Starting phenix.real_space_refine on Sun Nov 17 12:02:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ckv_45655/11_2024/9ckv_45655_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ckv_45655/11_2024/9ckv_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ckv_45655/11_2024/9ckv_45655.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ckv_45655/11_2024/9ckv_45655.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ckv_45655/11_2024/9ckv_45655_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ckv_45655/11_2024/9ckv_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-5513/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: 7.53, per 1000 atoms: 0.57 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: 3.71 Conformation dependent library (CDL) restraints added in 1.1 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: 1.27 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: 4.98 Time building geometry restraints manager: 4.36 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: 2.780 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: 0.230 Extract box with map and model: 0.470 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 32.020 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.800 ------------------------------------------------------------------------------- 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 : 0.959 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: 0.7673 time to fit residues: 77.0983 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 : 1.101 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 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 : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 ASP cc_start: 0.8132 (p0) cc_final: 0.7820 (t0) REVERT: A 269 ASP cc_start: 0.7352 (m-30) cc_final: 0.6810 (m-30) REVERT: A 449 ARG cc_start: 0.4099 (ttt90) cc_final: 0.3258 (ttp80) REVERT: B 200 LYS cc_start: 0.7863 (tttt) cc_final: 0.7313 (ttpt) REVERT: B 220 ARG cc_start: 0.8348 (mtm110) cc_final: 0.7922 (mtm110) REVERT: C 62 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7444 (mt-10) outliers start: 3 outliers final: 2 residues processed: 65 average time/residue: 0.8024 time to fit residues: 61.9382 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 : 1.331 ------------------------------------------------------------------------------- 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 43 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.1591 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= 0.291 Angle : 0.539 6.163 9548 Z= 0.272 Chirality : 0.046 0.215 1104 Planarity : 0.004 0.039 1226 Dihedral : 10.103 102.398 1333 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.56 % Allowed : 5.21 % 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: -0.37 (0.29), residues: 862 helix: 1.68 (0.46), residues: 125 sheet: -0.15 (0.31), residues: 285 loop : -0.82 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 121 HIS 0.004 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 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: 4 poor density : 51 time to evaluate : 1.059 Fit side-chains revert: symmetry clash REVERT: A 244 ASP cc_start: 0.8157 (p0) cc_final: 0.7925 (t0) REVERT: A 269 ASP cc_start: 0.7322 (m-30) cc_final: 0.6792 (m-30) REVERT: A 449 ARG cc_start: 0.3672 (ttt90) cc_final: 0.2912 (ttp80) REVERT: B 152 GLU cc_start: 0.7309 (tp30) cc_final: 0.7095 (tp30) REVERT: B 184 ARG cc_start: 0.7156 (mtm110) cc_final: 0.6908 (tpp80) REVERT: B 185 ASN cc_start: 0.8415 (p0) cc_final: 0.8150 (p0) REVERT: B 200 LYS cc_start: 0.7855 (tttt) cc_final: 0.7313 (ttpt) REVERT: B 220 ARG cc_start: 0.8310 (mtm110) cc_final: 0.7986 (mtm110) outliers start: 4 outliers final: 3 residues processed: 54 average time/residue: 0.8848 time to fit residues: 55.7806 Evaluate side-chains 48 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 1.122 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 5.9990 chunk 58 optimal weight: 0.6980 chunk 40 optimal weight: 0.4980 chunk 8 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 74 optimal weight: 20.0000 chunk 22 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.1840 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= 0.197 Angle : 0.492 4.883 9548 Z= 0.245 Chirality : 0.045 0.249 1104 Planarity : 0.003 0.042 1226 Dihedral : 9.226 103.284 1333 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.85 % Allowed : 6.20 % Favored : 92.96 % 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: 1.64 (0.46), residues: 132 sheet: -0.12 (0.31), residues: 284 loop : -0.85 (0.29), residues: 446 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 0.008 0.001 TYR A 327 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 54 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 1.154 Fit side-chains revert: symmetry clash REVERT: A 269 ASP cc_start: 0.7293 (m-30) cc_final: 0.6765 (m-30) REVERT: A 449 ARG cc_start: 0.3761 (ttt90) cc_final: 0.1674 (mtm110) REVERT: B 185 ASN