2110 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 5.49 % Allowed : 18.78 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.51 (0.27), residues: 1038 helix: 1.86 (0.18), residues: 772 sheet: -1.30 (1.04), residues: 20 loop : -1.65 (0.47), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 368 HIS 0.003 0.001 HIS A 395 PHE 0.019 0.002 PHE A 67 TYR 0.017 0.002 TYR C 52 ARG 0.005 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 125 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 80 time to evaluate : 0.839 Fit side-chains REVERT: A 208 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8620 (mm) REVERT: A 266 TYR cc_start: 0.9095 (m-10) cc_final: 0.8591 (m-80) REVERT: A 307 PHE cc_start: 0.8422 (m-80) cc_final: 0.7796 (m-10) REVERT: A 318 LEU cc_start: 0.8976 (mp) cc_final: 0.8688 (mp) REVERT: C 266 TYR cc_start: 0.8902 (m-10) cc_final: 0.8472 (m-80) REVERT: C 307 PHE cc_start: 0.8268 (m-80) cc_final: 0.7938 (m-10) REVERT: C 318 LEU cc_start: 0.8902 (mp) cc_final: 0.8701 (mp) outliers start: 45 outliers final: 30 residues processed: 118 average time/residue: 0.1386 time to fit residues: 25.6975 Evaluate side-chains 103 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 72 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU 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 162 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 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 108 LEU 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 162 VAL Chi-restraints excluded: chain C residue 163 LEU 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 383 LEU 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 90 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 100 optimal weight: 0.0270 chunk 83 optimal weight: 0.0370 chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 50.0000 chunk 97 optimal weight: 0.6980 overall best weight: 0.4716 ------------------------------------------------------------------------------- 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 ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8742 Z= 0.156 Angle : 0.587 7.101 11932 Z= 0.280 Chirality : 0.038 0.153 1398 Planarity : 0.004 0.041 1410 Dihedral : 10.277 149.187 2106 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.80 % Allowed : 21.22 % Favored : 75.98 % 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: 1.82 (0.28), residues: 1038 helix: 2.11 (0.18), residues: 774 sheet: None (None), residues: 0 loop : -1.66 (0.44), 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 348 PHE 0.012 0.001 PHE A 194 TYR 0.009 0.001 TYR C 444 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 108 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 85 time to evaluate : 0.945 Fit side-chains REVERT: A 208 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8587 (mm) REVERT: A 266 TYR cc_start: 0.9078 (m-10) cc_final: 0.8594 (m-80) REVERT: A 307 PHE cc_start: 0.8333 (m-80) cc_final: 0.7712 (m-10) REVERT: A 318 LEU cc_start: 0.8932 (mp) cc_final: 0.8611 (mp) REVERT: A 489 MET cc_start: 0.8009 (mmm) cc_final: 0.7671 (mmm) REVERT: C 266 TYR cc_start: 0.8952 (m-10) cc_final: 0.8535 (m-80) REVERT: C 307 PHE cc_start: 0.8167 (m-80) cc_final: 0.7843 (m-10) REVERT: C 318 LEU cc_start: 0.8930 (mp) cc_final: 0.8628 (mp) outliers start: 23 outliers final: 18 residues processed: 107 average time/residue: 0.1440 time to fit residues: 24.8145 Evaluate side-chains 97 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 78 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU 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 338 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 73 optimal weight: 0.0370 chunk 56 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 overall best weight: 0.9060 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.5070 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= 0.194 Angle : 0.608 7.088 11932 Z= 0.287 Chirality : 0.038 0.172 1398 Planarity : 0.004 0.032 1410 Dihedral : 10.084 148.084 2106 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 3.66 % Allowed : 20.98 % 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: 1.84 (0.28), residues: 1038 helix: 2.11 (0.18), residues: 774 sheet: -0.77 (1.11), residues: 20 loop : -1.63 (0.47), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 368 HIS 0.002 0.000 HIS A 395 PHE 0.013 