Starting phenix.real_space_refine on Wed Aug 5 00:07:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ygp_72937/08_2026/9ygp_72937.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ygp_72937/08_2026/9ygp_72937.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ygp_72937/08_2026/9ygp_72937.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ygp_72937/08_2026/9ygp_72937.map" model { file = "/net/cci-nas-00/data/ceres_data/9ygp_72937/08_2026/9ygp_72937.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ygp_72937/08_2026/9ygp_72937.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 4711 2.51 5 N 1209 2.21 5 O 1452 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7414 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2734 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 328} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 2779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2779 Classifications: {'peptide': 356} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 335} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 899 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 111} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "L" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 809 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 1.71, per 1000 atoms: 0.23 Number of scatterers: 7414 At special positions: 0 Unit cell: (93.84, 83.72, 120.52, 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 42 16.00 O 1452 8.00 N 1209 7.00 C 4711 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 156 " distance=2.03 Simple disulfide: pdb=" SG CYS B 151 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 292 " distance=2.03 Simple disulfide: pdb=" SG CYS B 819 " - pdb=" SG CYS B 825 " distance=2.03 Simple disulfide: pdb=" SG CYS C 327 " - pdb=" SG CYS C 352 " distance=2.03 Simple disulfide: pdb=" SG CYS C 370 " - pdb=" SG CYS C 423 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 603 " distance=2.03 Simple disulfide: pdb=" SG CYS C 466 " - pdb=" SG CYS C 546 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 495 " distance=2.03 Simple disulfide: pdb=" SG CYS C 476 " - pdb=" SG CYS C 565 " distance=2.03 Simple disulfide: pdb=" SG CYS C 485 " - pdb=" SG CYS C 516 " distance=2.03 Simple disulfide: pdb=" SG CYS C 504 " - pdb=" SG CYS C 518 " distance=2.03 Simple disulfide: pdb=" SG CYS C 520 " - pdb=" SG CYS C 533 " distance=2.03 Simple disulfide: pdb=" SG CYS C 556 " - pdb=" SG CYS C 567 " distance=2.03 Simple disulfide: pdb=" SG CYS C 580 " - pdb=" SG CYS C 586 " distance=2.03 Simple disulfide: pdb=" SG CYS C 619 " - pdb=" SG CYS C 672 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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 G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " NAG-ASN " NAG B1401 " - " ASN B 171 " " NAG B1402 " - " ASN B 19 " " NAG B1403 " - " ASN B 188 " " NAG B1404 " - " ASN B 192 " " NAG B1405 " - " ASN B 58 " " NAG C1401 " - " ASN C 335 " " NAG C1402 " - " ASN C 433 " " NAG C1403 " - " ASN C 355 " " NAG C1404 " - " ASN C 664 " " NAG C1405 " - " ASN C 454 " " NAG C1406 " - " ASN C 561 " " NAG G 1 " - " ASN B 132 " Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 401.1 milliseconds 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1728 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 16 sheets defined 15.9% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'B' and resid 42 through 46 removed outlier: 3.576A pdb=" N GLY B 45 " --> pdb=" O VAL B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 112 through 116 Processing helix chain 'B' and resid 285 through 295 Processing helix chain 'B' and resid 814 through 819 Processing helix chain 'B' and resid 822 through 830 Processing helix chain 'B' and resid 1041 through 1046 Processing helix chain 'B' and resid 1047 through 1049 No H-bonds generated for 'chain 'B' and resid 1047 through 1049' Processing helix chain 'B' and resid 1057 through 1062 Processing helix chain 'B' and resid 1066 through 1087 removed outlier: 3.776A pdb=" N GLN B1071 " --> pdb=" O PRO B1067 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N VAL B1072 " --> pdb=" O PRO B1068 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLN B1073 " --> pdb=" O GLU B1069 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 334 Processing helix chain 'C' and resid 340 through 344 removed outlier: 4.032A pdb=" N TRP C 344 " --> pdb=" O PRO C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 363 removed outlier: 3.639A pdb=" N VAL C 363 " --> pdb=" O LEU C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 378 removed outlier: 3.852A pdb=" N ILE C 378 " --> pdb=" O LYS C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 401 Processing helix chain 'C' and resid 407 through 413 Processing helix chain 'C' and resid 443 through 448 removed outlier: 3.772A pdb=" N TYR C 448 " --> pdb=" O TRP C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 483 removed outlier: 3.669A pdb=" N ASN C 483 " --> pdb=" O PRO C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 556 removed outlier: 3.530A pdb=" N CYS C 556 " --> pdb=" O GLU C 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 553 through 556' Processing helix chain 'C' and resid 568 through 570 No H-bonds generated for 'chain 'C' and resid 568 through 570' Processing helix chain 'L' and resid 26 through 29 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.624A pdb=" N GLU L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 