Starting phenix.real_space_refine on Tue Jul 29 16:33:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yg6_39237/07_2025/8yg6_39237.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yg6_39237/07_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_39237/07_2025/8yg6_39237.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yg6_39237/07_2025/8yg6_39237.map" model { file = "/net/cci-nas-00/data/ceres_data/8yg6_39237/07_2025/8yg6_39237.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yg6_39237/07_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-5711/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: 8.54, per 1000 atoms: 0.75 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: 2.97 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: 1.45 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: 3.43 Time building geometry restraints manager: 3.51 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: 0.09 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: 5.320 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: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 30.760 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.080 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:16.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.530 ------------------------------------------------------------------------------- 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 : 1.405 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: 1.6333 time to fit residues: 167.7294 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 : 1.451 ------------------------------------------------------------------------------- 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 = 0.3317 r_free = 0.3317 target = 0.071828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.061018 restraints weight = 44248.502| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 3.85 r_work: 0.2960 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 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 1.64598 ( 36) link_BETA1-4 : bond 0.00593 ( 6) link_BETA1-4 : angle 2.76601 ( 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 : 1.611 Fit side-chains revert: symmetry clash REVERT: A 104 MET cc_start: 0.9351 (tpt) cc_final: 0.9104 (tpt) REVERT: B 364 ASP cc_start: 0.9036 (p0) cc_final: 0.8666 (p0) REVERT: B 484 MET cc_start: 0.6306 (mmt) cc_final: 0.5723 (ttt) outliers start: 9 outliers final: 2 residues processed: 70 average time/residue: 1.7484 time to fit residues: 131.7636 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 : 1.413 ------------------------------------------------------------------------------- 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: 4.9990 chunk 58 optimal weight: 0.6980 chunk 127 optimal weight: 0.0980 chunk 70 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 115 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3332 r_free = 0.3332 target = 0.074115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.063325 restraints weight = 44271.962| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 3.88 r_work: 0.2984 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 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= 0.115 Angle : 0.552 7.825 15873 Z= 0.279 Chirality : 0.043 0.219 1782 Planarity : 0.002 0.023 2019 Dihedral : 11.427 82.636 1875 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.95 % Allowed : 7.60 % Favored : 91.45 % 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: 2.70 (0.31), residues: 318 sheet: 0.22 (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 285 PHE 0.025 0.001 PHE C 485 TYR 0.013 0.001 TYR B 383 ARG 0.004 0.000 ARG A 130 Details of bonding type rmsd link_NAG-ASN : bond 0.00353 ( 12) link_NAG-ASN : angle 1.42425 ( 36) link_BETA1-4 : bond 0.01289 ( 6) link_BETA1-4 : angle 3.42903 ( 18) hydrogen bonds : bond 0.05537 ( 393) hydrogen bonds : angle 4.90128 ( 1125) SS BOND : bond 0.00412 ( 21) SS BOND : angle 0.96165 ( 42) covalent geometry : bond 0.00249 (11664) covalent geometry : angle 0.53507 (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 77 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 1.240 Fit side-chains revert: symmetry clash REVERT: A 104 MET cc_start: 0.9413 (tpt) cc_final: 0.9154 (tpt) REVERT: B 87 ARG cc_start: 0.7172 (pmm-80) cc_final: 0.6811 (pmm-80) REVERT: B 364 ASP cc_start: 0.9062 (p0) cc_final: 0.8654 (p0) REVERT: B 484 MET cc_start: 0.6100 (mmt) cc_final: 0.5398 (ttt) outliers start: 12 outliers final: 2 residues processed: 71 average time/residue: 1.4013 time to fit residues: 107.8302 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 : 1.295 ------------------------------------------------------------------------------- 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: 7.9990 chunk 20 optimal weight: 0.6980 chunk 9 optimal weight: 0.0870 chunk 71 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 131 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- 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 = 0.3324 r_free = 0.3324 target = 0.073793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.062993 restraints weight = 44092.701| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 3.87 r_work: 0.2986 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11703 Z= 0.114 Angle : 0.550 8.542 15873 Z= 0.274 Chirality : 0.043 0.254 1782 Planarity : 0.002 0.019 2019 Dihedral : 10.213 71.922 1875 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 1.03 % Allowed : 9.42 % Favored : 89.55 % 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: -0.26 (0.22), residues: 1389 helix: 2.61 (0.31), residues: 321 sheet: 0.39 (0.27), residues: 351 loop : -1.90 (0.19), residues: 717 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 0.021 0.001 PHE C 485 TYR 0.012 0.001 TYR B 383 ARG 0.003 0.000 ARG C 288 Details of bonding type rmsd link_NAG-ASN : bond 0.00368 ( 12) link_NAG-ASN : angle 1.39526 ( 36) link_BETA1-4 : bond 0.00999 ( 6) link_BETA1-4 : angle 3.23391 ( 18) hydrogen bonds : bond 0.05381 ( 393) hydrogen bonds : angle 4.76168 ( 1125) SS BOND : bond 0.00394 ( 21) SS BOND : angle 0.88881 ( 42) covalent geometry : bond 0.00248 (11664) covalent geometry : angle 0.53508 (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 77 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 1.294 Fit side-chains revert: symmetry clash REVERT: A 104 MET cc_start: 0.9420 (tpt) cc_final: 0.9186 (tpt) REVERT: B 291 TYR cc_start: 0.5019 (OUTLIER) cc_final: 0.3798 (p90) REVERT: B 364 ASP cc_start: 0.9059 (p0) cc_final: 0.8654 (p0) REVERT: B 484 MET cc_start: 0.6094 (mmt) cc_final: 0.5389 (ttt) REVERT: C 370 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8303 (ptp) outliers start: 13 outliers final: 1 residues processed: 75 average time/residue: 1.2549 time to fit residues: 102.8076 Evaluate side-chains 65 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 291 TYR 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: 0.6980 chunk 17 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 123 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 82 optimal weight: 0.1980 chunk 2 optimal weight: 0.0270 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 = 0.3332 r_free = 0.3332 target = 0.074152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.063373 restraints weight = 43378.994| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 3.87 r_work: 0.2984 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 11703 Z= 0.107 Angle : 0.555 9.184 15873 Z= 0.273 Chirality : 0.042 0.257 1782 Planarity : 0.002 0.047 2019 Dihedral : 9.213 62.859 1875 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.71 % Allowed : 10.37 % Favored : 88.92 % 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: 2.70 (0.31), residues: 321 sheet: 0.87 (0.28), residues: 321 loop : -1.87 (0.19), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 138 HIS 0.003 0.001 HIS B 285 PHE 0.018 0.001 PHE B 485 TYR 0.011 0.001 TYR B 383 ARG 0.006 0.000 ARG B 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00379 ( 12) link_NAG-ASN : angle 1.29550 ( 36) link_BETA1-4 : bond 0.01121 ( 6) link_BETA1-4 : angle 3.41008 ( 18) hydrogen bonds : bond 0.05152 ( 393) hydrogen bonds : angle 4.68285 ( 1125) SS BOND : bond 0.00363 ( 21) SS BOND : angle 1.32651 ( 42) covalent geometry : bond 0.00234 (11664) covalent geometry : angle 0.53691 (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 72 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9390 (tpt) cc_final: 0.9134 (tpt) REVERT: B 364 ASP cc_start: 0.9081 (p0) cc_final: 0.8684 (p0) REVERT: B 484 MET cc_start: 0.6115 (mmt) cc_final: 0.5472 (ttt) REVERT: C 370 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8365 (ptp) outliers start: 9 outliers final: 4 residues processed: 69 average time/residue: 1.2921 time to fit residues: 97.4711 Evaluate side-chains 67 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain B residue 164 CYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 52 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 23 HIS C 245 HIS C 324 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.071554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.060935 restraints weight = 44970.496| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 