Starting phenix.real_space_refine on Fri Nov 15 16:39:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3j_36853/11_2024/8k3j_36853.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3j_36853/11_2024/8k3j_36853.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/8k3j_36853/11_2024/8k3j_36853.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3j_36853/11_2024/8k3j_36853.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3j_36853/11_2024/8k3j_36853.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3j_36853/11_2024/8k3j_36853.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= 0.000 sd= 0.038 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: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 5720 2.51 5 N 1576 2.21 5 O 1770 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 9108 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4448 Classifications: {'peptide': 574} Link IDs: {'PCIS': 5, 'PTRANS': 32, 'TRANS': 536} Chain: "B" Number of atoms: 4448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4448 Classifications: {'peptide': 574} Link IDs: {'PCIS': 5, 'PTRANS': 32, 'TRANS': 536} Chain: "C" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.90, per 1000 atoms: 0.76 Number of scatterers: 9108 At special positions: 0 Unit cell: (144.44, 164.68, 103.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 1770 8.00 N 1576 7.00 C 5720 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 111 " distance=2.03 Simple disulfide: pdb=" SG CYS A 155 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 261 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS A 348 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 440 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 111 " distance=2.03 Simple disulfide: pdb=" SG CYS B 155 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 261 " - pdb=" SG CYS B 306 " distance=2.03 Simple disulfide: pdb=" SG CYS B 348 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 440 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 530 " - pdb=" SG CYS B 587 " 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 ALPHA1-3 " BMA C 3 " - " MAN C 4 " " BMA E 3 " - " MAN E 4 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1101 " - " ASN A 76 " " NAG A1102 " - " ASN A 477 " " NAG B1101 " - " ASN B 76 " " NAG B1102 " - " ASN B 477 " " NAG C 1 " - " ASN A 498 " " NAG D 1 " - " ASN A 461 " " NAG E 1 " - " ASN B 498 " " NAG F 1 " - " ASN B 461 " Time building additional restraints: 2.54 Conformation dependent library (CDL) restraints added in 1.2 seconds 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2136 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 36 sheets defined 3.7% alpha, 45.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 101 through 106 removed outlier: 4.250A pdb=" N ALA A 106 " --> pdb=" O LYS A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 202 Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.521A pdb=" N GLU A 301 " --> pdb=" O PHE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 582 Processing helix chain 'B' and resid 101 through 106 removed outlier: 4.247A pdb=" N ALA B 106 " --> pdb=" O LYS B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 202 Processing helix chain 'B' and resid 297 through 301 removed outlier: 3.564A pdb=" N GLU B 301 " --> pdb=" O PHE B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 582 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 41 removed outlier: 5.935A pdb=" N GLY A 36 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N SER A 66 " --> pdb=" O GLY A 36 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ARG A 62 " --> pdb=" O GLU A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 49 removed outlier: 6.232A pdb=" N VAL A 46 " --> pdb=" O ARG A 128 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N GLY A 130 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N PHE A 48 " --> pdb=" O GLY A 130 " (cutoff:3.500A) removed outlier: 9.148A pdb=" N LEU A 132 " --> pdb=" O PHE A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 79 removed outlier: 3.597A pdb=" N THR A 78 " --> pdb=" O MET A 75 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 56 through 59 removed outlier: 3.539A pdb=" N VAL A 57 " --> pdb=" O ILE A 97 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 144 through 146 removed outlier: 3.814A pdb=" N GLY A 203 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 