Starting phenix.real_space_refine on Thu Sep 18 03:26:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ckv_45655/09_2025/9ckv_45655_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ckv_45655/09_2025/9ckv_45655.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ckv_45655/09_2025/9ckv_45655.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ckv_45655/09_2025/9ckv_45655.map" model { file = "/net/cci-nas-00/data/ceres_data/9ckv_45655/09_2025/9ckv_45655_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ckv_45655/09_2025/9ckv_45655_trim.cif" } resolution = 3.19 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= 0.034 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: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 Mn 3 7.51 5 S 23 5.16 5 C 4350 2.51 5 N 1128 2.21 5 O 1385 1.98 5 H 6375 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13268 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 6361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 6361 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 31, 'TRANS': 414} Chain breaks: 1 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 7, 'GLN:plan1': 1, 'ASP:plan': 3, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 5566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 5566 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 14, 'TRANS': 346} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 1083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1083 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" 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: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} 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 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 31 Unusual residues: {' MN': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.64, per 1000 atoms: 0.20 Number of scatterers: 13268 At special positions: 0 Unit cell: (75.174, 96.492, 136.884, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 3 24.99 Ca 4 19.99 S 23 16.00 O 1385 8.00 N 1128 7.00 C 4350 6.00 H 6375 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 58 " - pdb=" SG CYS A 67 " distance=2.03 Simple disulfide: pdb=" SG CYS A 115 " - pdb=" SG CYS A 135 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 187 " - pdb=" SG CYS B 193 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 281 " distance=2.03 Simple disulfide: pdb=" SG CYS B 381 " - pdb=" SG CYS B 395 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA G 3 " - " MAN G 6 " " MAN G 4 " - " MAN G 5 " ALPHA1-6 " BMA G 3 " - " MAN G 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG B 801 " - " ASN B 397 " " NAG B 802 " - " ASN B 386 " " NAG D 1 " - " ASN A 43 " " NAG E 1 " - " ASN A 256 " " NAG F 1 " - " ASN A 266 " " NAG G 1 " - " ASN A 275 " " NAG H 1 " - " ASN A 141 " " NAG I 1 " - " ASN B 343 " Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 426.1 milliseconds Enol-peptide restraints added in 1.2 microseconds 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1558 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 13 sheets defined 19.8% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 184 through 189 Processing helix chain 'A' and resid 196 through 204 Processing helix chain 'A' and resid 223 through 227 Processing helix chain 'B' and resid 132 through 136 Processing helix chain 'B' and resid 138 through 157 Processing helix chain 'B' and resid 172 through 176 Processing helix chain 'B' and resid 179 through 185 removed outlier: 3.969A pdb=" N ARG B 184 " --> pdb=" O PRO B 180 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 217 removed outlier: 4.063A pdb=" N PHE B 212 " --> pdb=" O LYS B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 241 removed outlier: 4.184A pdb=" N ALA B 234 " --> pdb=" O GLY B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 246 Processing helix chain 'B' and resid 266 through 272 removed outlier: 3.716A pdb=" N LYS B 269 " --> pdb=" O GLY B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 293 removed outlier: 4.497A pdb=" N HIS B 292 " --> pdb=" O THR B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 310 Processing helix chain 'B' and resid 321 through 332 removed outlier: 3.569A pdb=" N TYR B 325 " --> pdb=" O PHE B 321 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN B 330 " --> pdb=" O LYS B 326 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU B 331 " --> pdb=" O GLU B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 357 removed outlier: 3.696A pdb=" N ILE B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 384 No H-bonds generated for 'chain 'B' and resid 382 through 384' Processing helix chain 'B' and resid 390 through 392 No H-bonds generated for 'chain 'B' and resid 390 through 392' Processing helix chain 'C' and