34 through 39 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 34 through 39 current: chain 'B' and resid 197 through 205 removed outlier: 6.731A pdb=" N PHE B 209 " --> pdb=" O SER B 225 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N SER B 225 " --> pdb=" O PHE B 209 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ALA B 211 " --> pdb=" O LEU B 223 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 221 through 227 current: chain 'B' and resid 280 through 281 Processing sheet with id=AA2, first strand: chain 'B' and resid 54 through 55 removed outlier: 5.438A pdb=" N VAL B 55 " --> pdb=" O TYR C 649 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY C 657 " --> pdb=" O LEU C 648 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE C 656 " --> pdb=" O ILE C 669 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE C 658 " --> pdb=" O TYR C 667 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY C 631 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL C 620 " --> pdb=" O GLY C 631 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG C 319 " --> pdb=" O ASP C 623 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 80 through 81 removed outlier: 3.917A pdb=" N GLY B 81 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N THR B 241 " --> pdb=" O PRO B 159 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N THR B 161 " --> pdb=" O THR B 241 " (cutoff:3.500A) removed outlier: 10.782A pdb=" N TYR B 158 " --> pdb=" O HIS B 175 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N HIS B 175 " --> pdb=" O TYR B 158 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N HIS B 160 " --> pdb=" O SER B 173 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER B 173 " --> pdb=" O HIS B 160 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 96 through 97 removed outlier: 3.501A pdb=" N TYR B 235 " --> pdb=" O SER B 96 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N THR B 123 " --> pdb=" O MET B 238 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE B 124 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N CYS B 151 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU B 146 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ASN B 188 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ILE B 148 " --> pdb=" O LYS B 186 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LYS B 186 " --> pdb=" O ILE B 148 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ALA B 150 " --> pdb=" O LEU B 184 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 109 through 111 Processing sheet with id=AA6, first strand: chain 'C' and resid 337 through 338 removed outlier: 6.047A pdb=" N THR C 435 " --> pdb=" O VAL C 338 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 345 through 349 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 345 through 349 current: chain 'C' and resid 585 through 597 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 459 through 463 Processing sheet with id=AA9, first strand: chain 'C' and resid 466 through 468 removed outlier: 4.604A pdb=" N CYS C 466 " --> pdb=" O VAL C 538 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS C 536 " --> pdb=" O SER C 468 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 504 through 505 Processing sheet with id=AB2, first strand: chain 'C' and resid 550 through 551 Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.626A pdb=" N HIS H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AB5, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.704A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N TYR H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TRP H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 9 through 13 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 9 through 13 current: chain 'L' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 45 through 48 current: chain 'L' and resid 95B through 97 No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'L' and resid 19 through 24 146 hydrogen bonds defined for protein. 354 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.29 Time building geometry restraints manager: 0.87 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: 2302 1.34 - 1.46: 1821 1.46 - 1.58: 3432 1.58 - 1.70: 0 1.70 - 1.82: 45 Bond restraints: 7600 Sorted by residual: bond pdb=" N VAL L 106 " pdb=" CA VAL L 106 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.17e-02 7.31e+03 5.32e+00 bond pdb=" N ASN C 561 " pdb=" CA ASN C 561 " ideal model delta sigma weight residual 1.462 1.488 -0.026 1.31e-02 5.83e+03 3.90e+00 bond pdb=" N ASN C 454 " pdb=" CA ASN C 454 " ideal model delta sigma weight residual 1.462 1.483 -0.020 1.28e-02 6.10e+03 2.52e+00 bond pdb=" C2 BMA G 3 " pdb=" C3 BMA G 3 " ideal model delta sigma weight residual 1.544 1.514 0.030 2.00e-02 2.50e+03 2.28e+00 bond pdb=" N LEU L 106A" pdb=" CA LEU L 106A" ideal model delta sigma weight residual 1.458 1.486 -0.028 1.90e-02 2.77e+03 2.24e+00 ... (remaining 7595 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 9996 1.16 - 2.32: 251 2.32 - 3.48: 83 3.48 - 4.64: 15 4.64 - 5.79: 5 Bond angle restraints: 10350 Sorted by residual: angle pdb=" N SER B 165 " pdb=" CA SER B 165 " pdb=" C SER B 165 " ideal model delta sigma weight residual 114.62 109.95 4.67 1.14e+00 7.69e-01 1.68e+01 angle pdb=" CA ASN C 561 " pdb=" C ASN C 561 " pdb=" O ASN C 561 " ideal model delta sigma weight residual 122.44 118.38 4.06 1.32e+00 5.74e-01 9.48e+00 