Starting phenix.real_space_refine on Wed May 14 06:56:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yg6_39237/05_2025/8yg6_39237.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yg6_39237/05_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_39237/05_2025/8yg6_39237.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yg6_39237/05_2025/8yg6_39237.map" model { file = "/net/cci-nas-00/data/ceres_data/8yg6_39237/05_2025/8yg6_39237.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yg6_39237/05_2025/8yg6_39237.cif" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: "E" 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: D, F, C, B Time building chain proxies: 8.09, per 1000 atoms: 0.71 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 C 111 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 111 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 158 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 158 " distance=2.03 Simple disulfide: pdb=" SG CYS C 177 " - pdb=" SG CYS C 184 " distance=2.03 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 184 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS C 262 " - pdb=" SG CYS C 267 " distance=2.04 Simple disulfide: pdb=" SG CYS B 262 " - pdb=" SG CYS B 267 " distance=2.04 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 402 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 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: 3.16 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.25 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: 3.35 Time building geometry restraints manager: 3.62 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: 0.08 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 3.890 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: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 29.030 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.340 ------------------------------------------------------------------------------- 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 (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: -0.49 (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 TRP 0.013 0.001 TRP C 121 HIS 0.005 0.001 HIS B 285 PHE 0.010 0.001 PHE B 485 TYR 0.012 0.001 TYR B 383 ARG 0.004 0.000 ARG B 288 Details of bonding type rmsd link_NAG-ASN : bond 0.00408 ( 12) link_NAG-ASN : angle 1.66368 ( 36) link_BETA1-4 : bond 0.01130 ( 6) link_BETA1-4 : angle 2.27448 ( 18) hydrogen bonds : bond 0.17919 ( 393) hydrogen bonds : angle 6.85319 ( 1125) SS BOND : bond 0.07715 ( 21) SS BOND : angle 2.83616 ( 42) covalent geometry : bond 0.00344 (11664) covalent geometry : angle 0.66326 (15777) *********************** 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 : 1.396 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: 1.5681 time to fit residues: 161.1820 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 : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 41 optimal weight: 0.5980 chunk 65 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 125 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.071912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.061035 restraints weight = 44571.500| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 3.87 r_work: 0.2961 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11703 Z= 0.149 Angle : 0.617 7.105 15873 Z= 0.309 Chirality : 0.045 0.235 1782 Planarity : 0.004 0.061 2019 Dihedral : 13.493 89.715 1875 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 0.71 % Allowed : 6.02 % Favored : 93.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.22), residues: 1389 helix: 2.63 (0.30), residues: 318 sheet: 0.42 (0.28), residues: 324 loop : -1.93 (0.19), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 121 HIS 0.008 0.001 HIS C 23 PHE 0.032 0.002 PHE C 485 TYR 0.012 0.001 TYR C 72 ARG 0.009 0.000 ARG C 284 Details of bonding type rmsd link_NAG-ASN : bond 0.00410 ( 12) link_NAG-ASN : angle 1.64597 ( 36) link_BETA1-4 : bond 0.00593 ( 6) link_BETA1-4 : angle 2.76600 ( 18) hydrogen bonds : bond 0.05850 ( 393) hydrogen bonds : angle 5.17295 ( 1125) SS BOND : bond 0.00519 ( 21) SS BOND : angle 1.16516 ( 42) covalent geometry : bond 0.00331 (11664) covalent geometry : angle 0.60361 (15777) *********************** 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 