resid 12 through 26 removed outlier: 3.995A pdb=" N LEU C 16 " --> pdb=" O PRO C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 58 Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 6.151A pdb=" N ASP A 432 " --> pdb=" O GLY A 422 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 94 through 95 removed outlier: 3.797A pdb=" N SER A 120 " --> pdb=" O TYR A 95 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASP A 130 " --> pdb=" O TRP A 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 105 through 108 removed outlier: 3.649A pdb=" N ARG A 144 " --> pdb=" O THR A 139 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 172 removed outlier: 3.589A pdb=" N SER A 169 " --> pdb=" O GLY A 181 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 235 through 238 removed outlier: 6.546A pdb=" N VAL A 262 " --> pdb=" O ASN A 275 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASN A 275 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE A 264 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 289 through 292 Processing sheet with id=AA8, first strand: chain 'A' and resid 310 through 312 Processing sheet with id=AA9, first strand: chain 'A' and resid 355 through 359 removed outlier: 5.878A pdb=" N ASP A 368 " --> pdb=" O LEU A 358 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN A 400 " --> pdb=" O VAL A 386 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 66 through 72 removed outlier: 3.599A pdb=" N SER B 66 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP B 68 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLN B 98 " --> pdb=" O LYS B 70 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ASN B 72 " --> pdb=" O PRO B 96 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL B 362 " --> pdb=" O SER B 396 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N SER B 396 " --> pdb=" O VAL B 362 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N LEU B 364 " --> pdb=" O LYS B 394 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LYS B 394 " --> pdb=" O LEU B 364 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 109 through 116 removed outlier: 3.817A pdb=" N GLN B 405 " --> pdb=" O TYR B 380 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 200 through 206 removed outlier: 6.720A pdb=" N VAL B 202 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N SER B 166 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N SER B 204 " --> pdb=" O PHE B 164 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N PHE B 164 " --> pdb=" O SER B 204 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET B 129 " --> pdb=" O GLY B 165 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE B 167 " --> pdb=" O MET B 129 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ARG B 252 " --> pdb=" O GLN B 312 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N ILE B 314 " --> pdb=" O ARG B 252 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU B 254 " --> pdb=" O ILE B 314 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ALA B 316 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N PHE B 256 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N THR B 318 " --> pdb=" O PHE B 256 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N THR B 258 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N ALA B 336 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N THR B 313 " --> pdb=" O ALA B 336 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N GLY B 338 " --> pdb=" O THR B 313 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N PHE B 315 " --> pdb=" O GLY B 338 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU B 340 " --> pdb=" O PHE B 315 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL B 317 " --> pdb=" O LEU B 340 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 30 through 32 removed outlier: 3.600A pdb=" N ARG C 31 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU C 3 " --> pdb=" O LEU C 39 " (cutoff:3.500A) 243 hydrogen bonds defined for protein. 636 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: 2.58 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6374 1.03 - 1.23: 34 1.23 - 1.42: 2954 1.42 - 1.62: 4014 1.62 - 1.81: 33 Bond restraints: 13409 Sorted by residual: bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.57e+00 bond pdb=" C3 MAN G 4 " pdb=" O3 MAN G 4 " ideal model delta sigma weight residual 1.408 1.446 -0.038 2.00e-02 2.50e+03 3.53e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.43e+00 bond pdb=" N PHE A 1 " pdb=" CA PHE A 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.18e+00 bond pdb=" N SER C 1 " pdb=" CA SER C 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.84e+00 ... (remaining 13404 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 22947 1.34 - 2.68: 960 2.68 - 