3.90 r_work: 0.2884 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 11703 Z= 0.187 Angle : 0.639 10.315 15873 Z= 0.318 Chirality : 0.044 0.238 1782 Planarity : 0.003 0.047 2019 Dihedral : 7.809 59.364 1875 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 1.35 % Allowed : 11.08 % Favored : 87.57 % 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: -0.42 (0.21), residues: 1389 helix: 2.33 (0.30), residues: 318 sheet: 0.75 (0.28), residues: 321 loop : -2.07 (0.18), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 121 HIS 0.005 0.001 HIS C 285 PHE 0.011 0.001 PHE B 485 TYR 0.021 0.001 TYR B 383 ARG 0.011 0.001 ARG B 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00397 ( 12) link_NAG-ASN : angle 1.66961 ( 36) link_BETA1-4 : bond 0.01284 ( 6) link_BETA1-4 : angle 4.30940 ( 18) hydrogen bonds : bond 0.06663 ( 393) hydrogen bonds : angle 4.93258 ( 1125) SS BOND : bond 0.00557 ( 21) SS BOND : angle 1.95097 ( 42) covalent geometry : bond 0.00434 (11664) covalent geometry : angle 0.61061 (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: 17 poor density : 63 time to evaluate : 1.304 Fit side-chains revert: symmetry clash REVERT: A 104 MET cc_start: 0.9404 (tpt) cc_final: 0.9186 (tpt) REVERT: B 291 TYR cc_start: 0.5651 (OUTLIER) cc_final: 0.5248 (p90) REVERT: B 364 ASP cc_start: 0.9093 (p0) cc_final: 0.8721 (p0) REVERT: B 484 MET cc_start: 0.6090 (mmt) cc_final: 0.5523 (ttt) REVERT: C 370 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8465 (ptp) outliers start: 17 outliers final: 8 residues processed: 74 average time/residue: 1.1753 time to fit residues: 95.4494 Evaluate side-chains 71 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 476 LEU 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 370 MET Chi-restraints excluded: chain C residue 476 LEU 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: 0.9990 chunk 66 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 26 optimal weight: 0.1980 chunk 122 optimal weight: 2.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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** C 324 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.072590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.061954 restraints weight = 44911.753| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 3.90 r_work: 0.2930 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2229 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= 0.122 Angle : 0.579 8.774 15873 Z= 0.287 Chirality : 0.042 0.199 1782 Planarity : 0.002 0.031 2019 Dihedral : 6.835 55.984 1875 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 1.11 % Allowed : 11.24 % Favored : 87.65 % 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: -0.32 (0.22), residues: 1389 helix: 2.41 (0.31), residues: 321 sheet: 0.76 (0.28), residues: 321 loop : -2.00 (0.18), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 121 HIS 0.003 0.001 HIS B 23 PHE 0.011 0.001 PHE C 485 TYR 0.013 0.001 TYR A 383 ARG 0.007 0.000 ARG B 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00412 ( 12) link_NAG-ASN : angle 1.42721 ( 36) link_BETA1-4 : bond 0.01373 ( 6) link_BETA1-4 : angle 4.11583 ( 18) hydrogen bonds : bond 0.06008 ( 393) hydrogen bonds : angle 4.79244 ( 1125) SS BOND : bond 0.00366 ( 21) SS BOND : angle 1.33939 ( 42) covalent geometry : bond 0.00267 (11664) covalent geometry : angle 0.55546 (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 78 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 1.228 Fit side-chains revert: symmetry clash REVERT: A 104 MET cc_start: 0.9385 (tpt) cc_final: 0.9143 (tpt) REVERT: A 121 TRP cc_start: 0.8328 (m100) cc_final: 0.8023 (m100) REVERT: A 303 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.7665 (mtp) REVERT: B 121 TRP cc_start: 0.8184 (m100) cc_final: 0.7952 (m100) REVERT: B 291 TYR cc_start: 0.5680 (OUTLIER) cc_final: 0.5228 (p90) REVERT: B 364 ASP cc_start: 0.9107 (p0) cc_final: 0.8728 (p0) REVERT: B 484 MET cc_start: 0.6216 (mmt) cc_final: 0.5675 (ttt) REVERT: C 370 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.8432 (ptp) outliers start: 14 outliers final: 8 residues processed: 74 average time/residue: 1.1192 time to fit residues: 91.2382 Evaluate side-chains 75 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 1.218 ------------------------------------------------------------------------------- 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 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 164 CYS Chi-restraints excluded: chain C residue 370 MET 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: 1.9990 chunk 