angle pdb=" CA ASN C 454 " pdb=" C ASN C 454 " pdb=" O ASN C 454 " ideal model delta sigma weight residual 121.66 118.37 3.29 1.17e+00 7.31e-01 7.92e+00 angle pdb=" CA SER B 165 " pdb=" C SER B 165 " pdb=" N LYS B 166 " ideal model delta sigma weight residual 119.71 116.45 3.26 1.17e+00 7.31e-01 7.75e+00 angle pdb=" CA VAL L 106 " pdb=" C VAL L 106 " pdb=" O VAL L 106 " ideal model delta sigma weight residual 120.95 118.00 2.95 1.21e+00 6.83e-01 5.93e+00 ... (remaining 10345 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.30: 4535 21.30 - 42.60: 117 42.60 - 63.90: 21 63.90 - 85.20: 6 85.20 - 106.50: 4 Dihedral angle restraints: 4683 sinusoidal: 1988 harmonic: 2695 Sorted by residual: dihedral pdb=" O4 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C5 BMA G 3 " pdb=" O5 BMA G 3 " ideal model delta sinusoidal sigma weight residual -71.29 -177.79 106.50 1 3.00e+01 1.11e-03 1.37e+01 dihedral pdb=" C3 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C5 BMA G 3 " pdb=" O5 BMA G 3 " ideal model delta sinusoidal sigma weight residual 47.62 -56.86 104.48 1 3.00e+01 1.11e-03 1.33e+01 dihedral pdb=" CB CYS C 466 " pdb=" SG CYS C 466 " pdb=" SG CYS C 546 " pdb=" CB CYS C 546 " ideal model delta sinusoidal sigma weight residual -86.00 -115.69 29.69 1 1.00e+01 1.00e-02 1.26e+01 ... (remaining 4680 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 1179 0.128 - 0.256: 8 0.256 - 0.384: 1 0.384 - 0.512: 0 0.512 - 0.640: 1 Chirality restraints: 1189 Sorted by residual: chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.11e+01 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN B 132 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.35 -0.05 2.00e-02 2.50e+03 6.56e+00 ... (remaining 1186 not shown) Planarity restraints: 1312 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 1 " 0.085 2.00e-02 2.50e+03 7.20e-02 6.47e+01 pdb=" C7 NAG G 1 " -0.014 2.00e-02 2.50e+03 pdb=" C8 NAG G 1 " -0.023 2.00e-02 2.50e+03 pdb=" N2 NAG G 1 " -0.116 2.00e-02 2.50e+03 pdb=" O7 NAG G 1 " 0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 2 " -0.042 2.00e-02 2.50e+03 3.47e-02 1.51e+01 pdb=" C7 NAG G 2 " 0.009 2.00e-02 2.50e+03 pdb=" C8 NAG G 2 " -0.031 2.00e-02 2.50e+03 pdb=" N2 NAG G 2 " 0.056 2.00e-02 2.50e+03 pdb=" O7 NAG G 2 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B1066 " 0.034 5.00e-02 4.00e+02 5.08e-02 4.13e+00 pdb=" N PRO B1067 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO B1067 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B1067 " 0.028 5.00e-02 4.00e+02 ... (remaining 1309 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 3734 2.98 - 3.46: 6950 3.46 - 3.94: 12413 3.94 - 4.42: 13872 4.42 - 4.90: 23275 Nonbonded interactions: 60244 Sorted by model distance: nonbonded pdb=" OG SER H 98 " pdb=" NH2 ARG L 50 " model vdw 2.501 3.120 nonbonded pdb=" CB ARG C 396 " pdb=" NE ARG C 396 " model vdw 2.618 2.816 nonbonded pdb=" N VAL L 106 " pdb=" CG1 VAL L 106 " model vdw 2.623 2.832 nonbonded pdb=" N ARG H 100 " pdb=" O ARG H 100 " model vdw 2.632 2.496 nonbonded pdb=" N ASP C 578 " pdb=" O ASP C 578 " model vdw 2.633 2.496 ... (remaining 60239 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 8.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.630 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 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 : 0.002 0.031 7633 Z= 0.118 Angle : 0.530 10.507 10430 Z= 0.276 Chirality : 0.047 0.640 1189 Planarity : 0.004 0.072 1300 Dihedral : 10.499 106.502 2898 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.82 % Allowed : 5.83 % Favored : 92.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.29), residues: 906 helix: 0.27 (0.58), residues: 84 sheet: -0.23 (0.33), residues: 263 loop : -0.68 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 34 TYR 0.009 0.001 TYR B 191 PHE 0.011 0.001 PHE B 130 TRP 0.011 0.001 TRP H 47 HIS 0.002 0.001 HIS H 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.12 ( 7600) covalent geometry : angle 0.50970 / 0.27 (10350) SS BOND : bond 0.00112 / 0.08 ( 19) SS BOND : angle 0.53504 / 0.35 ( 38) hydrogen bonds : bond 0.24405 / 15.22 ( 146) hydrogen bonds : angle 9.76812 / 6.87 ( 354) link_BETA1-4 : bond 0.00689 / 0.36 ( 2) link_BETA1-4 : angle 1.93818 / 0.92 ( 6) link_NAG-ASN : bond 0.00309 / 0.19 ( 12) link_NAG-ASN : angle 2.42502 / 1.67 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 183 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 49 TYR cc_start: 0.8789 (p90) cc_final: 0.8550 (p90) REVERT: B 69 LYS cc_start: 0.8632 (ttmm) cc_final: 0.8421 (tttm) REVERT: B 213 TYR cc_start: 0.8334 (OUTLIER) cc_final: 0.7834 (t80) REVERT: B 266 TYR cc_start: 0.8436 (OUTLIER) cc_final: 0.6709 (t80) REVERT: B 271 ASP cc_start: 0.7453 (t70) cc_final: 0.7093 (t0) REVERT: B 273 HIS cc_start: 0.7002 (m-70) cc_final: 0.6660 (m90) REVERT: B 296 SER cc_start: 0.7972 (p) cc_final: 0.7742 (t) REVERT: B 828 LEU cc_start: 0.7254 (OUTLIER) cc_final: 0.7043 (mm) REVERT: B 1045 GLN cc_start: 0.8148 (mm-40) cc_final: 0.7780 (mm110) REVERT: C 353 ASN cc_start: 0.7780 (m-40) cc_final: 0.7550 (m-40) REVERT: C 372 ASN cc_start: 0.7818 (m110) cc_final: 0.7548 (m110) REVERT: C 406 SER cc_start: 0.8615 (t) cc_final: 0.8346 (t) REVERT: C 439 PHE cc_start: 0.7361 (t80) cc_final: 0.7002 (t80) REVERT: C 443 SER cc_start: 0.7720 (m) cc_final: 0.7408 (p) REVERT: C 577 PHE cc_start: 0.7552 (p90) cc_final: 0.7002 (p90) REVERT: L 45 LYS cc_start: 0.7285 (ttpp) cc_final: 0.6742 (ptpp) REVERT: L 56 SER cc_start: 0.8383 (m) cc_final: 0.8137 (p) REVERT: L 105 THR cc_start: 0.8266 (p) cc_final: 0.8014 (p) outliers start: 15 outliers final: 5 residues processed: 191 average time/residue: 0.0943 time to fit residues: 24.1459 Evaluate side-chains 134 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 106 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.1980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 201 HIS ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1059 GLN B1071 GLN C 351 ASN C 445 ASN ** C 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 646 ASN H 3 GLN H 39 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.126538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.107273 restraints weight = 9838.713| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.98 r_work: 0.3016 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7633 Z= 0.185 Angle : 0.601 7.621 10430 Z= 0.303 Chirality : 0.047 0.410 1189 Planarity : 0.004 0.037 1300 Dihedral : 6.780 57.428 1304 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.65 % Allowed : 11.30 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.29), residues: 906 helix: 0.37 (0.59), residues: 84 sheet: -0.24 (0.33), residues: 251 loop : -0.71 (0.27), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 38 TYR 0.021 0.002 TYR B 90 PHE 0.017 0.002 PHE B 130 TRP 0.018 0.001 TRP H 47 HIS 0.004 0.001 HIS H 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.18 ( 7600) covalent geometry : angle 0.58516 / 0.30 (10350) SS BOND : bond 0.00603 / 0.45 ( 19) SS BOND : angle 0.99731 / 0.64 ( 38) hydrogen bonds : bond 0.03771 / 2.36 ( 146) hydrogen bonds : angle 7.06770 / 4.86 ( 354) link_BETA1-4 : bond 0.00370 / 0.18 ( 2) link_BETA1-4 : angle 2.40310 / 1.19 ( 6) link_NAG-ASN : bond 0.00191 / 0.12 ( 12) link_NAG-ASN : angle 2.04439 / 1.30 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 0.278 Fit side-chains REVERT: B 84 TYR cc_start: 0.7680 (m-80) cc_final: 0.7397 (m-80) REVERT: B 213 TYR cc_start: 0.9068 (OUTLIER) cc_final: 0.8358 (t80) REVERT: B 272 GLU cc_start: 0.8449 (mt-10) cc_final: 0.7744 (pm20) REVERT: B 273 HIS cc_start: 0.7891 (m-70) cc_final: 0.7186 (m90) REVERT: B 828 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7586 (mm) REVERT: B 1045 GLN cc_start: 0.8441 (mm-40) cc_final: 0.8215 (mm110) REVERT: B 1078 ILE cc_start: 0.8492 (OUTLIER) cc_final: 0.8182 (mt) REVERT: C 330 ASP cc_start: 0.8777 (p0) cc_final: 0.8526 (p0) REVERT: C 406 SER cc_start: 0.9018 (t) cc_final: 0.8731 (t) REVERT: C 443 SER cc_start: 0.8397 (m) cc_final: 0.8176 (p) REVERT: C 577 PHE cc_start: 0.8671 (p90) cc_final: 0.8271 (p90) REVERT: C 641 TYR cc_start: 0.9000 (m-80) cc_final: 0.8726 (m-80) REVERT: H 20 LEU cc_start: 0.8758 (mt) cc_final: 0.8546 (mp) REVERT: L 45 LYS cc_start: 0.8533 (ttpp) cc_final: 0.8249 (ptpt) REVERT: L 95 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8629 (mp) REVERT: L 97 VAL cc_start: 0.9184 (p) cc_final: 0.8964 (m) outliers start: 30 outliers final: 16 residues processed: 145 average time/residue: 0.0766 time to fit residues: 15.5677 Evaluate side-chains 131 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 820 SER Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 106 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 64 optimal weight: 0.1980 chunk 51 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 142 HIS ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 353 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.123066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.103550 restraints weight = 9812.401| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.01 r_work: 0.2958 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7633 Z= 0.162 Angle : 0.555 7.480 10430 Z= 0.281 Chirality : 0.045 0.379 1189 Planarity : 0.004 0.039 1300 Dihedral : 5.683 53.509 1304 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.77 % Allowed : 11.91 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.28), residues: 906 helix: 0.05 (0.58), residues: 89 sheet: -0.38 (0.31), residues: 265 loop : -0.81 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 34 TYR 0.014 0.001 TYR B 213 PHE 0.018 0.002 PHE B 130 TRP 0.017 0.001 TRP H 47 HIS 0.006 0.001 HIS H 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 ( 7600) covalent geometry : angle 0.54009 / 0.28 (10350) SS BOND : bond 0.00337 / 0.24 ( 19) SS BOND : angle 0.82553 / 0.52 ( 38) hydrogen bonds : bond 0.03753 / 2.32 ( 146) hydrogen bonds : angle 6.78741 / 4.58 ( 354) link_BETA1-4 : bond 0.00333 / 0.16 ( 2) link_BETA1-4 : angle 1.90410 / 0.97 ( 6) link_NAG-ASN : bond 0.00211 / 0.15 ( 12) link_NAG-ASN : angle 1.98384 / 1.25 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 113 time to evaluate : 0.170 Fit side-chains REVERT: B 120 GLU cc_start: 0.8601 (pm20) cc_final: 0.8388 (pt0) REVERT: B 213 TYR cc_start: 0.9108 (OUTLIER) cc_final: 0.8427 (t80) REVERT: B 273 HIS cc_start: 0.8087 (m-70) cc_final: 0.7603 (m90) REVERT: B 828 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7553 (mm) REVERT: B 1045 GLN cc_start: 0.8433 (mm-40) cc_final: 0.8140 (mm110) REVERT: B 1078 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8067 (mt) REVERT: C 330 ASP cc_start: 0.8752 (p0) cc_final: 0.8514 (p0) REVERT: C 406 SER cc_start: 0.9165 (t) cc_final: 0.8919 (t) REVERT: C 577 PHE cc_start: 0.8801 (p90) cc_final: 0.8367 (p90) REVERT: C 627 ILE cc_start: 0.8780 (mm) cc_final: 0.8421 (mt) REVERT: H 58 GLU