Starting phenix.real_space_refine on Sat Aug 23 10:36:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yg6_39237/08_2025/8yg6_39237.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yg6_39237/08_2025/8yg6_39237.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yg6_39237/08_2025/8yg6_39237.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yg6_39237/08_2025/8yg6_39237.map" model { file = "/net/cci-nas-00/data/ceres_data/8yg6_39237/08_2025/8yg6_39237.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yg6_39237/08_2025/8yg6_39237.cif" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 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 87 5.16 5 C 7101 2.51 5 N 1968 2.21 5 O 2286 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11442 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3730 Classifications: {'peptide': 465} Link IDs: {'PTRANS': 12, 'TRANS': 452} Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: B, C, E, F Time building chain proxies: 3.32, per 1000 atoms: 0.29 Number of scatterers: 11442 At special positions: 0 Unit cell: (100.8, 99.84, 155.52, 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 87 16.00 O 2286 8.00 N 1968 7.00 C 7101 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 24 " - pdb=" SG CYS B 372 " distance=2.22 Simple disulfide: pdb=" SG CYS A 111 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 158 " distance=2.03 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 184 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS A 262 " - pdb=" SG CYS A 267 " distance=2.04 Simple disulfide: pdb=" SG CYS A 372 " - pdb=" SG CYS C 24 " distance=2.25 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 402 " distance=2.03 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS C 372 " distance=2.23 Simple disulfide: pdb=" SG CYS B 111 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 111 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 158 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 158 " distance=2.03 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 184 " distance=2.03 Simple disulfide: pdb=" SG CYS C 177 " - pdb=" SG CYS C 184 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 262 " - pdb=" SG CYS B 267 " distance=2.04 Simple disulfide: pdb=" SG CYS C 262 " - pdb=" SG CYS C 267 " distance=2.04 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 402 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 402 " 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " NAG D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " NAG E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " NAG F 3 " NAG-ASN " NAG A 501 " - " ASN A 197 " " NAG A 502 " - " ASN A 384 " " NAG A 503 " - " ASN A 426 " " NAG B 501 " - " ASN B 197 " " NAG B 502 " - " ASN B 384 " " NAG B 503 " - " ASN B 426 " " NAG C 501 " - " ASN C 197 " " NAG C 502 " - " ASN C 384 " " NAG C 503 " - " ASN C 426 " " NAG D 1 " - " ASN A 354 " " NAG E 1 " - " ASN B 354 " " NAG F 1 " - " ASN C 354 " Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 407.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2640 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 21 sheets defined 22.8% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 98 through 109 Processing helix chain 'A' and resid 126 through 130 removed outlier: 3.531A pdb=" N ARG A 130 " --> pdb=" O ASP A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 342 removed outlier: 3.582A pdb=" N LEU A 302 " --> pdb=" O THR A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 353 Processing helix chain 'A' and resid 439 through 456 removed outlier: 5.273A pdb=" N SER A 447 " --> pdb=" O ALA A 443 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ASN A 448 " --> pdb=" O GLN A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 487 removed outlier: 4.459A pdb=" N GLU A 473 " --> pdb=" O THR A 469 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU A 475 " --> pdb=" O MET A 471 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU A 476 " --> pdb=" O ALA A 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 109 Processing helix chain 'B' and resid 126 through 130 removed outlier: 3.530A pdb=" N ARG B 130 " --> pdb=" O ASP B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 342 removed outlier: 3.582A pdb=" N LEU B 302 " --> pdb=" O THR B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 353 Processing helix chain 'B' and resid 439 through 456 removed outlier: 5.272A pdb=" N SER B 447 " --> pdb=" O ALA B 443 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ASN B 448 " --> pdb=" O GLN B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 