Starting phenix.real_space_refine on Sun Jan 19 11:13:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ckv_45655/01_2025/9ckv_45655_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ckv_45655/01_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_45655/01_2025/9ckv_45655.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ckv_45655/01_2025/9ckv_45655.map" model { file = "/net/cci-nas-00/data/ceres_data/9ckv_45655/01_2025/9ckv_45655_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ckv_45655/01_2025/9ckv_45655_trim.cif" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: {'GLN:plan1': 1, 'GLU:plan': 7, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} 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: {'GLU:plan': 1, 'ARG: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: 7.82, per 1000 atoms: 0.59 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: 3.84 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.03 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: 4.75 Time building geometry restraints manager: 4.48 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: 2.050 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: 0.240 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 32.800 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.080 ------------------------------------------------------------------------------- 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 7034 Z= 0.298 Angle : 0.660 6.696 9548 Z= 0.305 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (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 TRP 0.037 0.002 TRP A 121 HIS 0.002 0.001 HIS C 34 PHE 0.012 0.001 PHE A 248 TYR 0.015 0.001 TYR B 325 ARG 0.007 0.000 ARG C 20 *********************** 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 : 1.054 Fit side-chains revert: symmetry clash 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: 0.6901 (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: 0.7773 (tp30) REVERT: C 20 ARG cc_start: 0.7646 (ttp80) cc_final: 0.7373 (ttt180) REVERT: C 21 GLU cc_start: 0.8108 (tm-30) cc_final: 0.7838 (tm-30) REVERT: C 62 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7287 (mt-10) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.7450 time to fit residues: 74.7595 Evaluate side-chains 61 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- 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 = 0.3626 r_free = 0.3626 target = 0.120214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.076172 restraints weight = 29604.658| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 3.11 r_work: 0.2853 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7034 Z= 0.268 Angle : 0.565 7.012 9548 Z= 0.287 Chirality : 0.046 0.222 1104 Planarity : 0.004 0.048 1226 Dihedral : 11.128 102.286 1333 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.42 % Allowed : 3.80 % Favored : 95.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.29), residues: 862 helix: 1.81 (0.47), residues: 125 sheet: -0.11 (0.31), residues: 284 loop : -0.73 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 121 HIS 0.003 0.001 HIS B 263 PHE 0.009 0.001 PHE B 212 TYR 0.011 0.001 TYR B 377 ARG 0.003 0.000 ARG A 271 *********************** 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: 3 poor density : 63 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 ASP cc_start: 0.8423 (p0) cc_final: 0.7890 (t0) REVERT: A 269 ASP cc_start: 0.7722 (m-30) cc_final: 0.7204 (m-30) REVERT: A 449 ARG cc_start: 0.5020 (ttt90) cc_final: 0.4197 (ttp80) REVERT: B 184 ARG cc_start: 0.7358 (mmp80) cc_final: 0.7138 (mtm110) REVERT: B 200 LYS cc_start: 0.8445 (tttt) cc_final: 0.7982 (ttpt) REVERT: B 220 ARG cc_start: 0.8704 (mtm110) cc_final: 0.8305 (mtm110) REVERT: C 62 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7753 (mt-10) outliers start: 3 outliers final: 2 residues processed: 65 average time/residue: 0.7906 time to fit residues: 60.9379 Evaluate side-chains 53 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 346 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 34 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 73 optimal weight: 9.9990 chunk 82 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 79 optimal weight: 9.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3619 r_free = 0.3619 target = 0.119913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.075934 restraints weight = 29732.786| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 3.11 r_work: 0.2844 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7034 Z= 0.235 Angle : 0.520 6.019 9548 Z= 0.261 Chirality : 0.045 0.215 1104 Planarity : 0.004 0.038 1226 Dihedral : 10.011 103.458 1333 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.28 % Allowed : 5.49 % Favored : 94.