144 through 146 removed outlier: 3.814A pdb=" N GLY A 203 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS A 218 " --> pdb=" O SER A 211 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 151 through 153 removed outlier: 3.843A pdb=" N ILE A 194 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A 153 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 240 through 243 removed outlier: 6.599A pdb=" N PHE A 262 " --> pdb=" O LYS A 242 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 248 through 252 removed outlier: 6.201A pdb=" N THR A 249 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N GLN A 324 " --> pdb=" O THR A 249 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ALA A 251 " --> pdb=" O GLN A 324 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 257 through 260 Processing sheet with id=AB2, first strand: chain 'A' and resid 328 through 331 removed outlier: 6.545A pdb=" N ALA A 349 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 336 through 339 Processing sheet with id=AB4, first strand: chain 'A' and resid 344 through 347 Processing sheet with id=AB5, first strand: chain 'A' and resid 427 through 431 removed outlier: 3.601A pdb=" N SER A 504 " --> pdb=" O ILE A 428 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 436 through 438 Processing sheet with id=AB7, first strand: chain 'A' and resid 510 through 513 removed outlier: 6.011A pdb=" N HIS A 531 " --> pdb=" O THR A 512 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 518 through 521 Processing sheet with id=AB9, first strand: chain 'A' and resid 526 through 528 Processing sheet with id=AC1, first strand: chain 'B' and resid 35 through 41 removed outlier: 5.953A pdb=" N GLY B 36 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N SER B 66 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ARG B 62 " --> pdb=" O GLU B 40 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 46 through 49 removed outlier: 6.219A pdb=" N VAL B 46 " --> pdb=" O ARG B 128 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N GLY B 130 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N PHE B 48 " --> pdb=" O GLY B 130 " (cutoff:3.500A) removed outlier: 9.154A pdb=" N LEU B 132 " --> pdb=" O PHE B 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 78 through 79 removed outlier: 3.694A pdb=" N THR B 78 " --> pdb=" O MET B 75 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 56 through 59 removed outlier: 3.600A pdb=" N VAL B 57 " --> pdb=" O ILE B 97 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 144 through 146 removed outlier: 7.494A pdb=" N ALA B 145 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY B 203 " --> pdb=" O LEU B 227 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 144 through 146 removed outlier: 7.494A pdb=" N ALA B 145 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY B 203 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS B 218 " --> pdb=" O SER B 211 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 151 through 153 removed outlier: 3.835A pdb=" N ILE B 194 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU B 153 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 237 through 243 removed outlier: 5.661A pdb=" N ALA B 238 " --> pdb=" O ASN B 266 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ASN B 266 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N PHE B 262 " --> pdb=" O LYS B 242 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 248 through 252 removed outlier: 6.007A pdb=" N THR B 249 " --> pdb=" O ILE B 322 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N GLN B 324 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA B 251 " --> pdb=" O GLN B 324 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 257 through 260 Processing sheet with id=AD2, first strand: chain 'B' and resid 328 through 331 removed outlier: 6.551A pdb=" N ALA B 349 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 336 through 339 Processing sheet with id=AD4, first strand: chain 'B' and resid 344 through 347 Processing sheet with id=AD5, first strand: chain 'B' and resid 427 through 431 removed outlier: 3.591A pdb=" N SER B 504 " --> pdb=" O ILE B 428 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 435 through 438 Processing sheet with id=AD7, first strand: chain 'B' and resid 510 through 513 removed outlier: 6.066A pdb=" N HIS B 531 " --> pdb=" O THR B 512 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 518 through 521 Processing sheet with id=AD9, first strand: chain 'B' and resid 526 through 528 332 hydrogen bonds defined for protein. 