487 removed outlier: 4.459A pdb=" N GLU B 473 " --> pdb=" O THR B 469 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU B 475 " --> pdb=" O MET B 471 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU B 476 " --> pdb=" O ALA B 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 109 Processing helix chain 'C' and resid 126 through 130 removed outlier: 3.530A pdb=" N ARG C 130 " --> pdb=" O ASP C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 342 removed outlier: 3.582A pdb=" N LEU C 302 " --> pdb=" O THR C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 353 Processing helix chain 'C' and resid 439 through 456 removed outlier: 5.273A pdb=" N SER C 447 " --> pdb=" O ALA C 443 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ASN C 448 " --> pdb=" O GLN C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 487 removed outlier: 4.459A pdb=" N GLU C 473 " --> pdb=" O THR C 469 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU C 475 " --> pdb=" O MET C 471 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N LEU C 476 " --> pdb=" O ALA C 472 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 219 through 226 removed outlier: 3.863A pdb=" N ILE A 268 " --> pdb=" O ASN A 261 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN A 261 " --> pdb=" O ILE A 268 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 168 Processing sheet with id=AA3, first strand: chain 'A' and resid 88 through 95 removed outlier: 4.341A pdb=" N LYS A 69 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N CYS A 158 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG A 120 " --> pdb=" O CYS A 158 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N LYS A 160 " --> pdb=" O ILE A 118 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ILE A 118 " --> pdb=" O LYS A 160 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 173 through 177 Processing sheet with id=AA5, first strand: chain 'A' and resid 228 through 232 Processing sheet with id=AA6, first strand: chain 'A' and resid 357 through 361 Processing sheet with id=AA7, first strand: chain 'A' and resid 386 through 389 Processing sheet with id=AA8, first strand: chain 'B' and resid 219 through 226 removed outlier: 3.863A pdb=" N ILE B 268 " --> pdb=" O ASN B 261 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN B 261 " --> pdb=" O ILE B 268 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 166 through 168 Processing sheet with id=AB1, first strand: chain 'B' and resid 88 through 95 removed outlier: 4.342A pdb=" N LYS B 69 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N CYS B 158 " --> pdb=" O ARG B 120 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG B 120 " --> pdb=" O CYS B 158 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N LYS B 160 " --> pdb=" O ILE B 118 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ILE B 118 " --> pdb=" O LYS B 160 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 173 through 177 Processing sheet with id=AB3, first strand: chain 'B' and resid 228 through 232 Processing sheet with id=AB4, first strand: chain 'B' and resid 357 through 361 Processing sheet with id=AB5, first strand: chain 'B' and resid 386 through 389 Processing sheet with id=AB6, first strand: chain 'C' and resid 219 through 226 removed outlier: 3.863A pdb=" N ILE C 268 " --> pdb=" O ASN C 261 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN C 261 " --> pdb=" O ILE C 268 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 166 through 168 Processing sheet with id=AB8, first strand: chain 'C' and resid 88 through 95 removed outlier: 4.340A pdb=" N LYS C 69 " --> pdb=" O LEU C 95 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N CYS C 158 " --> pdb=" O ARG C 120 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG C 120 " --> pdb=" O CYS C 158 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N LYS C 160 " --> pdb=" O ILE C 118 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ILE C 118 " --> pdb=" O LYS C 160 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 173 through 177 Processing sheet with id=AC1, first strand: chain 'C' and resid 228 through 232 Processing sheet with id=AC2, first strand: chain 'C' and resid 357 through 361 Processing sheet with id=AC3, first strand: chain 'C' and resid 386 through 389 393 hydrogen bonds defined for protein. 