cc_start: 0.8032 (tt0) cc_final: 0.7828 (tt0) REVERT: L 45 LYS cc_start: 0.8549 (ttpp) cc_final: 0.8220 (ptpt) REVERT: L 95 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8580 (mp) outliers start: 31 outliers final: 20 residues processed: 135 average time/residue: 0.0663 time to fit residues: 12.6937 Evaluate side-chains 129 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 820 SER Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 505 ASP Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 106 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 56 optimal weight: 0.0050 chunk 18 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 821 ASN C 552 ASN C 621 ASN C 630 GLN H 39 GLN L 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.120371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.100762 restraints weight = 9903.662| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.01 r_work: 0.2914 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7633 Z= 0.176 Angle : 0.572 9.855 10430 Z= 0.288 Chirality : 0.046 0.370 1189 Planarity : 0.004 0.050 1300 Dihedral : 5.271 55.231 1302 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 4.13 % Allowed : 13.37 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.28), residues: 906 helix: -0.06 (0.58), residues: 89 sheet: -0.46 (0.32), residues: 262 loop : -0.82 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 398 TYR 0.017 0.002 TYR C 622 PHE 0.018 0.002 PHE B 130 TRP 0.016 0.001 TRP H 47 HIS 0.004 0.001 HIS H 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 ( 7600) covalent geometry : angle 0.55784 / 0.29 (10350) SS BOND : bond 0.00379 / 0.24 ( 19) SS BOND : angle 0.88397 / 0.55 ( 38) hydrogen bonds : bond 0.03356 / 2.09 ( 146) hydrogen bonds : angle 6.65421 / 4.45 ( 354) link_BETA1-4 : bond 0.00349 / 0.17 ( 2) link_BETA1-4 : angle 1.57179 / 0.78 ( 6) link_NAG-ASN : bond 0.00147 / 0.11 ( 12) link_NAG-ASN : angle 1.98824 / 1.26 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 116 time to evaluate : 0.289 Fit side-chains REVERT: B 34 ARG cc_start: 0.7748 (tpm170) cc_final: 0.7440 (tpp-160) REVERT: B 169 ILE cc_start: 0.8686 (mp) cc_final: 0.8426 (mt) REVERT: B 213 TYR cc_start: 0.9120 (OUTLIER) cc_final: 0.8314 (t80) REVERT: B 273 HIS cc_start: 0.8178 (m-70) cc_final: 0.7691 (m90) REVERT: B 814 CYS cc_start: 0.7570 (m) cc_final: 0.7360 (p) REVERT: B 828 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7593 (mm) REVERT: B 1045 GLN cc_start: 0.8451 (mm-40) cc_final: 0.8116 (mm110) REVERT: B 1078 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.8055 (mt) REVERT: C 330 ASP cc_start: 0.8805 (p0) cc_final: 0.8568 (p0) REVERT: C 577 PHE cc_start: 0.8969 (p90) cc_final: 0.8514 (p90) REVERT: C 627 ILE cc_start: 0.8730 (mm) cc_final: 0.8354 (mt) REVERT: H 105 GLN cc_start: 0.8497 (mm-40) cc_final: 0.8254 (tp40) REVERT: L 20 THR cc_start: 0.8448 (m) cc_final: 0.8210 (t) REVERT: L 45 LYS cc_start: 0.8561 (ttpp) cc_final: 0.8221 (ptpt) outliers start: 34 outliers final: 24 residues processed: 140 average time/residue: 0.0784 time to fit residues: 15.4226 Evaluate side-chains 140 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 820 SER Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 505 ASP Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 27 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 62 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 51 optimal weight: 0.0050 chunk 79 optimal weight: 0.1980 chunk 56 optimal weight: 0.0570 overall best weight: 0.3712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.122876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.104200 restraints weight = 9807.024| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.86 r_work: 0.3023 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7633 Z= 0.114 Angle : 0.527 10.914 10430 Z= 0.266 Chirality : 0.044 0.339 1189 Planarity : 0.004 0.050 1300 Dihedral : 4.953 57.516 1301 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.40 % Allowed : 14.46 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.28), residues: 906 helix: -0.13 (0.57), residues: 95 sheet: -0.44 (0.32), residues: 255 loop : -0.87 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 398 TYR 0.014 0.001 TYR C 622 PHE 0.013 0.001 PHE B 130 TRP 0.014 0.001 TRP H 47 HIS 0.004 0.001 HIS H 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 ( 7600) covalent geometry : angle 0.51441 / 0.26 (10350) SS BOND : bond 0.00227 / 0.16 ( 19) SS BOND : angle 0.68079 / 0.42 ( 38) hydrogen bonds : bond 0.03125 / 1.97 ( 146) hydrogen bonds : angle 6.48845 / 4.32 ( 354) link_BETA1-4 : bond 0.00262 / 0.12 ( 2) link_BETA1-4 : angle 1.62529 / 0.83 ( 6) link_NAG-ASN : bond 0.00179 / 0.13 ( 12) link_NAG-ASN : angle 1.89206 / 1.20 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 0.433 Fit side-chains REVERT: B 34 ARG cc_start: 0.7637 (tpm170) cc_final: 0.7403 (tpp-160) REVERT: B 147 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7707 (tp30) REVERT: B 169 ILE cc_start: 0.8668 (mp) cc_final: 0.8400 (mt) REVERT: B 213 TYR cc_start: 0.9070 (OUTLIER) cc_final: 0.8408 (t80) REVERT: B 273 HIS cc_start: 0.8120 (m-70) cc_final: 0.7712 (m90) REVERT: B 828 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7492 (mm) REVERT: B 1045 GLN cc_start: 0.8405 (mm-40) cc_final: 0.8102 (mm110) REVERT: B 1078 ILE cc_start: 0.8330 (OUTLIER) cc_final: 0.7975 (mt) REVERT: C 330 ASP cc_start: 0.8773 (p0) cc_final: 0.8556 (p0) REVERT: C 406 SER cc_start: 