750 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: 3.65 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2966 1.34 - 1.46: 1709 1.46 - 1.58: 4579 1.58 - 1.70: 0 1.70 - 1.82: 60 Bond restraints: 9314 Sorted by residual: bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.541 -0.135 2.00e-02 2.50e+03 4.53e+01 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.510 -0.104 2.00e-02 2.50e+03 2.70e+01 bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.507 -0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.502 -0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" C5 MAN C 4 " pdb=" O5 MAN C 4 " ideal model delta sigma weight residual 1.418 1.463 -0.045 2.00e-02 2.50e+03 5.00e+00 ... (remaining 9309 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 12440 2.16 - 4.33: 203 4.33 - 6.49: 23 6.49 - 8.66: 3 8.66 - 10.82: 3 Bond angle restraints: 12672 Sorted by residual: angle pdb=" C ASN A 498 " pdb=" CA ASN A 498 " pdb=" CB ASN A 498 " ideal model delta sigma weight residual 109.99 115.83 -5.84 1.61e+00 3.86e-01 1.32e+01 angle pdb=" CB MET B 152 " pdb=" CG MET B 152 " pdb=" SD MET B 152 " ideal model delta sigma weight residual 112.70 123.52 -10.82 3.00e+00 1.11e-01 1.30e+01 angle pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " pdb=" C5 NAG C 1 " ideal model delta sigma weight residual 113.21 123.65 -10.44 3.00e+00 1.11e-01 1.21e+01 angle pdb=" CB MET A 152 " pdb=" CG MET A 152 " pdb=" SD MET A 152 " ideal model delta sigma weight residual 112.70 122.62 -9.92 3.00e+00 1.11e-01 1.09e+01 angle pdb=" CA ASN A 461 " pdb=" CB ASN A 461 " pdb=" CG ASN A 461 " ideal model delta sigma weight residual 112.60 115.36 -2.76 1.00e+00 1.00e+00 7.64e+00 ... (remaining 12667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.21: 5224 23.21 - 46.43: 480 46.43 - 69.64: 77 69.64 - 92.86: 41 92.86 - 116.07: 30 Dihedral angle restraints: 5852 sinusoidal: 2544 harmonic: 3308 Sorted by residual: dihedral pdb=" CB CYS A 348 " pdb=" SG CYS A 348 " pdb=" SG CYS A 395 " pdb=" CB CYS A 395 " ideal model delta sinusoidal sigma weight residual 93.00 176.17 -83.17 1 1.00e+01 1.00e-02 8.46e+01 dihedral pdb=" CB CYS B 155 " pdb=" SG CYS B 155 " pdb=" SG CYS B 207 " pdb=" CB CYS B 207 " ideal model delta sinusoidal sigma weight residual -86.00 -3.16 -82.84 1 1.00e+01 1.00e-02 8.40e+01 dihedral pdb=" CB CYS A 155 " pdb=" SG CYS A 155 " pdb=" SG CYS A 207 " pdb=" CB CYS A 207 " ideal model delta sinusoidal sigma weight residual -86.00 -3.73 -82.27 1 1.00e+01 1.00e-02 8.31e+01 ... (remaining 5849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1308 0.080 - 0.160: 145 0.160 - 0.240: 5 0.240 - 0.319: 2 0.319 - 0.399: 2 Chirality restraints: 1462 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN B 461 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.98e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 461 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 1459 not shown) Planarity restraints: 1648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 461 " -0.023 2.00e-02 2.50e+03 2.26e-02 6.37e+00 pdb=" CG ASN A 461 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN A 461 " -0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN A 461 " 0.028 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 498 " 0.020 2.00e-02 2.50e+03 2.02e-02 5.12e+00 pdb=" CG ASN A 498 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN A 498 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN A 498 " -0.010 2.00e-02 2.50e+03 pdb=" C1 NAG C 1 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 83 " 0.031 5.00e-02 4.00e+02 4.71e-02 3.55e+00 pdb=" N PRO B 84 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 84 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 84 " 0.026 5.00e-02 4.00e+02 ... (remaining 1645 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 257 2.69 - 3.24: 8050 3.24 - 3.80: 12984 3.80 - 4.35: 16991 4.35 - 4.90: 29008 Nonbonded interactions: 67290 Sorted by model distance: nonbonded pdb=" N GLN A 32 " pdb=" NE2 GLN A 32 " model vdw 2.138 3.200 nonbonded pdb=" NZ LYS A 144 " pdb=" O ALA A 145 " model vdw 2.223 3.120 nonbonded pdb=" NZ LYS B 144 " pdb=" O ALA B 145 " model vdw 2.245 3.120 nonbonded pdb=" OD1 ASN A 498 " pdb=" O6 NAG C 1 " model vdw 