1125 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.74 Time building geometry restraints manager: 1.36 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: 3794 1.34 - 1.47: 2697 1.47 - 1.59: 5041 1.59 - 1.72: 0 1.72 - 1.84: 132 Bond restraints: 11664 Sorted by residual: bond pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta sigma weight residual 1.453 1.487 -0.034 9.20e-03 1.18e+04 1.37e+01 bond pdb=" N ASP C 83 " pdb=" CA ASP C 83 " ideal model delta sigma weight residual 1.453 1.487 -0.034 9.20e-03 1.18e+04 1.36e+01 bond pdb=" N ASP A 83 " pdb=" CA ASP A 83 " ideal model delta sigma weight residual 1.453 1.487 -0.034 9.20e-03 1.18e+04 1.35e+01 bond pdb=" N VAL C 88 " pdb=" CA VAL C 88 " ideal model delta sigma weight residual 1.464 1.494 -0.031 1.13e-02 7.83e+03 7.33e+00 bond pdb=" N VAL A 88 " pdb=" CA VAL A 88 " ideal model delta sigma weight residual 1.464 1.494 -0.030 1.13e-02 7.83e+03 7.24e+00 ... (remaining 11659 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 15147 1.48 - 2.95: 514 2.95 - 4.43: 77 4.43 - 5.90: 21 5.90 - 7.38: 18 Bond angle restraints: 15777 Sorted by residual: angle pdb=" C LYS A 290 " pdb=" CA LYS A 290 " pdb=" CB LYS A 290 " ideal model delta sigma weight residual 116.54 109.87 6.67 1.15e+00 7.56e-01 3.37e+01 angle pdb=" C LYS C 290 " pdb=" CA LYS C 290 " pdb=" CB LYS C 290 " ideal model delta sigma weight residual 116.54 109.88 6.66 1.15e+00 7.56e-01 3.36e+01 angle pdb=" C LYS B 290 " pdb=" CA LYS B 290 " pdb=" CB LYS B 290 " ideal model delta sigma weight residual 116.54 109.91 6.63 1.15e+00 7.56e-01 3.32e+01 angle pdb=" N PRO B 84 " pdb=" CA PRO B 84 " pdb=" C PRO B 84 " ideal model delta sigma weight residual 114.27 108.24 6.03 1.35e+00 5.49e-01 1.99e+01 angle pdb=" N PRO C 84 " pdb=" CA PRO C 84 " pdb=" C PRO C 84 " ideal model delta sigma weight residual 114.27 108.25 6.02 1.35e+00 5.49e-01 1.99e+01 ... (remaining 15772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.12: 6822 21.12 - 42.24: 354 42.24 - 63.37: 72 63.37 - 84.49: 48 84.49 - 105.61: 36 Dihedral angle restraints: 7332 sinusoidal: 3252 harmonic: 4080 Sorted by residual: dihedral pdb=" CB CYS A 24 " pdb=" SG CYS A 24 " pdb=" SG CYS B 372 " pdb=" CB CYS B 372 " ideal model delta sinusoidal sigma weight residual 93.00 13.84 79.16 1 1.00e+01 1.00e-02 7.79e+01 dihedral pdb=" CB CYS A 372 " pdb=" SG CYS A 372 " pdb=" SG CYS C 24 " pdb=" CB CYS C 24 " ideal model delta sinusoidal sigma weight residual 93.00 13.90 79.10 1 1.00e+01 1.00e-02 7.78e+01 dihedral pdb=" CB CYS B 24 " pdb=" SG CYS B 24 " pdb=" SG CYS C 372 " pdb=" CB CYS C 372 " ideal model delta sinusoidal sigma weight residual 93.00 13.94 79.06 1 1.00e+01 1.00e-02 7.78e+01 ... (remaining 7329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1451 0.053 - 0.107: 249 0.107 - 0.160: 69 0.160 - 0.213: 7 0.213 - 0.267: 6 Chirality restraints: 1782 Sorted by residual: chirality pdb=" CA ASN C 85 " pdb=" N ASN C 85 " pdb=" C ASN C 85 " pdb=" CB ASN C 85 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CA ASN A 85 " pdb=" N ASN A 85 " pdb=" C ASN A 85 " pdb=" CB ASN A 85 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA ASN B 85 " pdb=" N ASN B 85 " pdb=" C ASN B 85 " pdb=" CB ASN B 85 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 1779 not shown) Planarity restraints: 2031 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 87 " -1.039 9.50e-02 1.11e+02 4.66e-01 1.31e+02 pdb=" NE ARG C 87 " 0.062 2.00e-02 2.50e+03 pdb=" CZ ARG C 87 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG C 87 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG C 87 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 87 " 1.038 9.50e-02 1.11e+02 4.65e-01 1.31e+02 pdb=" NE ARG A 87 " -0.062 2.00e-02 2.50e+03 pdb=" CZ ARG A 87 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 87 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 87 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 87 " -1.038 9.50e-02 1.11e+02 4.65e-01 1.31e+02 pdb=" NE ARG B 87 " 0.062 2.00e-02 2.50e+03 pdb=" CZ ARG B 87 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 87 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 87 " -0.022 2.00e-02 2.50e+03 ... (remaining 2028 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 370 2.70 - 3.25: 10658 3.25 - 3.80: 16642 3.80 - 4.35: 20506 4.35 - 4.90: 35964 Nonbonded interactions: 84140 Sorted by model distance: nonbonded pdb=" ND2 ASN A 236 " pdb=" OE1 GLN B 48 " model vdw 2.151 3.120 nonbonded pdb=" OG SER A 440 " pdb=" OE2 GLU C 346 " model vdw 2.152 3.040 nonbonded pdb=" OE2 GLU A 346 " pdb=" OG SER B 440 " model vdw 2.157 3.040 nonbonded pdb=" OE2 GLU B 346 " pdb=" OG SER C 440 " model vdw 2.163 3.040 nonbonded pdb=" ND2 ASN B 236 " pdb=" OE1 GLN C 48 " model vdw 2.166 3.120 ... (remaining 84135 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 12.540 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:6.