75 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 1.379 Fit side-chains revert: symmetry clash REVERT: A 104 MET cc_start: 0.9337 (tpt) cc_final: 0.9081 (tpt) REVERT: B 364 ASP cc_start: 0.9037 (p0) cc_final: 0.8666 (p0) REVERT: B 484 MET cc_start: 0.6265 (mmt) cc_final: 0.5702 (ttt) outliers start: 9 outliers final: 2 residues processed: 70 average time/residue: 1.4026 time to fit residues: 106.4624 Evaluate side-chains 66 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 MET 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 52 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 127 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 115 optimal weight: 0.0000 chunk 74 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- 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 = 0.3328 r_free = 0.3328 target = 0.073981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.063208 restraints weight = 44322.744| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 3.88 r_work: 0.2984 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11703 Z= 0.118 Angle : 0.554 8.139 15873 Z= 0.280 Chirality : 0.043 0.220 1782 Planarity : 0.002 0.020 2019 Dihedral : 11.460 82.825 1875 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.87 % Allowed : 7.60 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.22), residues: 1389 helix: 2.68 (0.31), residues: 318 sheet: 0.21 (0.27), residues: 360 loop : -1.92 (0.20), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 121 HIS 0.005 0.001 HIS C 23 PHE 0.025 0.001 PHE C 485 TYR 0.013 0.001 TYR B 383 ARG 0.004 0.000 ARG C 288 Details of bonding type rmsd link_NAG-ASN : bond 0.00355 ( 12) link_NAG-ASN : angle 1.44895 ( 36) link_BETA1-4 : bond 0.01260 ( 6) link_BETA1-4 : angle 3.37367 ( 18) hydrogen bonds : bond 0.05605 ( 393) hydrogen bonds : angle 4.91722 ( 1125) SS BOND : bond 0.00413 ( 21) SS BOND : angle 0.96312 ( 42) covalent geometry : bond 0.00256 (11664) covalent geometry : angle 0.53712 (15777) *********************** 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 76 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 1.460 Fit side-chains revert: symmetry clash REVERT: A 104 MET cc_start: 0.9421 (tpt) cc_final: 0.9158 (tpt) REVERT: B 364 ASP cc_start: 0.9050 (p0) cc_final: 0.8654 (p0) REVERT: B 484 MET cc_start: 0.6095 (mmt) cc_final: 0.5395 (ttt) outliers start: 11 outliers final: 2 residues processed: 70 average time/residue: 1.4341 time to fit residues: 108.9118 Evaluate side-chains 65 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 63 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 370 MET 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 109 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 43 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 HIS C 245 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.071183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.060606 restraints weight = 44855.738| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 3.85 r_work: 0.2881 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11703 Z= 0.210 Angle : 0.644 9.327 15873 Z= 0.327 Chirality : 0.045 0.246 1782 Planarity : 0.003 0.020 2019 Dihedral : 10.119 68.387 1875 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 1.50 % Allowed : 9.11 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.21), residues: 1389 helix: 2.27 (0.30), residues: 318 sheet: 0.59 (0.28), residues: 321 loop : -2.13 (0.18), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 121 HIS 0.006 0.001 HIS C 285 PHE 0.018 0.001 PHE C 485 TYR 0.021 0.001 TYR B 383 ARG 0.005 0.000 ARG B 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00413 ( 12) link_NAG-ASN : angle 1.73616 ( 36) link_BETA1-4 : bond 0.00947 ( 6) link_BETA1-4 : angle 3.82909 ( 18) hydrogen bonds : bond 0.07129 ( 393) hydrogen bonds : angle 5.06233 ( 1125) SS BOND : bond 0.00632 ( 21) SS BOND : angle 1.51569 ( 42) covalent geometry : bond 0.00480 (11664) covalent geometry : angle 0.62219 (15777) *********************** 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 83 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 1.314 Fit side-chains revert: symmetry clash REVERT: A 104 MET cc_start: 0.9425 (tpt) cc_final: 0.9182 (tpt) REVERT: B 291 TYR cc_start: 0.5669 (OUTLIER) cc_final: 0.5035 (p90) REVERT: B 364 ASP cc_start: 0.9140 (p0) cc_final: 0.8785 (p0) REVERT: B 484 MET cc_start: 0.6031 (mmt) cc_final: 0.5436 (ttt) REVERT: C 87 ARG cc_start: 0.8179 (pmm-80) cc_final: 0.7918 (pmm-80) REVERT: C 104 MET cc_start: 0.9558 (tpt) cc_final: 0.9347 (tpt) REVERT: C 370 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8395 (ptp) outliers start: 19 outliers final: 6 residues processed: 77 average time/residue: 1.2484 time to fit residues: 105.1997 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 : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 476 LEU 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 164 CYS Chi-restraints excluded: chain C residue 370 MET 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 72 optimal weight: 0.0000 chunk 17 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 123 optimal weight: 0.6980 chunk 77 optimal weight: 0.1980 chunk 120 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.5184 ------------------------------------------------------------------------------- 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 = 0.3298 r_free = 0.3298 target = 0.073017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.062423 restraints weight = 43633.204| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 3.84 r_work: 0.2934 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11703 Z= 0.116 Angle : 0.581 10.220 15873 Z= 0.288 Chirality : 0.043 0.258 1782 Planarity : 0.002 0.050 2019 Dihedral : 8.708 57.517 1875 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 0.95 % Allowed : 10.77 % 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 (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: -0.31 (0.22), residues: 1389 helix: 2.47 (0.31), residues: 321 sheet: 0.72 (0.28), residues: 321 loop : -1.99 (0.18), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 138 HIS 0.004 0.001 HIS B 285 PHE 0.017 0.001 PHE B 485 TYR 0.012 0.001 TYR B 383 ARG 0.006 0.000 ARG B 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00423 ( 12) link_NAG-ASN : angle 1.37261 ( 36) link_BETA1-4 : bond 0.01238 ( 6) link_BETA1-4 : angle 3.51853 ( 18) hydrogen bonds : bond 0.05859 ( 393) hydrogen bonds : angle 4.80478 ( 1125) SS BOND : bond 0.00520 ( 21) SS BOND : angle 1.70969 ( 42) covalent geometry : bond 0.00249 (11664) covalent geometry : angle 0.55997 (15777) *********************** 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 74 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 1.303 Fit side-chains REVERT: A 104 MET cc_start: 0.9346 (tpt) cc_final: 0.9101 (tpt) REVERT: B 291 TYR cc_start: 0.5561 (OUTLIER) cc_final: 0.4975 (p90) REVERT: B 364 ASP cc_start: 0.9064 (p0) cc_final: 0.8654 (p0) REVERT: B 484 MET cc_start: 0.6094 (mmt) cc_final: 0.5512 (ttt) outliers start: 12 outliers final: 3 residues processed: 69 average time/residue: 1.2489 time to fit residues: 94.4418 Evaluate side-chains 67 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain C residue 476 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 52 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 92 optimal weight: 0.0030 chunk 48 optimal weight: 0.0270 chunk 20 optimal weight: 0.7980 chunk 102 optimal weight: 0.0040 overall best weight: 0.3260 ------------------------------------------------------------------------------- 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 = 0.3328 r_free = 0.3328 target = 0.073818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.063057 restraints weight = 44259.456| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 3.88 r_work: 0.2979 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11703 Z= 0.104 Angle : 0.560 10.691 15873 Z= 0.272 Chirality : 0.042 0.203 1782 Planarity : 0.002 0.039 2019 Dihedral : 6.826 53.438 1875 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 1.19 % Allowed : 11.01 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.09 (0.22), residues: 1389 helix: 2.65 (0.31), residues: 321 sheet: 0.88 (0.28), residues: 321 loop : -1.86 (0.19), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 121 HIS 0.003 0.001 HIS B 285 PHE 0.012 0.001 PHE B 485 TYR 0.012 0.001 TYR B 383 ARG 0.009 0.000 ARG C 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00373 ( 12) link_NAG-ASN : angle 1.44866 ( 36) link_BETA1-4 : bond 0.01325 ( 6) link_BETA1-4 : angle 3.84827 ( 18) hydrogen bonds : bond 0.04945 ( 393) hydrogen bonds : angle 4.59813 ( 1125) SS BOND : bond 0.00345 ( 21) SS BOND : angle 1.14534 ( 42) covalent geometry : bond 0.00219 (11664) covalent geometry : angle 0.53844 (15777) *********************** 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 80 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 1.307 Fit side-chains revert: symmetry clash REVERT: B 121 TRP cc_start: 0.8202 (m100) cc_final: 0.7985 (m100) REVERT: B 291 TYR cc_start: 0.5486 (OUTLIER) cc_final: 0.4846 (p90) REVERT: B 364 ASP cc_start: 0.9116 (p0) cc_final: 0.8732 (p0) REVERT: B 484 MET cc_start: 0.6169 (mmt) cc_final: 0.5576 (ttt) REVERT: C 87 ARG cc_start: 0.8334 (pmm-80) cc_final: 0.7981 (pmm-80) REVERT: C 104 MET cc_start: 0.9546 (tpt) cc_final: 0.9343 (tpt) outliers start: 15 outliers final: 7 residues processed: 78 average time/residue: 1.1364 time to fit residues: 97.5376 Evaluate side-chains 70 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 1.377 ------------------------------------------------------------------------------- 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 88 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 164 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 6 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS B 335 HIS C 23 HIS C 324 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.067487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.057010 restraints weight = 46375.508| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 3.89 r_work: 0.2823 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 11703 Z= 0.295 Angle : 0.742 11.851 15873 Z= 0.376 Chirality : 0.047 0.186 1782 Planarity : 0.003 0.036 2019 Dihedral : 6.378 59.623 1875 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 1.50 % Allowed : 11.48 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.21), residues: 1389 helix: 2.27 (0.30), residues: 300 sheet: 0.78 (0.28), residues: 303 loop : -2.28 (0.18), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 121 HIS 0.009 0.002 HIS A 152 PHE 0.009 0.001 PHE A 405 TYR 0.025 0.002 TYR B 383 ARG 0.005 0.001 ARG B 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00445 ( 12) link_NAG-ASN : angle 2.10409 ( 36) link_BETA1-4 : bond 0.01621 ( 6) link_BETA1-4 : angle 5.14277 ( 18) hydrogen bonds : bond 0.07837 ( 393) hydrogen bonds : angle 5.19891 ( 1125) SS BOND : bond 0.00691 ( 21) SS BOND : angle 2.31141 ( 42) covalent geometry : bond 0.00688 (11664) covalent geometry : angle 0.70694 (15777) *********************** 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 82 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 1.506 Fit side-chains revert: symmetry clash REVERT: A 291 TYR cc_start: 0.7320 (OUTLIER) cc_final: 0.6217 (p90) REVERT: A 303 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8370 (mtt) REVERT: B 291 TYR cc_start: 0.6217 (OUTLIER) cc_final: 0.5718 (p90) REVERT: B 364 ASP cc_start: 0.9155 (p0) cc_final: 0.8830 (p0) REVERT: B 484 MET cc_start: 0.6247 (mmt) cc_final: 0.5718 (ttt) outliers start: 19 outliers final: 10 residues processed: 77 average time/residue: 1.1805 time to fit residues: 100.0896 Evaluate side-chains 74 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 1.273 ------------------------------------------------------------------------------- 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 A residue 476 LEU Chi-restraints excluded: chain B residue 113 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 164 CYS 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 80 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 72 optimal weight: 0.3980 chunk 54 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3248 r_free = 0.3248 target = 0.069755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.059223 restraints weight = 44676.756| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 3.89 r_work: 0.2871 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11703 Z= 0.127 Angle : 0.599 12.053 15873 Z= 0.298 Chirality : 0.043 0.150 1782 Planarity : 0.003 0.033 2019 Dihedral : 5.833 56.591 1875 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 1.11 % Allowed : 12.19 % 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 (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: -0.51 (0.21), residues: 