4.02: 89 4.02 - 5.36: 42 5.36 - 6.70: 8 Bond angle restraints: 24046 Sorted by residual: angle pdb=" C3 MAN G 4 " pdb=" C2 MAN G 4 " pdb=" O2 MAN G 4 " ideal model delta sigma weight residual 111.77 105.07 6.70 3.00e+00 1.11e-01 4.98e+00 angle pdb=" C3 BMA D 3 " pdb=" C2 BMA D 3 " pdb=" O2 BMA D 3 " ideal model delta sigma weight residual 112.95 106.57 6.38 3.00e+00 1.11e-01 4.52e+00 angle pdb=" C4 BMA D 3 " pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sigma weight residual 113.24 107.03 6.21 3.00e+00 1.11e-01 4.28e+00 angle pdb=" C4 BMA G 3 " pdb=" C3 BMA G 3 " pdb=" O3 BMA G 3 " ideal model delta sigma weight residual 113.17 106.99 6.18 3.00e+00 1.11e-01 4.24e+00 angle pdb=" C3 MAN G 6 " pdb=" C2 MAN G 6 " pdb=" O2 MAN G 6 " ideal model delta sigma weight residual 111.77 105.71 6.06 3.00e+00 1.11e-01 4.08e+00 ... (remaining 24041 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.49: 6201 24.49 - 48.98: 352 48.98 - 73.47: 91 73.47 - 97.95: 24 97.95 - 122.44: 5 Dihedral angle restraints: 6673 sinusoidal: 3767 harmonic: 2906 Sorted by residual: dihedral pdb=" CB CYS B 381 " pdb=" SG CYS B 381 " pdb=" SG CYS B 395 " pdb=" CB CYS B 395 " ideal model delta sinusoidal sigma weight residual 93.00 168.06 -75.06 1 1.00e+01 1.00e-02 7.12e+01 dihedral pdb=" CB CYS A 151 " pdb=" SG CYS A 151 " pdb=" SG CYS A 164 " pdb=" CB CYS A 164 " ideal model delta sinusoidal sigma weight residual 93.00 49.74 43.26 1 1.00e+01 1.00e-02 2.61e+01 dihedral pdb=" C2 MAN G 6 " pdb=" C1 MAN G 6 " pdb=" O5 MAN G 6 " pdb=" C5 MAN G 6 " ideal model delta sinusoidal sigma weight residual -57.62 64.82 -122.44 1 3.00e+01 1.11e-03 1.64e+01 ... (remaining 6670 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 900 0.056 - 0.111: 144 0.111 - 0.167: 55 0.167 - 0.222: 3 0.222 - 0.278: 2 Chirality restraints: 1104 Sorted by residual: chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 1.41e+00 ... (remaining 1101 not shown) Planarity restraints: 2055 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 121 " -0.010 2.00e-02 2.50e+03 1.16e-02 5.35e+00 pdb=" CG TRP A 121 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP A 121 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP A 121 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 121 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 121 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 121 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 121 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 121 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 121 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TRP A 121 " -0.008 2.00e-02 2.50e+03 pdb=" HE1 TRP A 121 " -0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP A 121 " 0.002 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 121 " 0.001 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 121 " -0.002 2.00e-02 2.50e+03 pdb=" HH2 TRP A 121 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 20 " 0.131 9.50e-02 1.11e+02 4.40e-02 2.33e+00 pdb=" NE ARG C 20 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG C 20 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG C 20 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 20 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG C 20 " -0.005 2.00e-02 2.50e+03 pdb="HH12 ARG C 20 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG C 20 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG C 20 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS B 415 " -0.021 5.00e-02 4.00e+02 3.17e-02 1.61e+00 pdb=" N PRO B 416 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO B 416 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 416 " -0.018 5.00e-02 4.00e+02 ... (remaining 2052 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.30: 2689 2.30 - 2.88: 28956 2.88 - 3.45: 32634 3.45 - 4.03: 46075 4.03 - 4.60: 69341 Nonbonded interactions: 179695 Sorted by model distance: nonbonded pdb=" O LYS B 305 " pdb="HD21 ASN B 309 " model vdw 1.726 2.450 nonbonded pdb=" OD2 ASP B 226 " pdb=" HE2 HIS B 263 " model vdw 1.730 2.450 nonbonded pdb=" OE2 GLU B 229 " pdb="MN MN B 803 " model vdw 1.734 2.200 nonbonded pdb=" OD2 ASP A 346 " pdb=" H GLY A 377 " model vdw 1.740 2.450 nonbonded pdb=" OE1 GLU A 320 " pdb=" HG SER B 298 " model vdw 1.741 2.450 ... (remaining 179690 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.340 Find NCS groups from input model: 0.070 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7059 Z= 0.201 Angle : 0.703 10.110 9617 Z= 0.315 Chirality : 0.049 0.278 1104 Planarity : 0.004 0.057 1226 Dihedral : 16.353 122.444 2833 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.29), residues: 862 helix: 2.07 (0.48), residues: 119 sheet: -0.05 (0.32), residues: 275 loop : -0.63 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 