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.29), residues: 862 helix: 1.74 (0.47), residues: 125 sheet: -0.11 (0.31), residues: 284 loop : -0.76 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 121 HIS 0.003 0.001 HIS B 263 PHE 0.007 0.001 PHE B 264 TYR 0.009 0.001 TYR A 327 ARG 0.002 0.000 ARG B 154 *********************** 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 55 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: A 244 ASP cc_start: 0.8454 (p0) cc_final: 0.7996 (t0) REVERT: A 269 ASP cc_start: 0.7697 (m-30) cc_final: 0.7190 (m-30) REVERT: A 449 ARG cc_start: 0.4802 (ttt90) cc_final: 0.4054 (ttp80) REVERT: B 152 GLU cc_start: 0.7854 (tp30) cc_final: 0.7653 (tp30) REVERT: B 185 ASN cc_start: 0.8794 (p0) cc_final: 0.8523 (p0) REVERT: B 200 LYS cc_start: 0.8458 (tttt) cc_final: 0.8005 (ttpt) outliers start: 2 outliers final: 1 residues processed: 54 average time/residue: 0.9439 time to fit residues: 59.6350 Evaluate side-chains 46 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 30 optimal weight: 0.9980 chunk 79 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 42 optimal weight: 0.8980 chunk 75 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 = 0.3597 r_free = 0.3597 target = 0.118452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.074525 restraints weight = 29617.936| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 3.12 r_work: 0.2817 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 7034 Z= 0.308 Angle : 0.533 5.182 9548 Z= 0.269 Chirality : 0.046 0.240 1104 Planarity : 0.004 0.039 1226 Dihedral : 9.319 100.492 1333 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.99 % Allowed : 6.34 % Favored : 92.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.28), residues: 862 helix: 1.45 (0.45), residues: 132 sheet: -0.20 (0.31), residues: 285 loop : -0.98 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 247 HIS 0.005 0.001 HIS B 263 PHE 0.008 0.001 PHE B 212 TYR 0.011 0.001 TYR A 287 ARG 0.004 0.000 ARG C 20 *********************** 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 55 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 1.040 Fit side-chains revert: symmetry clash REVERT: A 244 ASP cc_start: 0.8439 (p0) cc_final: 0.8030 (t0) REVERT: A 269 ASP cc_start: 0.7699 (m-30) cc_final: 0.7181 (m-30) REVERT: A 449 ARG cc_start: 0.4764 (ttt90) cc_final: 0.2558 (mtm110) REVERT: B 185 ASN cc_start: 0.8714 (p0) cc_final: 0.8355 (p0) REVERT: B 200 LYS cc_start: 0.8454 (tttt) cc_final: 0.7978 (ttpt) outliers start: 7 outliers final: 6 residues processed: 51 average time/residue: 0.7978 time to fit residues: 49.0272 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 : 1.008 ------------------------------------------------------------------------------- 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 16 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.3587 r_free = 0.3587 target = 0.117763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.073948 restraints weight = 29878.842| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 3.12 r_work: 0.2809 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 7034 Z= 0.305 Angle : 0.526 5.391 9548 Z= 0.265 Chirality : 0.045 0.222 1104 Planarity : 0.004 0.036 1226 Dihedral : 9.170 99.460 1333 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.27 % Allowed : 7.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.29), residues: 862 helix: 1.38 (0.45), residues: 132 sheet: -0.31 (0.31), residues: 295 loop : -0.96 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 247 HIS 0.005 0.001 HIS B 263 PHE 0.008 0.001 PHE B 164 TYR 0.010 0.001 TYR A 287 ARG 0.002 0.000 ARG C 20 *********************** 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 58 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 1.082 Fit side-chains REVERT: A 123 THR cc_start: 0.8167 (m) cc_final: 0.7503 (p) REVERT: A 244 ASP cc_start: 0.8418 (p0) cc_final: 0.8077 (t0) REVERT: A 269 ASP cc_start: 0.7695 (m-30) cc_final: 0.7182 (m-30) REVERT: A 449 ARG cc_start: 0.4974 (ttt90) cc_final: 0.2714 (mtm110) REVERT: B 185 ASN cc_start: 0.8761 (p0) cc_final: 0.8370 (p0) REVERT: B 200 LYS cc_start: 0.8403 (tttt) cc_final: 0.8014 (ttpt) outliers start: 9 outliers final: 7 residues processed: 52 average time/residue: 0.8003 time to fit residues: 50.3379 Evaluate side-chains 52 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 441 ASP Chi-restraints excluded: chain C residue 15 GLU 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 78 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 33 optimal weight: 0.2980 chunk 58 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.118854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.074858 restraints weight = 29906.118| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 3.14 r_work: 0.2825 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7034 Z= 0.203 Angle : 0.496 5.331 9548 Z= 0.247 Chirality : 0.045 0.237 1104 Planarity : 0.003 0.039 1226 Dihedral : 8.900 99.578 1333 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.13 % Allowed : 7.46 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.29), residues: 