0.9239 (t) cc_final: 0.8970 (p) REVERT: C 577 PHE cc_start: 0.8908 (p90) cc_final: 0.8482 (p90) REVERT: C 627 ILE cc_start: 0.8752 (mm) cc_final: 0.8387 (mt) REVERT: H 105 GLN cc_start: 0.8488 (mm-40) cc_final: 0.8274 (tp40) REVERT: L 20 THR cc_start: 0.8382 (m) cc_final: 0.8139 (t) REVERT: L 45 LYS cc_start: 0.8522 (ttpp) cc_final: 0.8267 (ptpt) outliers start: 28 outliers final: 21 residues processed: 137 average time/residue: 0.0708 time to fit residues: 13.4344 Evaluate side-chains 139 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 820 SER Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 505 ASP Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 106 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 25 optimal weight: 0.0670 chunk 10 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 57 optimal weight: 0.0000 chunk 29 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 overall best weight: 0.4522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 ASN ** 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 = 0.3297 r_free = 0.3297 target = 0.121206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.101596 restraints weight = 9935.654| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.01 r_work: 0.2936 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7633 Z= 0.127 Angle : 0.531 9.087 10430 Z= 0.267 Chirality : 0.044 0.331 1189 Planarity : 0.004 0.052 1300 Dihedral : 4.931 59.989 1300 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.89 % Allowed : 13.85 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.28), residues: 906 helix: -0.07 (0.57), residues: 95 sheet: -0.61 (0.31), residues: 267 loop : -0.82 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 398 TYR 0.015 0.001 TYR C 622 PHE 0.015 0.001 PHE B 130 TRP 0.013 0.001 TRP H 47 HIS 0.004 0.001 HIS H 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 7600) covalent geometry : angle 0.51830 / 0.26 (10350) SS BOND : bond 0.00322 / 0.20 ( 19) SS BOND : angle 0.70534 / 0.44 ( 38) hydrogen bonds : bond 0.03082 / 1.93 ( 146) hydrogen bonds : angle 6.46649 / 4.28 ( 354) link_BETA1-4 : bond 0.00380 / 0.18 ( 2) link_BETA1-4 : angle 1.63927 / 0.83 ( 6) link_NAG-ASN : bond 0.00157 / 0.11 ( 12) link_NAG-ASN : angle 1.85647 / 1.19 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 0.278 Fit side-chains REVERT: B 34 ARG cc_start: 0.7635 (tpm170) cc_final: 0.7428 (tpp-160) REVERT: B 147 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7734 (tp30) REVERT: B 169 ILE cc_start: 0.8715 (mp) cc_final: 0.8467 (mt) REVERT: B 213 TYR cc_start: 0.9085 (OUTLIER) cc_final: 0.8443 (t80) REVERT: B 273 HIS cc_start: 0.8136 (m-70) cc_final: 0.7707 (m90) REVERT: B 828 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7538 (mm) REVERT: B 1045 GLN cc_start: 0.8442 (mm-40) cc_final: 0.8111 (mm110) REVERT: B 1069 GLU cc_start: 0.7699 (tm-30) cc_final: 0.7400 (tm-30) REVERT: B 1078 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.7957 (mt) REVERT: C 330 ASP cc_start: 0.8778 (p0) cc_final: 0.8558 (p0) REVERT: C 406 SER cc_start: 0.9249 (t) cc_final: 0.8968 (p) REVERT: C 627 ILE cc_start: 0.8680 (mm) cc_final: 0.8320 (mt) REVERT: H 105 GLN cc_start: 0.8521 (mm-40) cc_final: 0.8314 (tp40) REVERT: L 20 THR cc_start: 0.8446 (m) cc_final: 0.8197 (t) REVERT: L 45 LYS cc_start: 0.8546 (ttpp) cc_final: 0.8233 (ptpt) outliers start: 32 outliers final: 24 residues processed: 136 average time/residue: 0.0808 time to fit residues: 15.2230 Evaluate side-chains 138 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 820 SER Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 505 ASP Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 106 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 44 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 17 optimal weight: 0.1980 chunk 50 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 445 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.116322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.096645 restraints weight = 10052.459| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.00 r_work: 0.2849 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 7633 Z= 0.223 Angle : 0.619 11.150 10430 Z= 0.312 Chirality : 0.047 0.377 1189 Planarity : 0.004 0.052 1300 Dihedral : 5.298 56.858 1300 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 4.37 % Allowed : 13.97 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.28), residues: 906 helix: -0.43 (0.55), residues: 96 sheet: -0.75 (0.31), residues: 274 loop : -0.88 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 38 TYR 0.020 0.002 TYR C 622 PHE 0.021 0.002 PHE B 130 TRP 0.017 0.002 TRP H 47 HIS 0.005 0.001 HIS B 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.22 ( 7600) covalent geometry : angle 0.60461 / 0.31 (10350) SS BOND : bond 0.00448 / 0.30 ( 19) SS BOND : angle 1.10041 / 0.70 ( 38) hydrogen bonds : bond 0.03487 / 2.15 ( 146) hydrogen bonds : angle 6.68566 / 4.42 ( 354) link_BETA1-4 : bond 0.00344 / 0.17 ( 2) link_BETA1-4 : angle 1.57002 / 0.79 ( 6) link_NAG-ASN : bond 0.00148 / 0.10 ( 12) link_NAG-ASN : angle 2.04077 / 1.32 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 114 time to evaluate : 0.292 Fit side-chains REVERT: B 147 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7890 (tp30) REVERT: B 169 ILE cc_start: 0.8832 (mp) cc_final: 0.8612 (mt) REVERT: B 213 TYR cc_start: 0.9210 (OUTLIER) cc_final: 0.8130 (t80) REVERT: B 273 HIS cc_start: 0.8215 (m-70) cc_final: 