20 TYR 0.015 0.001 TYR B 325 PHE 0.012 0.001 PHE A 248 TRP 0.037 0.002 TRP A 121 HIS 0.002 0.001 HIS C 34 Details of bonding type rmsd covalent geometry : bond 0.00453 ( 7034) covalent geometry : angle 0.66015 ( 9548) SS BOND : bond 0.00168 ( 6) SS BOND : angle 0.60618 ( 12) hydrogen bonds : bond 0.21657 ( 243) hydrogen bonds : angle 9.50873 ( 636) link_ALPHA1-3 : bond 0.00769 ( 2) link_ALPHA1-3 : angle 3.77253 ( 6) link_ALPHA1-6 : bond 0.00824 ( 1) link_ALPHA1-6 : angle 1.89533 ( 3) link_BETA1-4 : bond 0.01363 ( 8) link_BETA1-4 : angle 4.31099 ( 24) link_NAG-ASN : bond 0.00470 ( 8) link_NAG-ASN : angle 1.45798 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 75 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue LYS 397 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Evaluate side-chains 85 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 ARG cc_start: 0.8509 (mtm180) cc_final: 0.8096 (mtm180) REVERT: A 244 ASP cc_start: 0.8110 (p0) cc_final: 0.7713 (t0) REVERT: A 269 ASP cc_start: 0.7418 (m-30) cc_final: 0.6861 (m-30) REVERT: A 335 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7145 (mp0) REVERT: A 449 ARG cc_start: 0.4193 (ttt90) cc_final: 0.1788 (mtm110) REVERT: B 153 MET cc_start: 0.7152 (mmp) cc_final: 0.6909 (mmp) REVERT: B 184 ARG cc_start: 0.7270 (mmp80) cc_final: 0.7043 (mtm110) REVERT: B 200 LYS cc_start: 0.7765 (tttt) cc_final: 0.7286 (ttpt) REVERT: B 220 ARG cc_start: 0.8388 (mtm110) cc_final: 0.8050 (mtm110) REVERT: C 15 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7549 (mm-30) REVERT: C 20 ARG cc_start: 0.7646 (ttp80) cc_final: 0.7374 (ttt180) REVERT: C 21 GLU cc_start: 0.8108 (tm-30) cc_final: 0.7838 (tm-30) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.3953 time to fit residues: 39.2080 Evaluate side-chains 63 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.0470 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 overall best weight: 0.7282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.120848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.076718 restraints weight = 29620.915| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 3.12 r_work: 0.2863 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7059 Z= 0.148 Angle : 0.568 6.597 9617 Z= 0.284 Chirality : 0.045 0.205 1104 Planarity : 0.004 0.051 1226 Dihedral : 11.524 105.102 1333 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.28 % Allowed : 3.52 % Favored : 96.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.29), residues: 862 helix: 1.84 (0.47), residues: 125 sheet: -0.05 (0.31), residues: 284 loop : -0.68 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 271 TYR 0.009 0.001 TYR B 377 PHE 0.008 0.001 PHE B 212 TRP 0.012 0.001 TRP A 121 HIS 0.002 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 7034) covalent geometry : angle 0.54468 ( 9548) SS BOND : bond 0.00141 ( 6) SS BOND : angle 2.10310 ( 12) hydrogen bonds : bond 0.04945 ( 243) hydrogen bonds : angle 7.04967 ( 636) link_ALPHA1-3 : bond 0.00794 ( 2) link_ALPHA1-3 : angle 2.50963 ( 6) link_ALPHA1-6 : bond 0.00524 ( 1) link_ALPHA1-6 : angle 2.65902 ( 3) link_BETA1-4 : bond 0.00628 ( 8) link_BETA1-4 : angle 2.37497 ( 24) link_NAG-ASN : bond 0.00266 ( 8) link_NAG-ASN : angle 0.99429 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 75 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue LYS 397 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Evaluate side-chains 66 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 ARG cc_start: 0.8879 (mtm180) cc_final: 0.8551 (mtm180) REVERT: A 244 ASP cc_start: 0.8417 (p0) cc_final: 0.7874 (t0) REVERT: A 269 ASP cc_start: 0.7756 (m-30) cc_final: 0.7282 (m-30) REVERT: A 444 VAL cc_start: 0.9152 (m) cc_final: 0.8932 (t) REVERT: A 449 ARG cc_start: 0.4937 (ttt90) cc_final: 0.2320 (mtm110) REVERT: B 200 LYS cc_start: 0.8408 (tttt) cc_final: 0.7973 (ttpt) REVERT: B 220 ARG cc_start: 0.8722 (mtm110) cc_final: 0.8333 (mtm110) REVERT: C 62 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7733 (mt-10) outliers start: 2 outliers final: 1 residues processed: 65 average time/residue: 0.4740 time to fit residues: 35.5169 Evaluate side-chains 62 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 1 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 79 optimal weight: 8.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.119218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.074895 restraints weight = 29911.326| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 3.14 r_work: 0.2827 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7059 Z= 0.205 Angle : 0.574 6.638 9617 Z= 0.285 Chirality : 0.046 0.219 1104 Planarity : 0.004 0.037 1226 Dihedral : 10.069 101.236 1333 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.70 % Allowed : 5.21 % Favored : 94.