862 helix: 1.50 (0.46), residues: 133 sheet: -0.26 (0.31), residues: 294 loop : -0.91 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 247 HIS 0.003 0.001 HIS B 263 PHE 0.007 0.001 PHE A 172 TYR 0.007 0.001 TYR A 327 ARG 0.004 0.000 ARG C 20 *********************** 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 54 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 ASP cc_start: 0.8394 (p0) cc_final: 0.8052 (t0) REVERT: A 269 ASP cc_start: 0.7671 (m-30) cc_final: 0.7158 (m-30) REVERT: A 449 ARG cc_start: 0.5004 (ttt90) cc_final: 0.2780 (mtm110) REVERT: B 185 ASN cc_start: 0.8748 (p0) cc_final: 0.8340 (p0) REVERT: B 200 LYS cc_start: 0.8437 (tttt) cc_final: 0.7980 (ttpt) outliers start: 8 outliers final: 6 residues processed: 51 average time/residue: 0.7004 time to fit residues: 43.0048 Evaluate side-chains 51 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 1.095 ------------------------------------------------------------------------------- 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 30 VAL Chi-restraints excluded: chain C residue 32 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 67 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 12 optimal weight: 0.0370 chunk 7 optimal weight: 0.8980 overall best weight: 0.7658 ------------------------------------------------------------------------------- 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 = 0.118812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.074865 restraints weight = 29670.618| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 3.14 r_work: 0.2824 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7034 Z= 0.220 Angle : 0.497 5.395 9548 Z= 0.247 Chirality : 0.045 0.233 1104 Planarity : 0.003 0.040 1226 Dihedral : 8.786 99.156 1333 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.99 % Allowed : 7.61 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.29), residues: 862 helix: 1.51 (0.46), residues: 133 sheet: -0.27 (0.31), residues: 295 loop : -0.89 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 247 HIS 0.003 0.001 HIS B 263 PHE 0.007 0.001 PHE B 164 TYR 0.008 0.001 TYR A 327 ARG 0.004 0.000 ARG C 20 *********************** 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 53 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 1.134 Fit side-chains revert: symmetry clash REVERT: A 123 THR cc_start: 0.8070 (m) cc_final: 0.7420 (p) REVERT: A 244 ASP cc_start: 0.8381 (p0) cc_final: 0.8010 (t0) REVERT: A 269 ASP cc_start: 0.7681 (m-30) cc_final: 0.7189 (m-30) REVERT: A 449 ARG cc_start: 0.5124 (ttt90) cc_final: 0.2879 (mtm110) REVERT: B 185 ASN cc_start: 0.8747 (p0) cc_final: 0.8336 (p0) REVERT: B 200 LYS cc_start: 0.8382 (tttt) cc_final: 0.7970 (ttpt) outliers start: 7 outliers final: 6 residues processed: 52 average time/residue: 0.7464 time to fit residues: 48.0211 Evaluate side-chains 51 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 1.041 ------------------------------------------------------------------------------- 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 32 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 17 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3572 r_free = 0.3572 target = 0.116788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.074670 restraints weight = 29609.354| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 3.01 r_work: 0.2824 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7034 Z= 0.243 Angle : 0.504 5.449 9548 Z= 0.251 Chirality : 0.045 0.230 1104 Planarity : 0.003 0.041 1226 Dihedral : 8.755 98.632 1333 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.85 % Allowed : 8.31 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.29), residues: 862 helix: 1.51 (0.45), residues: 133 sheet: -0.28 (0.30), residues: 295 loop : -0.91 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 247 HIS 0.003 0.001 HIS B 263 PHE 0.008 0.001 PHE B 164 TYR 0.008 0.001 TYR A 327 ARG 0.005 0.000 ARG C 20 *********************** 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 51 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 1.075 Fit side-chains revert: symmetry clash REVERT: A 123 THR cc_start: 0.8168 (m) cc_final: 0.7543 (p) REVERT: A 244 ASP cc_start: 0.8357 (p0) cc_final: 0.8023 (t0) REVERT: A 269 ASP cc_start: 0.7725 (m-30) cc_final: 0.7236 (m-30) REVERT: A 449 ARG cc_start: 0.5170 (ttt90) cc_final: 0.2938 (mtm110) REVERT: B 185 ASN cc_start: 0.8775 (p0) cc_final: 0.8367 (p0) REVERT: B 200 LYS cc_start: 0.8448 (tttt) cc_final: 0.8049 (ttpt) outliers start: 6 outliers final: 5 residues processed: 49 average time/residue: 0.7729 time to fit residues: 46.2642 Evaluate side-chains 49 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 16 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 53 optimal weight: 0.3980 chunk 58 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 64 optimal weight: 0.0270 chunk 57 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.118977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.075486 restraints weight = 29641.981| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 3.11 r_work: 0.2837 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7034 Z= 0.177 Angle : 0.490 5.418 9548 Z= 0.243 Chirality : 0.045 0.237 1104 Planarity : 0.004 0.054 1226 Dihedral : 8.581 99.218 1333 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.13 % Allowed : 8.45 % Favored : 90.