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 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 : 0.005 0.222 11703 Z= 0.265 Angle : 0.686 7.380 15873 Z= 0.395 Chirality : 0.046 0.267 1782 Planarity : 0.023 0.466 2019 Dihedral : 16.651 105.611 4629 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 0.24 % Allowed : 0.95 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.22), residues: 1389 helix: 2.75 (0.31), residues: 315 sheet: -0.19 (0.28), residues: 315 loop : -1.84 (0.19), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 288 TYR 0.012 0.001 TYR B 383 PHE 0.010 0.001 PHE B 485 TRP 0.013 0.001 TRP C 121 HIS 0.005 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00344 (11664) covalent geometry : angle 0.66326 (15777) SS BOND : bond 0.07715 ( 21) SS BOND : angle 2.83616 ( 42) hydrogen bonds : bond 0.17919 ( 393) hydrogen bonds : angle 6.85319 ( 1125) link_BETA1-4 : bond 0.01130 ( 6) link_BETA1-4 : angle 2.27448 ( 18) link_NAG-ASN : bond 0.00408 ( 12) link_NAG-ASN : angle 1.66368 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 93 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: A 104 MET cc_start: 0.8906 (tpt) cc_final: 0.8575 (tpt) REVERT: A 484 MET cc_start: 0.4615 (mmt) cc_final: 0.4397 (ttt) REVERT: B 104 MET cc_start: 0.8781 (tpt) cc_final: 0.8377 (tpt) REVERT: B 364 ASP cc_start: 0.8497 (p0) cc_final: 0.8135 (p0) REVERT: B 484 MET cc_start: 0.5848 (mmt) cc_final: 0.5497 (ttt) REVERT: C 104 MET cc_start: 0.9230 (tpt) cc_final: 0.8971 (tpt) outliers start: 3 outliers final: 0 residues processed: 96 average time/residue: 0.7577 time to fit residues: 77.3748 Evaluate side-chains 63 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.0000 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN B 85 ASN C 85 ASN C 245 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.070405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.060004 restraints weight = 46121.101| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 3.79 r_work: 0.2899 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11703 Z= 0.210 Angle : 0.675 7.878 15873 Z= 0.341 Chirality : 0.047 0.250 1782 Planarity : 0.004 0.078 2019 Dihedral : 13.048 87.225 1875 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 0.87 % Allowed : 6.10 % Favored : 93.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.21), residues: 1389 helix: 2.36 (0.30), residues: 318 sheet: -0.08 (0.26), residues: 360 loop : -2.06 (0.19), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 284 TYR 0.016 0.002 TYR A 383 PHE 0.030 0.002 PHE C 485 TRP 0.011 0.001 TRP B 439 HIS 0.009 0.002 HIS C 23 Details of bonding type rmsd covalent geometry : bond 0.00479 (11664) covalent geometry : angle 0.65753 (15777) SS BOND : bond 0.00613 ( 21) SS BOND : angle 1.39882 ( 42) hydrogen bonds : bond 0.06735 ( 393) hydrogen bonds : angle 5.23532 ( 1125) link_BETA1-4 : bond 0.00753 ( 6) link_BETA1-4 : angle 3.34930 ( 18) link_NAG-ASN : bond 0.00450 ( 12) link_NAG-ASN : angle 1.85537 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: A 104 MET cc_start: 0.9415 (tpt) cc_final: 0.9165 (tpt) REVERT: A 484 MET cc_start: 0.5281 (mmt) cc_final: 0.5021 (tpt) REVERT: B 364 ASP cc_start: 0.9067 (p0) cc_final: 0.8706 (p0) REVERT: B 484 MET cc_start: 0.6367 (mmt) cc_final: 0.5717 (ttt) outliers start: 11 outliers final: 3 residues processed: 69 average time/residue: 0.7116 time to fit residues: 52.9497 Evaluate side-chains 64 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 MET Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain C residue 476 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 21 optimal weight: 0.0060 chunk 135 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 overall best weight: 2.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 HIS B 335 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.070179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.059670 restraints weight = 45428.684| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 3.88 r_work: 0.2857 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 11703 Z= 0.247 Angle : 0.682 8.553 15873 Z= 0.352 Chirality : 0.046 0.205 1782 Planarity : 0.004 0.054 2019 Dihedral : 11.168 78.072 1875 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 1.66 % Allowed : 8.71 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.21), residues: 1389 helix: 2.11 (0.30), residues: 318 sheet: 0.31 (0.27), residues: 321 loop : -2.26 (0.18), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 87 TYR 0.023 0.002 TYR B 383 PHE 0.021 0.002 