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.29), residues: 862 helix: 1.62 (0.46), residues: 125 sheet: -0.16 (0.31), residues: 285 loop : -0.84 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 271 TYR 0.011 0.001 TYR A 287 PHE 0.009 0.001 PHE B 164 TRP 0.008 0.001 TRP A 121 HIS 0.005 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00485 ( 7034) covalent geometry : angle 0.55082 ( 9548) SS BOND : bond 0.00822 ( 6) SS BOND : angle 1.73448 ( 12) hydrogen bonds : bond 0.04129 ( 243) hydrogen bonds : angle 6.40562 ( 636) link_ALPHA1-3 : bond 0.00527 ( 2) link_ALPHA1-3 : angle 3.06416 ( 6) link_ALPHA1-6 : bond 0.00499 ( 1) link_ALPHA1-6 : angle 2.59474 ( 3) link_BETA1-4 : bond 0.00557 ( 8) link_BETA1-4 : angle 2.37649 ( 24) link_NAG-ASN : bond 0.00334 ( 8) link_NAG-ASN : angle 1.07010 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 75 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue LYS 397 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Evaluate side-chains 60 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 244 ASP cc_start: 0.8447 (p0) cc_final: 0.7990 (t0) REVERT: A 269 ASP cc_start: 0.7722 (m-30) cc_final: 0.7196 (m-30) REVERT: A 449 ARG cc_start: 0.4891 (ttt90) cc_final: 0.4131 (ttp80) REVERT: B 184 ARG cc_start: 0.7438 (mtm110) cc_final: 0.7085 (tpp80) REVERT: B 185 ASN cc_start: 0.8734 (p0) cc_final: 0.8430 (p0) REVERT: B 200 LYS cc_start: 0.8456 (tttt) cc_final: 0.7998 (ttpt) REVERT: B 220 ARG cc_start: 0.8686 (mtm110) cc_final: 0.8392 (mtm110) outliers start: 5 outliers final: 4 residues processed: 58 average time/residue: 0.5251 time to fit residues: 34.7315 Evaluate side-chains 53 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 30 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 81 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 63 optimal weight: 0.3980 chunk 55 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 78 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.117790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.075542 restraints weight = 29340.034| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.99 r_work: 0.2826 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7059 Z= 0.178 Angle : 0.544 5.099 9617 Z= 0.268 Chirality : 0.046 0.232 1104 Planarity : 0.004 0.041 1226 Dihedral : 9.344 101.792 1333 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.99 % Allowed : 6.20 % Favored : 92.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.29), residues: 862 helix: 1.64 (0.47), residues: 126 sheet: -0.19 (0.31), residues: 285 loop : -0.94 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 20 TYR 0.010 0.001 TYR A 327 PHE 0.008 0.001 PHE B 212 TRP 0.007 0.001 TRP B 247 HIS 0.005 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 7034) covalent geometry : angle 0.52163 ( 9548) SS BOND : bond 0.00202 ( 6) SS BOND : angle 1.80020 ( 12) hydrogen bonds : bond 0.03516 ( 243) hydrogen bonds : angle 6.00473 ( 636) link_ALPHA1-3 : bond 0.00602 ( 2) link_ALPHA1-3 : angle 2.69873 ( 6) link_ALPHA1-6 : bond 0.00729 ( 1) link_ALPHA1-6 : angle 2.72405 ( 3) link_BETA1-4 : bond 0.00610 ( 8) link_BETA1-4 : angle 2.24602 ( 24) link_NAG-ASN : bond 0.00247 ( 8) link_NAG-ASN : angle 0.91701 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 75 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue LYS 397 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Evaluate side-chains 58 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 244 ASP cc_start: 0.8449 (p0) cc_final: 0.8059 (t0) REVERT: A 269 ASP cc_start: 0.7726 (m-30) cc_final: 0.7198 (m-30) REVERT: A 449 ARG cc_start: 0.4707 (ttt90) cc_final: 0.2477 (mtm110) REVERT: B 185 ASN cc_start: 0.8698 (p0) cc_final: 0.8367 (p0) REVERT: B 200 LYS cc_start: 0.8434 (tttt) cc_final: 0.7970 (ttpt) outliers start: 7 outliers final: 6 residues processed: 54 average time/residue: 0.3904 time to fit residues: 24.9677 Evaluate side-chains 54 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 32 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 54 optimal weight: 0.0970 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.119118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.075379 restraints weight = 29608.234| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 3.11 r_work: 0.2829 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7059 Z= 0.145 Angle : 0.521 5.203 9617 Z= 0.254 Chirality : 0.045 0.237 1104 Planarity : 0.003 0.034 1226 Dihedral : 9.041 100.472 1333 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.41 % Allowed : 6.20 % Favored : 92.