0.7809 (m90) REVERT: B 1045 GLN cc_start: 0.8507 (mm-40) cc_final: 0.8176 (mm110) REVERT: B 1069 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7469 (tm-30) REVERT: B 1078 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.7978 (mt) REVERT: C 566 PHE cc_start: 0.7492 (t80) cc_final: 0.7051 (t80) REVERT: H 105 GLN cc_start: 0.8583 (mm-40) cc_final: 0.8363 (tp40) REVERT: L 20 THR cc_start: 0.8540 (m) cc_final: 0.8303 (t) REVERT: L 45 LYS cc_start: 0.8503 (ttpp) cc_final: 0.8151 (ptpt) REVERT: L 93 ASP cc_start: 0.8415 (m-30) cc_final: 0.8187 (m-30) REVERT: L 103 LYS cc_start: 0.8401 (tppp) cc_final: 0.7865 (tptm) outliers start: 36 outliers final: 30 residues processed: 141 average time/residue: 0.0861 time to fit residues: 16.7798 Evaluate side-chains 142 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 109 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 820 SER Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain L residue 106 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 ASN ** 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 = 0.3241 r_free = 0.3241 target = 0.117110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.097526 restraints weight = 10076.345| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.00 r_work: 0.2866 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7633 Z= 0.170 Angle : 0.568 9.136 10430 Z= 0.287 Chirality : 0.045 0.348 1189 Planarity : 0.004 0.051 1300 Dihedral : 5.199 54.896 1300 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.89 % Allowed : 14.09 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.28), residues: 906 helix: -0.23 (0.57), residues: 90 sheet: -0.69 (0.32), residues: 262 loop : -0.90 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 38 TYR 0.016 0.001 TYR B 213 PHE 0.017 0.001 PHE B 130 TRP 0.016 0.001 TRP H 47 HIS 0.004 0.001 HIS B 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.17 ( 7600) covalent geometry : angle 0.55423 / 0.28 (10350) SS BOND : bond 0.00327 / 0.22 ( 19) SS BOND : angle 0.84369 / 0.52 ( 38) hydrogen bonds : bond 0.03232 / 2.02 ( 146) hydrogen bonds : angle 6.64212 / 4.39 ( 354) link_BETA1-4 : bond 0.00270 / 0.13 ( 2) link_BETA1-4 : angle 1.58676 / 0.82 ( 6) link_NAG-ASN : bond 0.00144 / 0.11 ( 12) link_NAG-ASN : angle 1.96970 / 1.26 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 0.290 Fit side-chains REVERT: B 25 ILE cc_start: 0.7560 (mm) cc_final: 0.7270 (mm) REVERT: B 147 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7729 (tp30) REVERT: B 169 ILE cc_start: 0.8850 (mp) cc_final: 0.8631 (mt) REVERT: B 213 TYR cc_start: 0.9156 (OUTLIER) cc_final: 0.8220 (t80) REVERT: B 273 HIS cc_start: 0.8226 (m-70) cc_final: 0.7830 (m90) REVERT: B 1045 GLN cc_start: 0.8516 (mm-40) cc_final: 0.8189 (mm110) REVERT: B 1069 GLU cc_start: 0.7806 (tm-30) cc_final: 0.7493 (tm-30) REVERT: B 1078 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.7896 (mt) REVERT: C 330 ASP cc_start: 0.8873 (p0) cc_final: 0.8576 (p0) REVERT: H 105 GLN cc_start: 0.8545 (mm-40) cc_final: 0.8319 (tp40) REVERT: L 20 THR cc_start: 0.8526 (m) cc_final: 0.8273 (t) REVERT: L 45 LYS cc_start: 0.8494 (ttpp) cc_final: 0.8102 (ptpt) REVERT: L 103 LYS cc_start: 0.8418 (tppp) cc_final: 0.7880 (tptm) outliers start: 32 outliers final: 29 residues processed: 135 average time/residue: 0.0867 time to fit residues: 16.1373 Evaluate side-chains 140 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 108 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 820 SER Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain L residue 106 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 55 optimal weight: 0.2980 chunk 4 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 56 optimal weight: 0.4980 chunk 38 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 37 optimal weight: 0.2980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 ASN ** 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 = 0.3266 r_free = 0.3266 target = 0.118947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.099337 restraints weight = 9939.841| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.00 r_work: 0.2895 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7633 Z= 0.131 Angle : 0.538 8.513 10430 Z= 0.273 Chirality : 0.044 0.326 1189 Planarity : 0.004 0.049 1300 Dihedral : 5.098 56.002 1300 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.89 % Allowed : 14.34 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.28), residues: 906 helix: -0.27 (0.57), residues: 90 sheet: -0.72 (0.32), residues: 263 loop : -0.85 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 94 TYR 0.015 0.001 TYR B 213 PHE 0.015 0.001 PHE B 130 TRP 0.014 0.001 TRP H 47 HIS 0.004 0.001 HIS B 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 ( 7600) covalent geometry : angle 0.52509 / 0.27 (10350) SS BOND : bond 0.00255 / 0.18 ( 19) SS BOND : angle 0.69272 / 0.43 ( 38) hydrogen bonds : bond 0.03080 / 1.93 ( 146) hydrogen bonds : angle 6.56053 / 4.33 ( 354) link_BETA1-4 : bond 0.00393 / 0.19 ( 2) link_BETA1-4 : angle 1.67597 / 0.85 ( 6) link_NAG-ASN : bond 0.00151 / 0.11 ( 12) link_NAG-ASN : angle 1.88288 / 1.20 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 0.308 Fit side-chains REVERT: B 25 ILE cc_start: 0.7569 (mm) cc_final: 0.7273 (mm) REVERT: B 147 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7702 (tp30) REVERT: B 169 ILE cc_start: 0.8851 (mp) cc_final: 0.8633 (mt) REVERT: B 213 TYR cc_start: 0.9124 (OUTLIER) cc_final: 0.8261 (t80) REVERT: B 273 HIS cc_start: 0.8208 (m-70) cc_final: 0.7834 (m90) REVERT: B 1045 GLN cc_start: 0.8475 (mm-40) cc_final: 0.8155 (mm110) REVERT: B 1069 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7538 (tm-30) REVERT: B 1078 ILE cc_start: 0.8272 (OUTLIER) cc_final: 0.7897 (mt) REVERT: H 105 GLN cc_start: 0.8557 (mm-40) cc_final: 0.8343 (tp40) REVERT: L 20 THR cc_start: 0.8483 (m) cc_final: 0.8215 (t) REVERT: L 45 LYS cc_start: 0.8483 (ttpp) cc_final: 0.8156 (ptpt) REVERT: L 103 LYS cc_start: 0.8443 (tppp) cc_final: 0.7907 (tptm) outliers start: 32 outliers final: 26 residues processed: 133 average time/residue: 0.0837 time to fit residues: 15.5771 Evaluate side-chains 136 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 107 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 820 SER Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 400 ASP Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain L residue 106 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 89 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 23 optimal weight: 0.3980 chunk 51 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 ASN ** 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 = 0.3247 r_free = 0.3247 target = 0.117497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.098484 restraints weight = 9932.182| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.88 r_work: 0.2952 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7633 Z= 0.182 Angle : 0.580 8.132 10430 Z= 0.293 Chirality : 0.046 0.350 1189 Planarity : 0.004 0.048 1300 Dihedral : 5.219 54.893 1300 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.52 % Allowed : 14.82 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.28), residues: 906 helix: -0.40 (0.56), residues: 90 sheet: -0.67 (0.32), residues: 267 loop : -0.91 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 94 TYR 0.017 0.001 TYR C 622 PHE 0.019 0.002 PHE B 130 TRP 0.015 0.001 TRP H 47 HIS 0.005 0.001 HIS B 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.18 ( 7600) covalent geometry : angle 0.56651 / 0.29 (10350) SS BOND : bond 0.00361 / 0.25 ( 19) SS BOND : angle 0.87420 / 0.54 ( 38) hydrogen bonds : bond 0.03227 / 2.01 ( 146) hydrogen bonds : angle 6.62645 / 4.38 ( 354) link_BETA1-4 : bond 0.00419 / 0.20 ( 2) link_BETA1-4 : angle 1.65835 / 0.84 ( 6) link_NAG-ASN : bond 0.00144 / 0.11 ( 12) link_NAG-ASN : angle 1.95543 / 1.25 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 106 time to evaluate : 0.271 Fit side-chains REVERT: B 25 ILE cc_start: 0.7783 (mm) cc_final: 0.7564 (mm) REVERT: B 147 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7743 (tp30) REVERT: B 169 ILE cc_start: 0.8897 (mp) cc_final: 0.8683 (mt) REVERT: B 213 TYR cc_start: 0.9199 (OUTLIER) cc_final: 0.8276 (t80) REVERT: B 273 HIS cc_start: 0.8248 (m-70) cc_final: 0.7910 (m90) REVERT: B 1045 GLN cc_start: 0.8496 (mm-40) cc_final: 0.8191 (mm110) REVERT: B 1078 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.7950 (mt) REVERT: H 94 ARG cc_start: 0.9005 (mtm110) cc_final: 0.8757 (mtm180) REVERT: H 105 GLN cc_start: 0.8563 (mm-40) cc_final: 0.8330 (tp40) REVERT: L 20 THR cc_start: 0.8474 (m) cc_final: 0.8233 (t) REVERT: L 45 LYS cc_start: 0.8490 (ttpp) cc_final: 0.8152 (ptpt) REVERT: L 103 LYS cc_start: 0.8509 (tppp) cc_final: 0.8007 (tptm) outliers start: 29 outliers final: 25 residues processed: 127 average time/residue: 0.0908 time to fit residues: 15.8762 Evaluate side-chains 131 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 820 SER Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 400 ASP Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain L residue 106 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 84 optimal weight: 0.9990 chunk 75 optimal weight: 0.4980 chunk 31 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 54 optimal weight: 0.0020 chunk 2 optimal weight: 1.9990 chunk 55 optimal weight: 0.2980 chunk 89 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 overall best weight: 0.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 GLN ** C 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.119120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.099485 restraints weight = 9875.667| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.00 r_work: 0.2898 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7633 Z= 0.125 Angle : 0.547 7.714 10430 Z= 0.278 Chirality : 0.044 0.320 1189 Planarity : 0.004 0.050 1300 Dihedral : 5.025 48.375 1300 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.28 % Allowed : 15.19 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.28), residues: 906 helix: -0.28 (0.57), residues: 90 sheet: -0.59 (0.33), residues: 257 loop : -0.93 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 94 TYR 0.015 0.001 TYR B 213 PHE 0.017 0.001 PHE C 566 TRP 0.013 0.001 TRP H 47 HIS 0.004 0.001 HIS B 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.12 ( 7600) covalent geometry : angle 0.53527 / 0.28 (10350) SS BOND : bond 0.00238 / 0.17 ( 19) SS BOND : angle 0.64699 / 0.40 ( 38) hydrogen bonds : bond 0.03030 / 1.91 ( 146) hydrogen bonds : angle 6.53467 / 4.31 ( 354) link_BETA1-4 : bond 0.00369 / 0.18 ( 2) link_BETA1-4 : angle 1.69817 / 0.87 ( 6) link_NAG-ASN : bond 0.00158 / 0.12 ( 12) link_NAG-ASN : angle 1.87937 / 1.19 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2098.67 seconds wall clock time: 36 minutes 47.23 seconds (2207.23 seconds total)