1389 helix: 2.31 (0.30), residues: 318 sheet: 0.67 (0.28), residues: 321 loop : -2.14 (0.18), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 121 HIS 0.004 0.001 HIS B 23 PHE 0.010 0.001 PHE B 485 TYR 0.014 0.001 TYR A 383 ARG 0.007 0.000 ARG B 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00479 ( 12) link_NAG-ASN : angle 1.55239 ( 36) link_BETA1-4 : bond 0.01561 ( 6) link_BETA1-4 : angle 4.31503 ( 18) hydrogen bonds : bond 0.06471 ( 393) hydrogen bonds : angle 4.90279 ( 1125) SS BOND : bond 0.00363 ( 21) SS BOND : angle 1.44400 ( 42) covalent geometry : bond 0.00278 (11664) covalent geometry : angle 0.57307 (15777) *********************** 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 78 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 1.486 Fit side-chains revert: symmetry clash REVERT: A 303 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.8014 (mtt) REVERT: B 121 TRP cc_start: 0.8221 (m100) cc_final: 0.8005 (m100) REVERT: B 291 TYR cc_start: 0.6098 (OUTLIER) cc_final: 0.5590 (p90) REVERT: B 364 ASP cc_start: 0.9105 (p0) cc_final: 0.8748 (p0) REVERT: B 484 MET cc_start: 0.6228 (mmt) cc_final: 0.5784 (ttt) REVERT: C 87 ARG cc_start: 0.8228 (pmm-80) cc_final: 0.7912 (pmm-80) REVERT: C 291 TYR cc_start: 0.6827 (OUTLIER) cc_final: 0.5877 (p90) outliers start: 14 outliers final: 8 residues processed: 75 average time/residue: 1.2902 time to fit residues: 107.0852 Evaluate side-chains 74 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 1.301 ------------------------------------------------------------------------------- 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 303 MET Chi-restraints excluded: chain B residue 113 VAL 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 88 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 24 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 67 optimal weight: 0.0030 chunk 64 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.5796 ------------------------------------------------------------------------------- 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 = 0.3220 r_free = 0.3220 target = 0.068533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.058106 restraints weight = 45102.428| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 3.87 r_work: 0.2855 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 11703 Z= 0.188 Angle : 0.633 9.891 15873 Z= 0.318 Chirality : 0.044 0.164 1782 Planarity : 0.003 0.035 2019 Dihedral : 5.699 57.984 1875 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 1.43 % Allowed : 11.96 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.21), residues: 1389 helix: 2.47 (0.31), residues: 300 sheet: 0.68 (0.27), residues: 318 loop : -2.26 (0.18), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 121 HIS 0.004 0.001 HIS C 285 PHE 0.010 0.001 PHE C 483 TYR 0.018 0.001 TYR B 383 ARG 0.006 0.000 ARG B 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00414 ( 12) link_NAG-ASN : angle 1.72143 ( 36) link_BETA1-4 : bond 0.01555 ( 6) link_BETA1-4 : angle 4.59922 ( 18) hydrogen bonds : bond 0.06892 ( 393) hydrogen bonds : angle 4.99546 ( 1125) SS BOND : bond 0.00471 ( 21) SS BOND : angle 1.73817 ( 42) covalent geometry : bond 0.00435 (11664) covalent geometry : angle 0.60363 (15777) *********************** 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 81 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 1.354 Fit side-chains revert: symmetry clash REVERT: A 291 TYR cc_start: 0.7284 (OUTLIER) cc_final: 0.6320 (p90) REVERT: A 303 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8136 (mtt) REVERT: B 121 TRP cc_start: 0.8164 (m100) cc_final: 0.7900 (m100) REVERT: B 291 TYR cc_start: 0.6253 (OUTLIER) cc_final: 0.5655 (p90) REVERT: B 364 ASP cc_start: 0.9127 (p0) cc_final: 0.8783 (p0) REVERT: B 484 MET cc_start: 0.6183 (mmt) cc_final: 0.5697 (ttt) REVERT: C 291 TYR cc_start: 0.6926 (OUTLIER) cc_final: 0.6021 (p90) REVERT: C 484 MET cc_start: 0.7027 (mmp) cc_final: 0.5857 (ptt) outliers start: 18 outliers final: 11 residues processed: 77 average time/residue: 1.1202 time to fit residues: 94.9020 Evaluate side-chains 77 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 1.358 ------------------------------------------------------------------------------- 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 