42 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 102 optimal weight: 0.4980 chunk 105 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 = 0.3270 r_free = 0.3270 target = 0.071953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.061430 restraints weight = 44394.756| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 3.89 r_work: 0.2901 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2355 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= 0.146 Angle : 0.602 10.197 15873 Z= 0.297 Chirality : 0.043 0.160 1782 Planarity : 0.002 0.033 2019 Dihedral : 5.928 55.492 1875 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 1.27 % Allowed : 11.72 % 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: -0.36 (0.21), residues: 1389 helix: 2.35 (0.31), residues: 321 sheet: 0.75 (0.28), residues: 321 loop : -2.01 (0.18), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 121 HIS 0.003 0.001 HIS C 285 PHE 0.009 0.001 PHE C 485 TYR 0.016 0.001 TYR B 383 ARG 0.007 0.000 ARG C 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00384 ( 12) link_NAG-ASN : angle 1.59649 ( 36) link_BETA1-4 : bond 0.01476 ( 6) link_BETA1-4 : angle 4.46647 ( 18) hydrogen bonds : bond 0.06162 ( 393) hydrogen bonds : angle 4.79674 ( 1125) SS BOND : bond 0.00406 ( 21) SS BOND : angle 1.48571 ( 42) covalent geometry : bond 0.00332 (11664) covalent geometry : angle 0.57438 (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 81 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 1.484 Fit side-chains revert: symmetry clash REVERT: A 104 MET cc_start: 0.9385 (tpt) cc_final: 0.9151 (tpt) REVERT: A 121 TRP cc_start: 0.8403 (m100) cc_final: 0.8064 (m100) REVERT: A 303 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.7775 (mtp) REVERT: B 121 TRP cc_start: 0.8203 (m100) cc_final: 0.7915 (m100) REVERT: B 291 TYR cc_start: 0.5802 (OUTLIER) cc_final: 0.5397 (p90) REVERT: B 364 ASP cc_start: 0.9091 (p0) cc_final: 0.8724 (p0) REVERT: B 484 MET cc_start: 0.6148 (mmt) cc_final: 0.5670 (ttt) REVERT: C 484 MET cc_start: 0.6866 (mmp) cc_final: 0.5677 (ptt) outliers start: 16 outliers final: 7 residues processed: 76 average time/residue: 1.2552 time to fit residues: 104.5928 Evaluate side-chains 73 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 1.252 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 24 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 44 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 67 optimal weight: 0.0040 chunk 64 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.9394 ------------------------------------------------------------------------------- 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 = 0.3275 r_free = 0.3275 target = 0.072039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.061474 restraints weight = 44434.673| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.90 r_work: 0.2911 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11703 Z= 0.132 Angle : 0.586 12.193 15873 Z= 0.289 Chirality : 0.043 0.163 1782 Planarity : 0.002 0.032 2019 Dihedral : 5.549 55.600 1875 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 1.19 % Allowed : 11.96 % Favored : 86.86 % 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: -0.35 (0.22), residues: 1389 helix: 2.39 (0.31), residues: 321 sheet: 0.75 (0.28), residues: 321 loop : -2.02 (0.18), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 121 HIS 0.003 0.001 HIS C 285 PHE 0.009 0.001 PHE B 485 TYR 0.014 0.001 TYR B 383 ARG 0.010 0.000 ARG C 288 Details of bonding type rmsd link_NAG-ASN : bond 0.00406 ( 12) link_NAG-ASN : angle 1.52583 ( 36) link_BETA1-4 : bond 0.01500 ( 6) link_BETA1-4 : angle 4.32100 ( 18) hydrogen bonds : bond 0.06013 ( 393) hydrogen bonds : angle 4.77434 ( 1125) SS BOND : bond 0.00365 ( 21) SS BOND : angle 1.33760 ( 42) covalent geometry : bond 0.00294 (11664) covalent geometry : angle 0.56025 (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 80 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 1.303 Fit side-chains revert: symmetry clash REVERT: A 121 TRP cc_start: 0.8432 (m100) cc_final: 0.8163 (m100) REVERT: A 291 TYR cc_start: 0.7026 (OUTLIER) cc_final: 0.5881 (p90) REVERT: A 303 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.7696 (mtp) REVERT: B 121 TRP cc_start: 0.8217 (m100) cc_final: 0.7989 (m100) REVERT: B 291 TYR cc_start: 0.5809 (OUTLIER) cc_final: 0.5379 (p90) REVERT: B 364 ASP cc_start: 0.9113 (p0) cc_final: 0.8755 (p0) REVERT: B 484 MET cc_start: 0.6236 (mmt) cc_final: 0.5765 (ttt) REVERT: C 87 ARG cc_start: 0.8405 (pmm-80) cc_final: 0.8192 (pmm-80) REVERT: C 192 GLU cc_start: 0.8770 (mp0) cc_final: 