2.276 3.040 nonbonded pdb=" OD1 ASP A 535 " pdb=" OG1 THR A 537 " model vdw 2.277 3.040 ... (remaining 67285 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' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.690 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 26.190 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 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 : 0.004 0.135 9314 Z= 0.272 Angle : 0.687 10.824 12672 Z= 0.341 Chirality : 0.049 0.399 1462 Planarity : 0.004 0.047 1640 Dihedral : 20.459 116.072 3680 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.72 % Favored : 95.10 % Rotamer: Outliers : 0.31 % Allowed : 23.19 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.25), residues: 1144 helix: None (None), residues: 0 sheet: 0.82 (0.23), residues: 500 loop : -1.13 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 149 HIS 0.003 0.001 HIS A 559 PHE 0.008 0.001 PHE B 135 TYR 0.007 0.001 TYR B 405 ARG 0.002 0.000 ARG B 480 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 1.034 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 54 average time/residue: 0.1783 time to fit residues: 15.0867 Evaluate side-chains 51 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLN Chi-restraints excluded: chain B residue 549 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.0578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9314 Z= 0.212 Angle : 0.671 11.362 12672 Z= 0.321 Chirality : 0.050 0.384 1462 Planarity : 0.004 0.049 1640 Dihedral : 15.969 109.507 1575 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.33 % Favored : 94.49 % Rotamer: Outliers : 3.31 % Allowed : 22.15 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.25), residues: 1144 helix: -3.19 (1.54), residues: 12 sheet: 0.72 (0.23), residues: 524 loop : -1.31 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 149 HIS 0.003 0.001 HIS B 146 PHE 0.009 0.001 PHE B 245 TYR 0.009 0.001 TYR B 405 ARG 0.004 0.000 ARG A 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 53 time to evaluate : 1.004 Fit side-chains REVERT: A 544 TRP cc_start: 0.5730 (m100) cc_final: 0.5101 (m-10) REVERT: A 573 THR cc_start: 0.7101 (m) cc_final: 0.6901 (p) outliers start: 32 outliers final: 17 residues processed: 82 average time/residue: 0.1929 time to fit residues: 23.5546 Evaluate side-chains 66 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 49 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 549 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 83 optimal weight: 0.0470 overall best weight: 1.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN B 146 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9314 Z= 0.305 Angle : 0.727 11.926 12672 Z= 0.349 Chirality : 0.051 0.432 1462 Planarity : 0.005 0.059 1640 Dihedral : 13.290 109.415 1572 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 5.38 % Allowed : 20.50 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.25), residues: 1144 helix: -3.80 (1.13), residues: 12 sheet: 0.80 (0.23), residues: 498 loop : -1.41 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 149 HIS 0.007 0.001 HIS A 146 PHE 0.012 0.002 PHE A 245 TYR 0.019 0.002 TYR A 161 ARG 0.003 0.000 ARG B 182 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 58 time to evaluate : 0.932 Fit side-chains REVERT: A 135 PHE cc_start: 0.4420 (OUTLIER) cc_final: 0.2693 (t80) REVERT: A 176 PHE cc_start: 0.6094 (OUTLIER) cc_final: 0.5473 (m-80) REVERT: B 128 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7607 (mtm180) REVERT: B 135 PHE cc_start: 0.4332 (OUTLIER) cc_final: 0.2571 (t80) REVERT: B 176 PHE cc_start: 0.5838 (OUTLIER) cc_final: 0.5147 (m-80) outliers start: 52 outliers final: 26 residues processed: 102 average time/residue: 0.1909 time to fit residues: 28.8729 Evaluate side-chains 79 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 48 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 176 PHE Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 212 HIS Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 549 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 110 optimal weight: 0.0970 chunk 54 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9314 Z= 0.232 Angle : 0.683 11.711 12672 Z= 0.324 Chirality : 0.049 0.404 1462 Planarity : 0.004 0.066 1640 Dihedral : 12.502 107.612 1572 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.59 % Favored : 94.32 % Rotamer: Outliers : 4.76 % Allowed : 