PHE C 485 TRP 0.013 0.001 TRP C 121 HIS 0.009 0.002 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00572 (11664) covalent geometry : angle 0.65789 (15777) SS BOND : bond 0.00729 ( 21) SS BOND : angle 1.72853 ( 42) hydrogen bonds : bond 0.07994 ( 393) hydrogen bonds : angle 5.30360 ( 1125) link_BETA1-4 : bond 0.01383 ( 6) link_BETA1-4 : angle 4.09530 ( 18) link_NAG-ASN : bond 0.00375 ( 12) link_NAG-ASN : angle 1.89546 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 62 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: A 104 MET cc_start: 0.9403 (tpt) cc_final: 0.9182 (tpt) REVERT: B 291 TYR cc_start: 0.5905 (OUTLIER) cc_final: 0.5488 (p90) REVERT: B 364 ASP cc_start: 0.9154 (p0) cc_final: 0.8806 (p0) REVERT: B 484 MET cc_start: 0.6179 (mmt) cc_final: 0.5565 (ttt) REVERT: C 87 ARG cc_start: 0.8177 (pmm-80) cc_final: 0.7861 (pmm-80) REVERT: C 104 MET cc_start: 0.9591 (tpt) cc_final: 0.9371 (tpt) outliers start: 21 outliers final: 7 residues processed: 75 average time/residue: 0.6108 time to fit residues: 49.9035 Evaluate side-chains 69 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 476 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 28 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 70 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 22 optimal weight: 0.2980 chunk 7 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 102 optimal weight: 0.3980 chunk 79 optimal weight: 0.8980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 HIS ** 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 = 0.3272 r_free = 0.3272 target = 0.072141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.061730 restraints weight = 44308.286| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 3.84 r_work: 0.2888 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11703 Z= 0.122 Angle : 0.599 8.891 15873 Z= 0.300 Chirality : 0.044 0.258 1782 Planarity : 0.003 0.033 2019 Dihedral : 9.579 66.641 1875 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 0.87 % Allowed : 10.85 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.21), residues: 1389 helix: 2.44 (0.31), residues: 318 sheet: 0.53 (0.28), residues: 306 loop : -2.14 (0.18), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 87 TYR 0.014 0.001 TYR A 383 PHE 0.023 0.001 PHE C 485 TRP 0.017 0.001 TRP C 121 HIS 0.005 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00263 (11664) covalent geometry : angle 0.57594 (15777) SS BOND : bond 0.00407 ( 21) SS BOND : angle 1.92224 ( 42) hydrogen bonds : bond 0.06421 ( 393) hydrogen bonds : angle 4.93225 ( 1125) link_BETA1-4 : bond 0.01076 ( 6) link_BETA1-4 : angle 3.41456 ( 18) link_NAG-ASN : bond 0.00426 ( 12) link_NAG-ASN : angle 1.57382 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.412 Fit side-chains REVERT: B 291 TYR cc_start: 0.5885 (OUTLIER) cc_final: 0.5413 (p90) REVERT: B 364 ASP cc_start: 0.9095 (p0) cc_final: 0.8709 (p0) REVERT: B 484 MET cc_start: 0.6257 (mmt) cc_final: 0.5722 (ttt) outliers start: 11 outliers final: 4 residues processed: 70 average time/residue: 0.5103 time to fit residues: 39.1351 Evaluate side-chains 65 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 476 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 113 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 37 optimal weight: 0.0670 chunk 34 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 133 optimal weight: 0.3980 chunk 89 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 HIS ** 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 = 0.3273 r_free = 0.3273 target = 0.070406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.059848 restraints weight = 44806.305| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 3.89 r_work: 0.2907 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11703 Z= 0.118 Angle : 0.576 9.907 15873 Z= 0.284 Chirality : 0.043 0.238 1782 Planarity : 0.002 0.030 2019 Dihedral : 7.770 55.273 1875 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 1.27 % Allowed : 11.64 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.21), residues: 1389 helix: 2.49 (0.31), residues: 321 sheet: 0.64 (0.27), residues: 321 loop : -2.05 (0.18), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 87 TYR 0.014 0.001 TYR B 383 PHE 0.015 0.001 PHE B 485 TRP 0.014 0.001 TRP C 121 HIS 0.004 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00257 (11664) covalent geometry : angle 0.55320 (15777) SS BOND : bond 0.00361 ( 21) SS BOND : angle 1.47106 ( 42) hydrogen bonds : bond 0.05817 ( 393) hydrogen bonds : angle 4.78524 ( 1125) link_BETA1-4 : bond 0.01262 ( 6) link_BETA1-4 : angle 