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.29), residues: 862 helix: 1.48 (0.46), residues: 133 sheet: -0.20 (0.31), residues: 285 loop : -0.91 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 20 TYR 0.007 0.001 TYR B 325 PHE 0.008 0.001 PHE A 172 TRP 0.008 0.001 TRP B 247 HIS 0.004 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 7034) covalent geometry : angle 0.50108 ( 9548) SS BOND : bond 0.00204 ( 6) SS BOND : angle 1.40455 ( 12) hydrogen bonds : bond 0.03284 ( 243) hydrogen bonds : angle 5.82681 ( 636) link_ALPHA1-3 : bond 0.00687 ( 2) link_ALPHA1-3 : angle 2.77023 ( 6) link_ALPHA1-6 : bond 0.00764 ( 1) link_ALPHA1-6 : angle 2.66165 ( 3) link_BETA1-4 : bond 0.00612 ( 8) link_BETA1-4 : angle 2.05721 ( 24) link_NAG-ASN : bond 0.00238 ( 8) link_NAG-ASN : angle 0.92723 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 75 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue LYS 397 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Evaluate side-chains 61 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: A 244 ASP cc_start: 0.8351 (p0) cc_final: 0.8054 (t0) REVERT: A 269 ASP cc_start: 0.7717 (m-30) cc_final: 0.7192 (m-30) REVERT: A 449 ARG cc_start: 0.4924 (ttt90) cc_final: 0.2936 (mtp85) REVERT: B 185 ASN cc_start: 0.8718 (p0) cc_final: 0.8387 (p0) REVERT: B 200 LYS cc_start: 0.8435 (tttt) cc_final: 0.7959 (ttpt) outliers start: 10 outliers final: 8 residues processed: 55 average time/residue: 0.3845 time to fit residues: 25.0322 Evaluate side-chains 57 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 43 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 26 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 12 optimal weight: 0.0470 chunk 75 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.119681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.075489 restraints weight = 29545.303| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 3.15 r_work: 0.2832 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7059 Z= 0.130 Angle : 0.511 5.151 9617 Z= 0.248 Chirality : 0.045 0.238 1104 Planarity : 0.003 0.041 1226 Dihedral : 8.848 100.844 1333 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.13 % Allowed : 7.04 % Favored : 91.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.29), residues: 862 helix: 1.57 (0.46), residues: 133 sheet: -0.19 (0.31), residues: 285 loop : -0.89 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 20 TYR 0.007 0.001 TYR B 325 PHE 0.008 0.001 PHE A 172 TRP 0.005 0.001 TRP B 247 HIS 0.003 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 7034) covalent geometry : angle 0.49115 ( 9548) SS BOND : bond 0.00135 ( 6) SS BOND : angle 1.61122 ( 12) hydrogen bonds : bond 0.03072 ( 243) hydrogen bonds : angle 5.68303 ( 636) link_ALPHA1-3 : bond 0.00686 ( 2) link_ALPHA1-3 : angle 2.65762 ( 6) link_ALPHA1-6 : bond 0.00918 ( 1) link_ALPHA1-6 : angle 2.73557 ( 3) link_BETA1-4 : bond 0.00603 ( 8) link_BETA1-4 : angle 1.99233 ( 24) link_NAG-ASN : bond 0.00206 ( 8) link_NAG-ASN : angle 0.89386 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 75 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue LYS 397 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Evaluate side-chains 57 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: A 244 ASP cc_start: 0.8341 (p0) cc_final: 0.8033 (t0) REVERT: A 269 ASP cc_start: 0.7701 (m-30) cc_final: 0.7175 (m-30) REVERT: A 449 ARG cc_start: 0.4981 (ttt90) cc_final: 0.2746 (mtm110) REVERT: B 185 ASN cc_start: 0.8708 (p0) cc_final: 0.8368 (p0) REVERT: B 200 LYS cc_start: 0.8406 (tttt) cc_final: 0.7948 (ttpt) outliers start: 8 outliers final: 6 residues processed: 53 average time/residue: 0.3925 time to fit residues: 24.6932 Evaluate side-chains 54 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 43 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 47 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 58 optimal weight: 0.4980 chunk 74 optimal weight: 9.9990 chunk 36 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.117820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.075571 restraints weight = 29424.722| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.99 r_work: 0.2823 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7059 Z= 0.158 Angle : 0.524 5.369 9617 Z= 0.255 Chirality : 0.045 0.233 1104 Planarity : 0.004 0.040 1226 Dihedral : 8.799 99.701 1333 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.13 % Allowed : 7.18 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.29), residues: 862 helix: 1.51 (0.46), residues: 133 sheet: -0.25 (0.30), residues: 294 loop : -0.87 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 20 TYR 0.008 0.001 TYR B 325 PHE 0.007 0.001 PHE B 164 TRP 0.008 0.001 TRP B 247 HIS 0.004 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 7034) covalent geometry : angle 0.50240 ( 9548) SS BOND : bond 0.00219 ( 6) SS BOND : angle 1.81728 ( 12) hydrogen bonds : bond 0.03151 ( 243) hydrogen bonds : angle 