21.74 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.25), residues: 1144 helix: -3.62 (1.25), residues: 12 sheet: 0.86 (0.24), residues: 498 loop : -1.35 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 149 HIS 0.002 0.001 HIS A 146 PHE 0.010 0.001 PHE B 245 TYR 0.009 0.001 TYR B 405 ARG 0.002 0.000 ARG B 480 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 53 time to evaluate : 1.034 Fit side-chains REVERT: A 135 PHE cc_start: 0.4413 (OUTLIER) cc_final: 0.2572 (t80) REVERT: A 176 PHE cc_start: 0.5987 (OUTLIER) cc_final: 0.5350 (m-80) REVERT: A 387 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8457 (mm) REVERT: A 544 TRP cc_start: 0.6038 (m100) cc_final: 0.5779 (m-10) REVERT: B 128 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7587 (mtm180) REVERT: B 135 PHE cc_start: 0.4568 (OUTLIER) cc_final: 0.2757 (t80) REVERT: B 387 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8505 (mm) outliers start: 46 outliers final: 28 residues processed: 92 average time/residue: 0.1683 time to fit residues: 24.1243 Evaluate side-chains 81 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 47 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 212 HIS Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 549 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 2.9990 chunk 62 optimal weight: 0.0570 chunk 1 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 chunk 0 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 overall best weight: 1.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9314 Z= 0.266 Angle : 0.699 11.665 12672 Z= 0.333 Chirality : 0.050 0.410 1462 Planarity : 0.005 0.069 1640 Dihedral : 12.191 105.796 1572 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.12 % Favored : 93.71 % Rotamer: Outliers : 4.97 % Allowed : 22.46 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.25), residues: 1144 helix: -3.68 (1.22), residues: 12 sheet: 0.86 (0.23), residues: 502 loop : -1.42 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 149 HIS 0.004 0.001 HIS B 559 PHE 0.011 0.001 PHE A 245 TYR 0.011 0.001 TYR B 405 ARG 0.002 0.000 ARG B 480 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 48 time to evaluate : 1.020 Fit side-chains REVERT: A 135 PHE cc_start: 0.4709 (OUTLIER) cc_final: 0.2774 (t80) REVERT: A 176 PHE cc_start: 0.6040 (OUTLIER) cc_final: 0.5390 (m-80) REVERT: A 387 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8473 (mm) REVERT: B 128 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7596 (mtm180) REVERT: B 135 PHE cc_start: 0.4759 (OUTLIER) cc_final: 0.2800 (t80) REVERT: B 176 PHE cc_start: 0.5948 (OUTLIER) cc_final: 0.5296 (m-80) REVERT: B 387 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8529 (mm) outliers start: 48 outliers final: 31 residues processed: 88 average time/residue: 0.1666 time to fit residues: 23.0743 Evaluate side-chains 85 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 47 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 176 PHE Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 212 HIS Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 549 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 0.0050 chunk 27 optimal weight: 0.9990 chunk 110 optimal weight: 0.0040 chunk 91 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.8012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9314 Z= 0.203 Angle : 0.661 11.654 12672 Z= 0.313 Chirality : 0.048 0.391 1462 Planarity : 0.004 0.070 1640 Dihedral : 11.839 104.519 1572 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.90 % Favored : 94.93 % Rotamer: Outliers : 5.38 % Allowed : 22.05 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.26), residues: 1144 helix: -3.43 (1.38), residues: 12 sheet: 0.93 (0.23), residues: 512 loop : -1.32 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 168 HIS 0.003 0.001 HIS A 559 PHE 0.009 0.001 PHE A 245 TYR 0.009 0.001 TYR B 405 ARG 0.002 0.000 ARG B 480 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 50 time to evaluate : 1.046 Fit side-chains REVERT: A 135 PHE cc_start: 0.4728 (OUTLIER) cc_final: 0.2794 (t80) REVERT: A 164 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.7174 (mt) REVERT: A 176 PHE cc_start: 0.5896 (OUTLIER) cc_final: 0.5245 (m-80) REVERT: B 128 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7592 (mtm180) REVERT: B 135 PHE cc_start: 0.4648 (OUTLIER) cc_final: 0.2732 (t80) REVERT: B 176 PHE cc_start: 0.5866 (OUTLIER) cc_final: 0.5184 (m-80) REVERT: B 229 LEU cc_start: 0.1579 (OUTLIER) cc_final: 0.1279 (pp) outliers start: 52 outliers final: 39 residues processed: 94 average time/residue: 0.1644 time to fit residues: 24.4623 Evaluate side-chains 90 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 44 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 176 PHE Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 212 HIS Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 549 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 62 optimal weight: 0.0050 chunk 80 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 109 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 66 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9314 Z= 0.180 Angle : 0.650 11.782 12672 Z= 0.304 Chirality : 0.048 0.377 1462 Planarity : 0.004 0.069 1640 Dihedral : 11.506 103.325 1572 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.63 % Favored : 95.19 % Rotamer: Outliers : 5.18 % Allowed : 22.46 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.26), residues: 1144 helix: -3.31 (1.45), residues: 12 sheet: 1.02 (0.23), residues: 512 loop : -1.24 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 544 HIS 0.003 0.000 HIS A 146 PHE 0.008 0.001 PHE A 245 TYR 0.008 0.001 TYR A 405 ARG 0.002 0.000 ARG A 562 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 53 time to evaluate : 0.959 Fit side-chains REVERT: A 135 PHE cc_start: 0.4742 (OUTLIER) cc_final: 0.2693 (t80) REVERT: A 176 PHE cc_start: 0.5906 (OUTLIER) cc_final: 0.5254 (m-80) REVERT: A 544 TRP cc_start: 0.5738 (m-10) cc_final: 0.5218 (m-10) REVERT: B 128 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7623 (mtm180) REVERT: B 135 PHE cc_start: 0.4722 (OUTLIER) cc_final: 0.2664 (t80) REVERT: B 176 PHE cc_start: 0.5874 (OUTLIER) cc_final: 0.5196 (m-80) REVERT: B 229 LEU cc_start: 0.1665 (OUTLIER) cc_final: 0.1348 (pp) REVERT: B 387 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8497 (mm) outliers start: 50 outliers final: 37 residues processed: 94 average time/residue: 0.1664 time to fit residues: 24.5507 Evaluate side-chains 91 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 47 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 176 PHE Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 212 HIS Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 549 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 69 optimal weight: 0.0060 chunk 74 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 10 optimal weight: 0.4980 chunk 86 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9314 Z= 0.178 Angle : 0.654 11.798 12672 Z= 0.306 Chirality : 0.048 0.369 1462 Planarity : 0.004 0.065 1640 Dihedral : 11.358 102.698 1572 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.37 % Favored : 95.45 % Rotamer: Outliers : 5.28 % Allowed : 22.05 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.25), residues: 1144 helix: -3.26 (1.49), residues: 12 sheet: 1.12 (0.23), residues: 490 loop : -1.24 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 544 HIS 0.002 0.001 HIS B 146 PHE 0.008 0.001 PHE A 245 TYR 0.015 0.001 TYR A 161 ARG 0.002 0.000 ARG B 480 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 48 time to evaluate : 1.022 Fit side-chains REVERT: A 135 PHE cc_start: 0.4732 (OUTLIER) cc_final: 0.2761 (t80) REVERT: A 176 PHE cc_start: 0.5893 (OUTLIER) cc_final: 0.5241 (m-80) REVERT: A 544 TRP cc_start: 0.5603 (m-10) cc_final: 0.5025 (m-10) REVERT: B 128 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7631 (mtm180) REVERT: B 135 PHE cc_start: 0.4726 (OUTLIER) cc_final: 0.2690 (t80) REVERT: B 176 PHE cc_start: 0.5896 (OUTLIER) cc_final: 0.5206 (m-80) REVERT: B 229 LEU cc_start: 0.1865 (OUTLIER) cc_final: 0.1522 (pp) outliers start: 51 outliers final: 40 residues processed: 91 average time/residue: 0.1556 time to fit residues: 22.1652 Evaluate side-chains 93 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 47 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 176 PHE Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 212 HIS Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 573 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 108 optimal weight: 0.0470 chunk 66 optimal weight: 0.6980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9314 Z= 0.183 Angle : 0.653 11.816 12672 Z= 0.305 Chirality : 0.048 0.366 1462 Planarity : 0.004 0.066 1640 Dihedral : 11.156 