3.80024 ( 18) link_NAG-ASN : bond 0.00358 ( 12) link_NAG-ASN : angle 1.54746 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.509 Fit side-chains revert: symmetry clash REVERT: A 121 TRP cc_start: 0.8296 (m100) cc_final: 0.7998 (m100) REVERT: B 121 TRP cc_start: 0.8206 (m100) cc_final: 0.7906 (m100) REVERT: B 291 TYR cc_start: 0.5772 (OUTLIER) cc_final: 0.5353 (p90) REVERT: B 364 ASP cc_start: 0.9047 (p0) cc_final: 0.8676 (p0) REVERT: B 484 MET cc_start: 0.6086 (mmt) cc_final: 0.5560 (ttt) REVERT: C 192 GLU cc_start: 0.8871 (mp0) cc_final: 0.8648 (mp0) outliers start: 16 outliers final: 5 residues processed: 77 average time/residue: 0.5454 time to fit residues: 45.8569 Evaluate side-chains 71 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain C residue 164 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 129 optimal weight: 0.0270 chunk 131 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 68 optimal weight: 0.4980 chunk 117 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 1 optimal weight: 0.4980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.070989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.060394 restraints weight = 44594.966| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.88 r_work: 0.2930 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11703 Z= 0.106 Angle : 0.567 10.015 15873 Z= 0.276 Chirality : 0.042 0.204 1782 Planarity : 0.002 0.029 2019 Dihedral : 6.582 54.274 1875 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 1.58 % Allowed : 11.72 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.22), residues: 1389 helix: 2.60 (0.31), residues: 321 sheet: 0.77 (0.27), residues: 321 loop : -2.01 (0.18), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 87 TYR 0.012 0.001 TYR B 383 PHE 0.014 0.001 PHE C 485 TRP 0.014 0.001 TRP C 121 HIS 0.003 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00225 (11664) covalent geometry : angle 0.54509 (15777) SS BOND : bond 0.00313 ( 21) SS BOND : angle 1.10164 ( 42) hydrogen bonds : bond 0.05382 ( 393) hydrogen bonds : angle 4.67605 ( 1125) link_BETA1-4 : bond 0.01307 ( 6) link_BETA1-4 : angle 3.92264 ( 18) link_NAG-ASN : bond 0.00394 ( 12) link_NAG-ASN : angle 1.50611 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 0.531 Fit side-chains revert: symmetry clash REVERT: A 121 TRP cc_start: 0.8422 (m100) cc_final: 0.8155 (m100) REVERT: A 291 TYR cc_start: 0.6966 (OUTLIER) cc_final: 0.5691 (p90) REVERT: B 121 TRP cc_start: 0.8188 (m100) cc_final: 0.7925 (m100) REVERT: B 291 TYR cc_start: 0.5822 (OUTLIER) cc_final: 0.5424 (p90) REVERT: B 364 ASP cc_start: 0.9085 (p0) cc_final: 0.8700 (p0) REVERT: B 484 MET cc_start: 0.6214 (mmt) cc_final: 0.5696 (ttt) REVERT: C 87 ARG cc_start: 0.8261 (pmm-80) cc_final: 0.7891 (pmm-80) REVERT: C 192 GLU cc_start: 0.8828 (mp0) cc_final: 0.8594 (mp0) REVERT: C 484 MET cc_start: 0.7048 (OUTLIER) cc_final: 0.6637 (tpp) REVERT: C 487 HIS cc_start: 0.5012 (OUTLIER) cc_final: 0.4232 (t-170) outliers start: 20 outliers final: 8 residues processed: 84 average time/residue: 0.5372 time to fit residues: 49.5630 Evaluate side-chains 76 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 484 MET Chi-restraints excluded: chain C residue 487 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 90 optimal weight: 7.9990 chunk 120 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 23 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.067654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.057362 restraints weight = 45622.429| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 3.84 r_work: 0.2823 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 11703 Z= 0.252 Angle : 0.704 10.858 15873 Z= 0.355 Chirality : 0.046 0.182 1782 Planarity : 0.003 0.033 2019 Dihedral : 6.183 59.987 1875 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 2.06 % Allowed : 11.88 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.21), residues: 1389 helix: 2.37 (0.31), residues: 300 sheet: 0.67 (0.27), residues: 318 loop : -2.34 (0.18), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 288 TYR 0.023 0.002 TYR B 383 PHE 0.007 0.001 PHE A 405 TRP 0.008 0.001 TRP A 121 HIS 0.006 0.001 HIS C 285 Details of bonding type rmsd covalent geometry : bond 0.00582 (11664) covalent geometry : angle 0.66948 (15777) SS BOND : bond 0.00845 ( 21) SS BOND : angle 2.20175 ( 42) hydrogen bonds : bond 0.07623 ( 393) hydrogen bonds : angle 5.11239 ( 1125) link_BETA1-4 : bond 0.01561 ( 6) link_BETA1-4 : angle 5.01306 ( 18) link_NAG-ASN : bond 0.00428 ( 12) link_NAG-ASN : angle 1.98949 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 