0.001 PHE A 67 TYR 0.009 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 109 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 79 time to evaluate : 0.910 Fit side-chains REVERT: A 208 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8570 (mm) REVERT: A 266 TYR cc_start: 0.9117 (m-10) cc_final: 0.8643 (m-80) REVERT: A 307 PHE cc_start: 0.8355 (m-80) cc_final: 0.7730 (m-10) REVERT: A 318 LEU cc_start: 0.8979 (mp) cc_final: 0.8659 (mp) REVERT: A 441 ASN cc_start: 0.7319 (m-40) cc_final: 0.6756 (p0) REVERT: A 489 MET cc_start: 0.8053 (mmm) cc_final: 0.7642 (mmm) REVERT: C 266 TYR cc_start: 0.8986 (m-10) cc_final: 0.8571 (m-80) REVERT: C 307 PHE cc_start: 0.8158 (m-80) cc_final: 0.7851 (m-10) REVERT: C 318 LEU cc_start: 0.8971 (mp) cc_final: 0.8664 (mp) REVERT: C 339 GLN cc_start: 0.8724 (tt0) cc_final: 0.8445 (mt0) outliers start: 30 outliers final: 25 residues processed: 107 average time/residue: 0.1344 time to fit residues: 22.8514 Evaluate side-chains 101 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 75 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 233 VAL Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 338 MET 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 415 SER 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 30 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 91 optimal weight: 0.4980 chunk 96 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 485 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.5184 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= 0.168 Angle : 0.589 7.415 11932 Z= 0.279 Chirality : 0.038 0.181 1398 Planarity : 0.004 0.039 1410 Dihedral : 9.973 147.266 2106 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 3.41 % Allowed : 21.22 % 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: 1.94 (0.28), residues: 1038 helix: 2.10 (0.18), residues: 784 sheet: -0.53 (1.14), residues: 20 loop : -1.45 (0.49), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 452 HIS 0.001 0.000 HIS C 348 PHE 0.011 0.001 PHE A 257 TYR 0.006 0.001 TYR C 52 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 106 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 78 time to evaluate : 0.887 Fit side-chains REVERT: A 208 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8561 (mm) REVERT: A 266 TYR cc_start: 0.9114 (m-10) cc_final: 0.8680 (m-80) REVERT: A 307 PHE cc_start: 0.8333 (m-80) cc_final: 0.7723 (m-10) REVERT: A 313 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8524 (tm-30) REVERT: A 318 LEU cc_start: 0.8974 (mp) cc_final: 0.8662 (mp) REVERT: A 441 ASN cc_start: 0.7284 (m-40) cc_final: 0.6745 (p0) REVERT: A 489 MET cc_start: 0.8000 (mmm) cc_final: 0.7590 (mmm) REVERT: C 266 TYR cc_start: 0.9011 (m-10) cc_final: 0.8567 (m-80) REVERT: C 307 PHE cc_start: 0.8160 (m-80) cc_final: 0.7849 (m-10) REVERT: C 318 LEU cc_start: 0.8976 (mp) cc_final: 0.8668 (mp) REVERT: C 339 GLN cc_start: 0.8746 (tt0) cc_final: 0.8477 (mt0) REVERT: C 413 MET cc_start: 0.8730 (tpp) cc_final: 0.8529 (ttm) outliers start: 28 outliers final: 21 residues processed: 103 average time/residue: 0.1349 time to fit residues: 22.0559 Evaluate side-chains 99 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 77 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 40 optimal weight: 0.0020 chunk 73 optimal weight: 2.9990 chunk 28 optimal weight: 0.0980 chunk 84 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 93 optimal weight: 0.5980 chunk 61 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 overall best weight: 0.4588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.5275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8742 Z= 0.150 Angle : 0.588 8.270 11932 Z= 0.277 Chirality : 0.038 0.196 1398 Planarity : 0.004 0.032 1410 Dihedral : 9.829 146.302 2106 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.17 % Allowed : 21.59 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.98 (0.28), residues: 1038 helix: 2.13 (0.18), residues: 784 sheet: -0.43 (1.17), 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 348 PHE 0.011 0.001 PHE A 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 110 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 84 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: A 208 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8524 (mm) REVERT: A 266 TYR cc_start: 0.9128 (m-10) cc_final: 0.8673 (m-80) REVERT: A 307 PHE cc_start: 0.8327 (m-80) cc_final: 0.7719 (m-10) REVERT: A 313 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8490 (tm-30) REVERT: A 318 LEU cc_start: 0.8978 (mp) cc_final: 0.8661 (mp) REVERT: A 428 ASN cc_start: 0.8670 (OUTLIER) cc_final: 0.8206 (t0) REVERT: A 441 ASN cc_start: 0.7106 (m-40) cc_final: 0.6647 (p0) REVERT: A 489 MET cc_start: 0.7990 (mmm) cc_final: 0.7566 (mmm) REVERT: C 266 TYR cc_start: 0.8949 (m-10) cc_final: 0.8521 (m-80) REVERT: C 307 PHE cc_start: 0.8162 (m-80) cc_final: 0.7851 (m-10) REVERT: C 318 LEU cc_start: 0.8972 (mp) cc_final: 0.8634 (mp) REVERT: C 339 GLN cc_start: 0.8747 (tt0) cc_final: 0.8487 (mt0) REVERT: C 413 MET cc_start: 0.8726 (tpp) cc_final: 0.8517 (ttm) REVERT: C 441 ASN cc_start: 0.6964 (m-40) cc_final: 0.6523 (p0) outliers start: 26 outliers final: 19 residues processed: 107 average time/residue: 0.1519 time to fit residues: 25.3631 Evaluate side-chains 102 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 81 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 370 THR Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 176 THR 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 46 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 103 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 63 optimal weight: 0.0470 chunk 50 optimal weight: 0.9990 chunk 65 optimal weight: 8.9990 chunk 87 optimal weight: 0.2980 chunk 25 optimal weight: 6.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.5365 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= 0.156 Angle : 0.591 8.096 11932 Z= 0.277 Chirality : 0.038 0.198 1398 Planarity : 0.004 0.037 1410 Dihedral : 9.718 145.731 2106 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 2.44 % Allowed : 22.68 % 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: 1.99 (0.28), residues: 1038 helix: 2.12 (0.18), residues: 788 sheet: -0.25 (1.18), residues: 20 loop : -1.47 (0.49), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 368 HIS 0.001 0.000 HIS A 348 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 104 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 84 time to evaluate : 0.893 Fit side-chains REVERT: A 113 TYR cc_start: 0.8606 (t80) cc_final: 0.8350 (t80) REVERT: A 208 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8511 (mm) REVERT: A 266 TYR cc_start: 0.9117 (m-10) cc_final: 0.8644 (m-80) REVERT: A 307 PHE cc_start: 0.8322 (m-80) cc_final: 0.7716 (m-10) REVERT: A 313 GLU cc_start: 0.8664 (tm-30) cc_final: 0.8447 (tm-30) REVERT: A 318 LEU cc_start: 0.8981 (mp) cc_final: 0.8650 (mp) REVERT: A 441 ASN cc_start: 0.7119 (m-40) cc_final: 0.6676 (p0) REVERT: A 489 MET cc_start: 0.8009 (mmm) cc_final: 0.7594 (mmm) REVERT: C 113 TYR cc_start: 0.8391 (t80) cc_final: 0.7992 (t80) REVERT: C 266 TYR cc_start: 0.8936 (m-10) cc_final: 0.8516 (m-80) REVERT: C 307 PHE cc_start: 0.8158 (m-80) cc_final: 0.7837 (m-10) REVERT: C 318 LEU cc_start: 0.8958 (mp) cc_final: 0.8621 (mp) REVERT: C 339 GLN cc_start: 0.8736 (tt0) cc_final: 0.8477 (mt0) REVERT: C 413 MET cc_start: 0.8726 (tpp) cc_final: 0.8522 (ttm) REVERT: C 441 ASN cc_start: 0.6982 (m-40) cc_final: 0.6589 (p0) outliers start: 20 outliers final: 18 residues processed: 101 average time/residue: 0.1412 time to fit residues: 22.5786 Evaluate side-chains 98 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 79 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 76 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3821 r_free = 0.3821 target = 0.113531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.089476 restraints weight = 18483.194| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 3.07 r_work: 0.3262 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 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= 0.184 Angle : 0.598 7.786 11932 Z= 0.283 Chirality : 0.038 0.189 1398 Planarity : 0.004 0.031 1410 Dihedral : 9.653 145.737 2106 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 2.68 % Allowed : 22.68 % 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: 1.99 (0.28), residues: 1038 helix: 2.11 (0.18), residues: 788 sheet: 0.09 (1.22), residues: 20 loop : -1.46 (0.49), residues: 230 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 0.016 0.001 PHE A 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: 1714.06 seconds wall clock time: 31 minutes 32.60 seconds (1892.60 seconds total)