101.796 1570 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.46 % Favored : 95.37 % Rotamer: Outliers : 4.97 % Allowed : 22.46 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.25), residues: 1144 helix: -3.25 (1.50), residues: 12 sheet: 1.13 (0.23), residues: 490 loop : -1.22 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 544 HIS 0.001 0.000 HIS A 146 PHE 0.009 0.001 PHE A 245 TYR 0.012 0.001 TYR A 161 ARG 0.002 0.000 ARG B 480 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 50 time to evaluate : 1.122 Fit side-chains REVERT: A 135 PHE cc_start: 0.4760 (OUTLIER) cc_final: 0.2732 (t80) REVERT: A 176 PHE cc_start: 0.5920 (OUTLIER) cc_final: 0.5258 (m-80) REVERT: A 544 TRP cc_start: 0.5442 (m-10) cc_final: 0.4851 (m-10) REVERT: B 128 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7600 (mtm180) REVERT: B 135 PHE cc_start: 0.4748 (OUTLIER) cc_final: 0.2693 (t80) REVERT: B 173 PHE cc_start: 0.4579 (OUTLIER) cc_final: 0.4162 (m-80) REVERT: B 176 PHE cc_start: 0.5874 (OUTLIER) cc_final: 0.5183 (m-80) REVERT: B 229 LEU cc_start: 0.2185 (OUTLIER) cc_final: 0.1833 (pp) REVERT: B 544 TRP cc_start: 0.5580 (m-10) cc_final: 0.4900 (m-10) outliers start: 48 outliers final: 38 residues processed: 90 average time/residue: 0.1657 time to fit residues: 23.3601 Evaluate side-chains 93 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 48 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 176 PHE Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 212 HIS Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 540 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.4980 chunk 75 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9314 Z= 0.201 Angle : 0.667 12.043 12672 Z= 0.311 Chirality : 0.048 0.368 1462 Planarity : 0.004 0.066 1640 Dihedral : 11.024 100.759 1570 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.63 % Favored : 95.19 % Rotamer: Outliers : 4.97 % Allowed : 22.67 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.26), residues: 1144 helix: -3.24 (1.51), residues: 12 sheet: 1.02 (0.23), residues: 514 loop : -1.19 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 544 HIS 0.002 0.001 HIS B 559 PHE 0.009 0.001 PHE A 245 TYR 0.013 0.001 TYR A 161 ARG 0.002 0.000 ARG B 480 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 48 time to evaluate : 1.057 Fit side-chains REVERT: A 135 PHE cc_start: 0.4881 (OUTLIER) cc_final: 0.2823 (t80) REVERT: A 176 PHE cc_start: 0.6097 (OUTLIER) cc_final: 0.5460 (m-80) REVERT: A 544 TRP cc_start: 0.5483 (m-10) cc_final: 0.4854 (m-10) REVERT: B 128 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7574 (mtm180) REVERT: B 135 PHE cc_start: 0.4908 (OUTLIER) cc_final: 0.2818 (t80) REVERT: B 173 PHE cc_start: 0.4573 (OUTLIER) cc_final: 0.4113 (m-80) REVERT: B 176 PHE cc_start: 0.5872 (OUTLIER) cc_final: 0.5174 (m-80) REVERT: B 544 TRP cc_start: 0.5526 (m-10) cc_final: 0.4885 (m-10) outliers start: 48 outliers final: 38 residues processed: 89 average time/residue: 0.1615 time to fit residues: 22.7215 Evaluate side-chains 90 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 46 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 176 PHE Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 212 HIS Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 540 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 90 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN ** B 559 HIS ** 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 = 0.4076 r_free = 0.4076 target = 0.138986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.112204 restraints weight = 19371.299| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 4.92 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9314 Z= 0.203 Angle : 0.665 11.753 12672 Z= 0.311 Chirality : 0.047 0.368 1462 Planarity : 0.004 0.066 1640 Dihedral : 10.838 99.193 1570 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.90 % Favored : 94.93 % Rotamer: Outliers : 5.07 % Allowed : 22.57 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.26), residues: 1144 helix: -3.23 (1.51), residues: 12 sheet: 1.01 (0.23), residues: 514 loop : -1.17 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 544 HIS 0.003 0.001 HIS A 146 PHE 0.009 0.001 PHE A 245 TYR 0.012 0.001 TYR A 161 ARG 0.002 0.000 ARG B 480 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2258.18 seconds wall clock time: 42 minutes 14.08 seconds (2534.08 seconds total)