63 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: A 121 TRP cc_start: 0.8309 (m100) cc_final: 0.7931 (m100) REVERT: A 291 TYR cc_start: 0.7390 (OUTLIER) cc_final: 0.6376 (p90) REVERT: A 303 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.8233 (mtt) REVERT: B 291 TYR cc_start: 0.6360 (OUTLIER) cc_final: 0.5811 (p90) REVERT: B 364 ASP cc_start: 0.9122 (p0) cc_final: 0.8787 (p0) REVERT: B 484 MET cc_start: 0.6081 (mmt) cc_final: 0.5629 (ttt) REVERT: C 192 GLU cc_start: 0.8949 (mp0) cc_final: 0.8411 (pm20) REVERT: C 291 TYR cc_start: 0.7029 (OUTLIER) cc_final: 0.6065 (p90) outliers start: 26 outliers final: 13 residues processed: 81 average time/residue: 0.5020 time to fit residues: 44.5227 Evaluate side-chains 78 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 291 TYR Chi-restraints excluded: chain C residue 476 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 34 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.069489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.059057 restraints weight = 44813.451| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 3.84 r_work: 0.2868 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11703 Z= 0.130 Angle : 0.598 11.274 15873 Z= 0.298 Chirality : 0.042 0.148 1782 Planarity : 0.002 0.031 2019 Dihedral : 5.684 56.270 1875 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 1.66 % Allowed : 12.67 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.21), residues: 1389 helix: 2.29 (0.30), residues: 321 sheet: 0.60 (0.27), residues: 321 loop : -2.19 (0.18), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 288 TYR 0.014 0.001 TYR A 383 PHE 0.011 0.001 PHE A 153 TRP 0.021 0.001 TRP B 121 HIS 0.003 0.001 HIS B 23 Details of bonding type rmsd covalent geometry : bond 0.00287 (11664) covalent geometry : angle 0.57104 (15777) SS BOND : bond 0.00438 ( 21) SS BOND : angle 1.65585 ( 42) hydrogen bonds : bond 0.06371 ( 393) hydrogen bonds : angle 4.86692 ( 1125) link_BETA1-4 : bond 0.01562 ( 6) link_BETA1-4 : angle 4.26364 ( 18) link_NAG-ASN : bond 0.00477 ( 12) link_NAG-ASN : angle 1.53712 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 121 TRP cc_start: 0.8399 (m100) cc_final: 0.8149 (m100) REVERT: A 291 TYR cc_start: 0.7264 (OUTLIER) cc_final: 0.6187 (p90) REVERT: A 303 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.8028 (mtt) REVERT: B 121 TRP cc_start: 0.8222 (m100) cc_final: 0.8005 (m100) REVERT: B 291 TYR cc_start: 0.6283 (OUTLIER) cc_final: 0.5747 (p90) REVERT: B 364 ASP cc_start: 0.9101 (p0) cc_final: 0.8735 (p0) REVERT: B 484 MET cc_start: 0.6192 (mmt) cc_final: 0.5633 (ttt) REVERT: C 87 ARG cc_start: 0.8248 (pmm-80) cc_final: 0.7849 (pmm-80) REVERT: C 192 GLU cc_start: 0.8932 (mp0) cc_final: 0.8383 (pm20) REVERT: C 291 TYR cc_start: 0.7017 (OUTLIER) cc_final: 0.6010 (p90) outliers start: 21 outliers final: 10 residues processed: 81 average time/residue: 0.4564 time to fit residues: 40.5774 Evaluate side-chains 79 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 291 TYR Chi-restraints excluded: chain C residue 476 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 64 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 2 optimal weight: 0.3980 chunk 95 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.069918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.059492 restraints weight = 44469.585| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 3.84 r_work: 0.2894 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11703 Z= 0.123 Angle : 0.594 11.750 15873 Z= 0.292 Chirality : 0.042 0.147 1782 Planarity : 0.003 0.033 2019 Dihedral : 5.281 54.730 1875 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 1.35 % Allowed : 13.30 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.22), residues: 1389 helix: 2.43 (0.31), residues: 321 sheet: 0.73 (0.27), residues: 321 loop : -2.10 (0.18), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 288 TYR 0.014 0.001 TYR B 383 PHE 0.008 0.001 PHE C 483 TRP 0.016 0.001 TRP B 121 HIS 0.003 0.001 HIS C 487 Details of bonding type rmsd covalent geometry : bond 0.00271 (11664) covalent geometry : angle 0.56926 (15777) SS BOND : bond 0.00385 ( 21) SS BOND : angle 1.41947 ( 42) hydrogen bonds : bond 0.05891 ( 393) hydrogen bonds : angle 4.78555 ( 1125) link_BETA1-4 : bond 0.01512 ( 6) link_BETA1-4 : angle 4.21570 ( 18) link_NAG-ASN : bond 0.00414 ( 12) link_NAG-ASN : angle 1.50037 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.560 Fit side-chains revert: symmetry clash REVERT: A 121 TRP cc_start: 0.8341 (m100) cc_final: 0.8057 (m100) REVERT: A 291 TYR cc_start: 0.7241 (OUTLIER) cc_final: 0.6207 (p90) REVERT: B 121 TRP cc_start: 0.8185 (m100) cc_final: 0.7932 (m100) REVERT: B 291 TYR cc_start: 0.6150 (OUTLIER) cc_final: 0.5538 (p90) REVERT: B 364 ASP cc_start: 0.9069 (p0) cc_final: 0.8719 (p0) REVERT: B 484 MET cc_start: 0.6062 (mmt) cc_final: 0.5589 (ttt) REVERT: C 87 ARG cc_start: 0.8216 (pmm-80) cc_final: 0.7855 (pmm-80) REVERT: C 192 GLU cc_start: 0.8891 (mp0) cc_final: 0.8329 (pm20) REVERT: C 291 TYR cc_start: 0.6948 (OUTLIER) cc_final: 0.6102 (p90) REVERT: C 484 MET cc_start: 0.6807 (mmp) cc_final: 0.5749 (ptt) outliers start: 17 outliers final: 9 residues processed: 79 average time/residue: 0.5141 time to fit residues: 44.5724 Evaluate side-chains 76 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 291 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 97 optimal weight: 7.9990 chunk 19 optimal weight: 0.5980 chunk 112 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 60 optimal weight: 0.2980 chunk 61 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.069088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.058977 restraints weight = 45969.107| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 3.80 r_work: 0.2856 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11703 Z= 0.170 Angle : 0.619 10.600 15873 Z= 0.310 Chirality : 0.043 0.147 1782 Planarity : 0.003 0.030 2019 Dihedral : 5.488 58.293 1875 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 1.27 % Allowed : 13.62 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.21), residues: 1389 helix: 2.54 (0.31), residues: 303 sheet: 0.66 (0.27), residues: 321 loop : -2.23 (0.18), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 288 TYR 0.017 0.001 TYR A 383 PHE 0.008 0.001 PHE B 485 TRP 0.015 0.001 TRP B 121 HIS 0.004 0.001 HIS C 285 Details of bonding type rmsd covalent geometry : bond 0.00392 (11664) covalent geometry : angle 0.59227 (15777) SS BOND : bond 0.00453 ( 21) SS BOND : angle 1.69022 ( 42) hydrogen bonds : bond 0.06505 ( 393) hydrogen bonds : angle 4.87559 ( 1125) link_BETA1-4 : bond 0.01511 ( 6) link_BETA1-4 : angle 4.30470 ( 18) link_NAG-ASN : bond 0.00421 ( 12) link_NAG-ASN : angle 1.67117 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.489 Fit side-chains revert: symmetry clash REVERT: A 121 TRP cc_start: 0.8438 (m100) cc_final: 0.8155 (m100) REVERT: A 291 TYR cc_start: 0.7370 (OUTLIER) cc_final: 0.6421 (p90) REVERT: A 303 MET cc_start: 0.8367 (mpp) cc_final: 0.8062 (mtt) REVERT: B 121 TRP cc_start: 0.8227 (m100) cc_final: 0.7994 (m100) REVERT: B 291 TYR cc_start: 0.6498 (OUTLIER) cc_final: 0.5804 (p90) REVERT: B 364 ASP cc_start: 0.9096 (p0) cc_final: 0.8760 (p0) REVERT: B 484 MET cc_start: 0.6234 (mmt) cc_final: 0.5773 (ttt) REVERT: C 87 ARG cc_start: 0.8253 (pmm-80) cc_final: 0.7939 (pmm-80) REVERT: C 192 GLU cc_start: 0.8883 (mp0) cc_final: 0.8325 (pm20) REVERT: C 291 TYR cc_start: 0.7024 (OUTLIER) cc_final: 0.6094 (p90) REVERT: C 484 MET cc_start: 0.6963 (mmp) cc_final: 0.6663 (tpp) outliers start: 16 outliers final: 10 residues processed: 79 average time/residue: 0.5469 time to fit residues: 47.5090 Evaluate side-chains 78 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 291 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 23 optimal weight: 0.4980 chunk 39 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.069166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.058792 restraints weight = 45117.224| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 3.87 r_work: 0.2857 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11703 Z= 0.154 Angle : 0.613 10.889 15873 Z= 0.305 Chirality : 0.043 0.149 1782 Planarity : 0.003 0.040 2019 Dihedral : 5.429 57.400 1875 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 1.58 % Allowed : 13.38 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.21), residues: 1389 helix: 2.54 (0.31), residues: 303 sheet: 0.61 (0.27), residues: 321 loop : -2.23 (0.18), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 288 TYR 0.015 0.001 TYR A 383 PHE 0.009 0.001 PHE B 485 TRP 0.017 0.001 TRP B 121 HIS 0.003 0.001 HIS C 285 Details of bonding type rmsd covalent geometry : bond 0.00353 (11664) covalent geometry : angle 0.58802 (15777) SS BOND : bond 0.00430 ( 21) SS BOND : angle 1.58362 ( 42) hydrogen bonds : bond 0.06438 ( 393) hydrogen bonds : angle 4.88309 ( 1125) link_BETA1-4 : bond 0.01534 ( 6) link_BETA1-4 : angle 4.18417 ( 18) link_NAG-ASN : bond 0.00439 ( 12) link_NAG-ASN : angle 1.58713 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3499.24 seconds wall clock time: 60 minutes 31.35 seconds (3631.35 seconds total)