5.61419 ( 636) link_ALPHA1-3 : bond 0.00685 ( 2) link_ALPHA1-3 : angle 2.79734 ( 6) link_ALPHA1-6 : bond 0.00817 ( 1) link_ALPHA1-6 : angle 2.71211 ( 3) link_BETA1-4 : bond 0.00611 ( 8) link_BETA1-4 : angle 2.01854 ( 24) link_NAG-ASN : bond 0.00259 ( 8) link_NAG-ASN : angle 0.96900 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 75 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue LYS 397 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Evaluate side-chains 59 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 123 THR cc_start: 0.8175 (m) cc_final: 0.7547 (p) REVERT: A 244 ASP cc_start: 0.8336 (p0) cc_final: 0.8035 (t0) REVERT: A 269 ASP cc_start: 0.7711 (m-30) cc_final: 0.7203 (m-30) REVERT: A 449 ARG cc_start: 0.5070 (ttt90) cc_final: 0.2851 (mtm110) REVERT: B 185 ASN cc_start: 0.8716 (p0) cc_final: 0.8373 (p0) REVERT: B 200 LYS cc_start: 0.8382 (tttt) cc_final: 0.7983 (ttpt) outliers start: 8 outliers final: 7 residues processed: 56 average time/residue: 0.3715 time to fit residues: 24.6117 Evaluate side-chains 56 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 32 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 79 optimal weight: 9.9990 chunk 17 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.118735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.075156 restraints weight = 29405.520| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 3.10 r_work: 0.2828 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7059 Z= 0.142 Angle : 0.530 9.586 9617 Z= 0.258 Chirality : 0.045 0.235 1104 Planarity : 0.003 0.042 1226 Dihedral : 8.683 99.446 1333 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.13 % Allowed : 7.61 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.29), residues: 862 helix: 1.57 (0.46), residues: 133 sheet: -0.21 (0.30), residues: 294 loop : -0.85 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 20 TYR 0.008 0.001 TYR B 325 PHE 0.007 0.001 PHE B 164 TRP 0.007 0.001 TRP B 247 HIS 0.003 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 7034) covalent geometry : angle 0.49888 ( 9548) SS BOND : bond 0.00226 ( 6) SS BOND : angle 3.40142 ( 12) hydrogen bonds : bond 0.03042 ( 243) hydrogen bonds : angle 5.54321 ( 636) link_ALPHA1-3 : bond 0.00737 ( 2) link_ALPHA1-3 : angle 2.74439 ( 6) link_ALPHA1-6 : bond 0.00862 ( 1) link_ALPHA1-6 : angle 2.69298 ( 3) link_BETA1-4 : bond 0.00617 ( 8) link_BETA1-4 : angle 1.97721 ( 24) link_NAG-ASN : bond 0.00236 ( 8) link_NAG-ASN : angle 0.92758 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 75 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue LYS 397 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Evaluate side-chains 59 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 244 ASP cc_start: 0.8325 (p0) cc_final: 0.7999 (t0) REVERT: A 269 ASP cc_start: 0.7715 (m-30) cc_final: 0.7213 (m-30) REVERT: A 449 ARG cc_start: 0.5137 (ttt90) cc_final: 0.2825 (mtm110) REVERT: B 185 ASN cc_start: 0.8703 (p0) cc_final: 0.8350 (p0) REVERT: B 200 LYS cc_start: 0.8379 (tttt) cc_final: 0.7975 (ttpt) outliers start: 8 outliers final: 7 residues processed: 55 average time/residue: 0.3760 time to fit residues: 24.5828 Evaluate side-chains 54 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 32 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 2 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 3 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 405 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 = 0.3608 r_free = 0.3608 target = 0.119208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.075199 restraints weight = 29775.370| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 3.16 r_work: 0.2827 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7059 Z= 0.135 Angle : 0.522 6.051 9617 Z= 0.254 Chirality : 0.045 0.235 1104 Planarity : 0.004 0.047 1226 Dihedral : 8.615 99.100 1333 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.99 % Allowed : 8.03 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.29), residues: 862 helix: 1.60 (0.46), residues: 133 sheet: -0.20 (0.30), residues: 294 loop : -0.83 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 317 TYR 0.007 0.001 TYR B 325 PHE 0.007 0.001 PHE B 164 TRP 0.007 0.001 TRP B 247 HIS 0.003 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 7034) covalent geometry : angle 0.49795 ( 9548) SS BOND : bond 0.00145 ( 6) SS BOND : angle 2.52355 ( 12) hydrogen bonds : bond 0.03025 ( 243) hydrogen bonds : angle 5.49408 ( 636) link_ALPHA1-3 : bond 0.00753 ( 2) link_ALPHA1-3 : angle 2.74254 ( 6) link_ALPHA1-6 : bond 0.00899 ( 1) link_ALPHA1-6 : angle 2.69332 ( 3) link_BETA1-4 : bond 0.00625 ( 8) link_BETA1-4 : angle 1.97153 ( 24) link_NAG-ASN : bond 0.00229 ( 8) link_NAG-ASN : angle 0.92268 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 