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.29), residues: 862 helix: 1.66 (0.46), residues: 133 sheet: -0.18 (0.30), residues: 294 loop : -0.82 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 247 HIS 0.002 0.000 HIS B 263 PHE 0.007 0.001 PHE B 164 TYR 0.007 0.001 TYR B 325 ARG 0.010 0.000 ARG A 317 *********************** 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 51 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 1.070 Fit side-chains revert: symmetry clash REVERT: A 244 ASP cc_start: 0.8280 (p0) cc_final: 0.8050 (t0) REVERT: A 269 ASP cc_start: 0.7669 (m-30) cc_final: 0.7186 (m-30) REVERT: A 449 ARG cc_start: 0.5187 (ttt90) cc_final: 0.2866 (mtm110) REVERT: B 185 ASN cc_start: 0.8746 (p0) cc_final: 0.8348 (p0) REVERT: B 200 LYS cc_start: 0.8372 (tttt) cc_final: 0.7967 (ttpt) REVERT: C 20 ARG cc_start: 0.7802 (ttp80) cc_final: 0.7418 (ttt180) outliers start: 8 outliers final: 5 residues processed: 49 average time/residue: 0.7503 time to fit residues: 44.5005 Evaluate side-chains 48 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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 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 21 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 0.0040 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 42 optimal weight: 0.0570 chunk 74 optimal weight: 20.0000 chunk 11 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 overall best weight: 0.5710 ------------------------------------------------------------------------------- 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 = 0.3601 r_free = 0.3601 target = 0.118806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.075479 restraints weight = 29587.183| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 3.10 r_work: 0.2837 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7034 Z= 0.180 Angle : 0.486 5.449 9548 Z= 0.240 Chirality : 0.044 0.234 1104 Planarity : 0.003 0.039 1226 Dihedral : 8.432 98.902 1333 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.70 % Allowed : 9.01 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.29), residues: 862 helix: 1.72 (0.46), residues: 133 sheet: -0.16 (0.30), residues: 294 loop : -0.76 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 121 HIS 0.002 0.001 HIS B 263 PHE 0.007 0.001 PHE B 164 TYR 0.007 0.001 TYR A 327 ARG 0.009 0.000 ARG A 317 ********************** 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 48 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 1.108 Fit side-chains revert: symmetry clash REVERT: A 244 ASP cc_start: 0.8271 (p0) cc_final: 0.8051 (t0) REVERT: A 269 ASP cc_start: 0.7695 (m-30) cc_final: 0.7151 (m-30) REVERT: A 449 ARG cc_start: 0.5239 (ttt90) cc_final: 0.2893 (mtm110) REVERT: B 185 ASN cc_start: 0.8749 (p0) cc_final: 0.8364 (p0) REVERT: B 200 LYS cc_start: 0.8388 (tttt) cc_final: 0.7977 (ttpt) outliers start: 5 outliers final: 5 residues processed: 47 average time/residue: 0.7789 time to fit residues: 44.4484 Evaluate side-chains 48 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.999 ------------------------------------------------------------------------------- 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 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 25 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 51 optimal weight: 0.0060 chunk 36 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 73 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.6796 ------------------------------------------------------------------------------- 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 = 0.118903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.075314 restraints weight = 29647.205| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 3.13 r_work: 0.2834 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7034 Z= 0.196 Angle : 0.489 5.565 9548 Z= 0.241 Chirality : 0.044 0.223 1104 Planarity : 0.004 0.044 1226 Dihedral : 8.377 98.217 1333 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.85 % Allowed : 9.15 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.29), residues: 862 helix: 1.70 (0.46), residues: 133 sheet: -0.15 (0.30), residues: 294 loop : -0.74 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 247 HIS 0.002 0.001 HIS B 263 PHE 0.007 0.001 PHE B 164 TYR 0.007 0.001 TYR B 325 ARG 0.008 0.000 ARG A 317 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7320.04 seconds wall clock time: 129 minutes 24.34 seconds (7764.34 seconds total)