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 88 VAL 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 73 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 46 optimal weight: 0.0010 chunk 39 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 0.0570 chunk 99 optimal weight: 2.9990 overall best weight: 1.8110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.067907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.057840 restraints weight = 46083.867| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 3.78 r_work: 0.2825 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 11703 Z= 0.212 Angle : 0.673 13.416 15873 Z= 0.339 Chirality : 0.045 0.154 1782 Planarity : 0.003 0.035 2019 Dihedral : 5.860 59.739 1875 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 1.27 % Allowed : 12.11 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.21), residues: 1389 helix: 2.32 (0.30), residues: 300 sheet: 0.54 (0.27), residues: 318 loop : -2.38 (0.18), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 121 HIS 0.005 0.001 HIS C 285 PHE 0.009 0.001 PHE B 485 TYR 0.019 0.002 TYR A 383 ARG 0.006 0.000 ARG C 288 Details of bonding type rmsd link_NAG-ASN : bond 0.00480 ( 12) link_NAG-ASN : angle 1.82992 ( 36) link_BETA1-4 : bond 0.01669 ( 6) link_BETA1-4 : angle 4.58271 ( 18) hydrogen bonds : bond 0.07454 ( 393) hydrogen bonds : angle 5.13006 ( 1125) SS BOND : bond 0.00513 ( 21) SS BOND : angle 1.87608 ( 42) covalent geometry : bond 0.00492 (11664) covalent geometry : angle 0.64426 (15777) ********************** 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 78 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 1.372 Fit side-chains revert: symmetry clash REVERT: A 291 TYR cc_start: 0.7540 (OUTLIER) cc_final: 0.6670 (p90) REVERT: B 121 TRP cc_start: 0.8125 (m100) cc_final: 0.7917 (m100) REVERT: B 291 TYR cc_start: 0.6658 (OUTLIER) cc_final: 0.5810 (p90) REVERT: B 364 ASP cc_start: 0.9153 (p0) cc_final: 0.8811 (p0) REVERT: B 484 MET cc_start: 0.6202 (mmt) cc_final: 0.5818 (ttt) REVERT: C 87 ARG cc_start: 0.8312 (pmm-80) cc_final: 0.7835 (pmm-80) REVERT: C 291 TYR cc_start: 0.7139 (OUTLIER) cc_final: 0.6140 (p90) REVERT: C 484 MET cc_start: 0.7001 (mmp) cc_final: 0.6799 (tpp) outliers start: 16 outliers final: 9 residues processed: 75 average time/residue: 1.1739 time to fit residues: 96.8114 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 : 1.343 ------------------------------------------------------------------------------- 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 338 ILE 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 64 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 37 optimal weight: 0.4980 chunk 96 optimal weight: 0.8980 chunk 127 optimal weight: 0.9980 chunk 119 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 117 optimal weight: 0.0000 overall best weight: 0.5584 ------------------------------------------------------------------------------- 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 = 0.3255 r_free = 0.3255 target = 0.069965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.059533 restraints weight = 44590.091| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 3.87 r_work: 0.2902 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11703 Z= 0.117 Angle : 0.590 11.521 15873 Z= 0.293 Chirality : 0.043 0.205 1782 Planarity : 0.003 0.033 2019 Dihedral : 5.355 54.494 1875 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 0.95 % Allowed : 12.43 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.21), residues: 1389 helix: 2.51 (0.31), residues: 303 sheet: 0.59 (0.27), residues: 321 loop : -2.19 (0.18), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 121 HIS 0.007 0.001 HIS B 285 PHE 0.009 0.001 PHE A 485 TYR 0.012 0.001 TYR A 383 ARG 0.007 0.000 ARG B 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00528 ( 12) link_NAG-ASN : angle 1.45931 ( 36) link_BETA1-4 : bond 0.01495 ( 6) link_BETA1-4 : angle 3.92583 ( 18) hydrogen bonds : bond 0.06021 ( 393) hydrogen bonds : angle 4.87443 ( 1125) SS BOND : bond 0.00441 ( 21) SS BOND : angle 1.33354 ( 42) covalent geometry : bond 0.00245 (11664) covalent geometry : angle 0.56800 (15777) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7001.58 seconds wall clock time: 121 minutes 46.70 seconds (7306.70 seconds total)