75 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue LYS 397 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Evaluate side-chains 54 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: A 244 ASP cc_start: 0.8301 (p0) cc_final: 0.8060 (t0) REVERT: A 269 ASP cc_start: 0.7695 (m-30) cc_final: 0.7197 (m-30) REVERT: A 449 ARG cc_start: 0.5137 (ttt90) cc_final: 0.2826 (mtm110) REVERT: B 185 ASN cc_start: 0.8696 (p0) cc_final: 0.8338 (p0) REVERT: B 200 LYS cc_start: 0.8377 (tttt) cc_final: 0.7965 (ttpt) outliers start: 7 outliers final: 5 residues processed: 52 average time/residue: 0.4071 time to fit residues: 24.9671 Evaluate side-chains 52 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 32 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 12 optimal weight: 0.0980 chunk 61 optimal weight: 0.9980 chunk 44 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 74 optimal weight: 20.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 405 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 = 0.3591 r_free = 0.3591 target = 0.118122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.074871 restraints weight = 29521.181| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 3.09 r_work: 0.2826 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7059 Z= 0.146 Angle : 0.523 5.556 9617 Z= 0.254 Chirality : 0.045 0.230 1104 Planarity : 0.004 0.043 1226 Dihedral : 8.545 97.985 1333 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.85 % Allowed : 8.45 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.29), residues: 862 helix: 1.59 (0.46), residues: 133 sheet: -0.21 (0.30), residues: 295 loop : -0.85 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 317 TYR 0.008 0.001 TYR A 327 PHE 0.007 0.001 PHE B 164 TRP 0.007 0.001 TRP B 247 HIS 0.003 0.001 HIS C 34 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 7034) covalent geometry : angle 0.50090 ( 9548) SS BOND : bond 0.00139 ( 6) SS BOND : angle 1.98746 ( 12) hydrogen bonds : bond 0.03036 ( 243) hydrogen bonds : angle 5.45596 ( 636) link_ALPHA1-3 : bond 0.00769 ( 2) link_ALPHA1-3 : angle 2.77853 ( 6) link_ALPHA1-6 : bond 0.00889 ( 1) link_ALPHA1-6 : angle 2.64603 ( 3) link_BETA1-4 : bond 0.00621 ( 8) link_BETA1-4 : angle 1.99987 ( 24) link_NAG-ASN : bond 0.00248 ( 8) link_NAG-ASN : angle 0.95111 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 75 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue LYS 397 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Evaluate side-chains 53 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 123 THR cc_start: 0.8154 (m) cc_final: 0.7546 (p) REVERT: A 244 ASP cc_start: 0.8286 (p0) cc_final: 0.8061 (t0) REVERT: A 269 ASP cc_start: 0.7702 (m-30) cc_final: 0.7208 (m-30) REVERT: A 449 ARG cc_start: 0.5246 (ttt90) cc_final: 0.2941 (mtm110) REVERT: B 185 ASN cc_start: 0.8733 (p0) cc_final: 0.8381 (p0) REVERT: B 200 LYS cc_start: 0.8387 (tttt) cc_final: 0.7990 (ttpt) outliers start: 6 outliers final: 6 residues processed: 52 average time/residue: 0.4133 time to fit residues: 25.3760 Evaluate side-chains 52 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 121 TRP Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 32 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 53 optimal weight: 0.3980 chunk 61 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 30 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.118557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.075159 restraints weight = 29389.058| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 3.10 r_work: 0.2831 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7059 Z= 0.127 Angle : 0.512 5.673 9617 Z= 0.247 Chirality : 0.044 0.227 1104 Planarity : 0.004 0.042 1226 Dihedral : 8.424 97.517 1333 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.99 % Allowed : 8.03 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.29), residues: 862 helix: 1.65 (0.46), residues: 133 sheet: -0.15 (0.30), residues: 294 loop : -0.80 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 317 TYR 0.007 0.001 TYR B 325 PHE 0.007 0.001 PHE B 164 TRP 0.006 0.001 TRP B 247 HIS 0.003 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 7034) covalent geometry : angle 0.49057 ( 9548) SS BOND : bond 0.00120 ( 6) SS BOND : angle 1.78013 ( 12) hydrogen bonds : bond 0.02944 ( 243) hydrogen bonds : angle 5.40421 ( 636) link_ALPHA1-3 : bond 0.00811 ( 2) link_ALPHA1-3 : angle 2.73885 ( 6) link_ALPHA1-6 : bond 0.00887 ( 1) link_ALPHA1-6 : angle 2.62410 ( 3) link_BETA1-4 : bond 0.00636 ( 8) link_BETA1-4 : angle 1.98230 ( 24) link_NAG-ASN : bond 0.00222 ( 8) link_NAG-ASN : angle 0.92082 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4136.78 seconds wall clock time: 70 minutes 50.55 seconds (4250.55 seconds total)