0.8448 (pm20) REVERT: C 484 MET cc_start: 0.7048 (mmp) cc_final: 0.6764 (tpp) outliers start: 15 outliers final: 8 residues processed: 77 average time/residue: 1.1425 time to fit residues: 96.9783 Evaluate side-chains 75 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 1.287 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 73 optimal weight: 8.9990 chunk 108 optimal weight: 2.9990 chunk 46 optimal weight: 0.4980 chunk 39 optimal weight: 3.9990 chunk 67 optimal weight: 0.1980 chunk 134 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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** B 324 HIS 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 = 0.068591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.058345 restraints weight = 44578.827| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 3.78 r_work: 0.2860 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 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 : 0.004 0.058 11703 Z= 0.190 Angle : 0.641 9.648 15873 Z= 0.321 Chirality : 0.044 0.157 1782 Planarity : 0.003 0.039 2019 Dihedral : 5.613 58.682 1875 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 1.11 % Allowed : 12.43 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.21), residues: 1389 helix: 2.49 (0.31), residues: 300 sheet: 0.75 (0.28), residues: 318 loop : -2.20 (0.18), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 121 HIS 0.006 0.001 HIS C 285 PHE 0.009 0.001 PHE B 485 TYR 0.019 0.001 TYR B 383 ARG 0.008 0.000 ARG C 288 Details of bonding type rmsd link_NAG-ASN : bond 0.00432 ( 12) link_NAG-ASN : angle 1.75200 ( 36) link_BETA1-4 : bond 0.01560 ( 6) link_BETA1-4 : angle 4.56190 ( 18) hydrogen bonds : bond 0.06870 ( 393) hydrogen bonds : angle 4.94501 ( 1125) SS BOND : bond 0.00484 ( 21) SS BOND : angle 1.75527 ( 42) covalent geometry : bond 0.00438 (11664) covalent geometry : angle 0.61212 (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 77 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 1.685 Fit side-chains revert: symmetry clash REVERT: A 121 TRP cc_start: 0.8364 (m100) cc_final: 0.8049 (m100) REVERT: A 291 TYR cc_start: 0.7263 (OUTLIER) cc_final: 0.6267 (p90) REVERT: A 303 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.8195 (mtt) REVERT: B 121 TRP cc_start: 0.8195 (m100) cc_final: 0.7896 (m100) REVERT: B 291 TYR cc_start: 0.6187 (OUTLIER) cc_final: 0.5690 (p90) REVERT: B 364 ASP cc_start: 0.9111 (p0) cc_final: 0.8771 (p0) REVERT: B 484 MET cc_start: 0.6324 (mmt) cc_final: 0.5883 (ttt) REVERT: C 87 ARG cc_start: 0.8444 (pmm-80) cc_final: 0.8216 (pmm-80) REVERT: C 192 GLU cc_start: 0.8703 (mp0) cc_final: 0.8393 (pm20) outliers start: 14 outliers final: 9 residues processed: 74 average time/residue: 1.5684 time to fit residues: 127.4333 Evaluate side-chains 75 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 1.495 ------------------------------------------------------------------------------- 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 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 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: 0.9980 chunk 24 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 127 optimal weight: 0.7980 chunk 119 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3249 r_free = 0.3249 target = 0.069521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.059122 restraints weight = 44648.945| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 3.85 r_work: 0.2881 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2605 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= 0.135 Angle : 0.594 12.011 15873 Z= 0.296 Chirality : 0.043 0.164 1782 Planarity : 0.003 0.037 2019 Dihedral : 5.418 56.579 1875 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 1.03 % Allowed : 12.51 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.21), residues: 1389 helix: 2.33 (0.31), residues: 318 sheet: 0.66 (0.27), residues: 321 loop : -2.12 (0.18), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 121 HIS 0.003 0.001 HIS C 285 PHE 0.009 0.001 PHE B 485 TYR 0.014 0.001 TYR B 383 ARG 0.008 0.000 ARG C 288 Details of bonding type rmsd link_NAG-ASN : bond 0.00467 ( 12) link_NAG-ASN : angle 1.54817 ( 36) link_BETA1-4 : bond 0.01525 ( 6) link_BETA1-4 : angle 4.20187 ( 18) hydrogen bonds : bond 0.06326 ( 393) hydrogen bonds : angle 4.85123 ( 1125) SS BOND : bond 0.00383 ( 21) SS BOND : angle 1.42673 ( 42) covalent geometry : bond 0.00303 (11664) covalent geometry : angle 0.56921 (15777) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8564.48 seconds wall clock time: 152 minutes 45.67 seconds (9165.67 seconds total)