cc_start: 0.8411 (p0) cc_final: 0.8123 (p0) REVERT: B 200 LYS cc_start: 0.7801 (tttt) cc_final: 0.7293 (ttpt) REVERT: C 20 ARG cc_start: 0.7717 (ttp80) cc_final: 0.7316 (ttt180) outliers start: 6 outliers final: 4 residues processed: 50 average time/residue: 0.7369 time to fit residues: 44.6667 Evaluate side-chains 49 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 GLU 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 69 optimal weight: 0.5980 chunk 47 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.2011 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= 0.252 Angle : 0.502 5.116 9548 Z= 0.251 Chirality : 0.045 0.230 1104 Planarity : 0.003 0.032 1226 Dihedral : 9.054 100.968 1333 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.85 % Allowed : 6.76 % 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 (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: -0.44 (0.29), residues: 862 helix: 1.59 (0.46), residues: 132 sheet: -0.21 (0.31), residues: 285 loop : -0.89 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 247 HIS 0.004 0.001 HIS B 263 PHE 0.008 0.001 PHE B 164 TYR 0.008 0.001 TYR A 287 ARG 0.002 0.000 ARG C 52 *********************** 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 55 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 1.080 Fit side-chains revert: symmetry clash REVERT: A 269 ASP cc_start: 0.7306 (m-30) cc_final: 0.6791 (m-30) REVERT: A 449 ARG cc_start: 0.3616 (ttt90) cc_final: 0.1796 (mtm110) REVERT: B 185 ASN cc_start: 0.8445 (p0) cc_final: 0.8129 (p0) REVERT: B 200 LYS cc_start: 0.7848 (tttt) cc_final: 0.7297 (ttpt) outliers start: 6 outliers final: 4 residues processed: 52 average time/residue: 0.6998 time to fit residues: 44.5106 Evaluate side-chains 50 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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 32 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 6 optimal weight: 0.4980 chunk 43 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7034 Z= 0.228 Angle : 0.496 5.137 9548 Z= 0.247 Chirality : 0.045 0.235 1104 Planarity : 0.003 0.034 1226 Dihedral : 8.935 100.790 1333 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.85 % Allowed : 7.04 % Favored : 92.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.29), residues: 862 helix: 1.60 (0.46), residues: 132 sheet: -0.21 (0.31), residues: 285 loop : -0.88 (0.29), residues: 445 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 0.007 0.001 PHE A 172 TYR 0.008 0.001 TYR A 327 ARG 0.003 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 52 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.911 Fit side-chains revert: symmetry clash REVERT: A 269 ASP cc_start: 0.7304 (m-30) cc_final: 0.6794 (m-30) REVERT: A 449 ARG cc_start: 0.3688 (ttt90) cc_final: 0.2011 (mtp85) REVERT: B 185 ASN cc_start: 0.8450 (p0) cc_final: 0.8111 (p0) REVERT: B 200 LYS cc_start: 0.7841 (tttt) cc_final: 0.7293 (ttpt) outliers start: 6 outliers final: 5 residues processed: 49 average time/residue: 0.7460 time to fit residues: 44.3110 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 : 1.015 ------------------------------------------------------------------------------- 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 32 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 0.9980 chunk 47 optimal weight: 10.0000 chunk 60 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 33 optimal weight: 0.3980 chunk 49 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.2222 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= 0.212 Angle : 0.489 5.158 9548 Z= 0.243 Chirality : 0.045 0.241 1104 Planarity : 0.003 0.048 1226 Dihedral : 8.702 100.609 1333 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.99 % Allowed : 7.32 % 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 (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: -0.38 (0.29), residues: 862 helix: 1.59 (0.46), residues: 133 sheet: -0.23 (0.30), residues: 294 loop : -0.81 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 247 HIS 0.004 0.001 HIS B 263 PHE 0.007 0.001 PHE A 172 TYR 0.008 0.001 TYR B 325 ARG 0.006 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 : 1.045 Fit side-chains revert: symmetry clash REVERT: A 269 ASP cc_start: 0.7333 (m-30) cc_final: 0.6829 (m-30) REVERT: A 449 ARG cc_start: 0.3880 (ttt90) cc_final: 0.2161 (mtp85) REVERT: B 185 ASN cc_start: 0.8454 (p0) cc_final: 0.8116 (p0) REVERT: B 200 LYS cc_start: 0.7827 (tttt) cc_final: 0.7281 (ttpt) REVERT: C 20 ARG cc_start: 0.7745 (ttp80) cc_final: 0.7391 (ttt180) outliers start: 7 outliers final: 4 residues processed: 51 average time/residue: 0.7286 time to fit residues: 45.1847 Evaluate side-chains 51 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 56 optimal weight: 0.2980 chunk 40 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 79 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.2331 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 : 0.524 5.436 9548 Z= 0.262 Chirality : 0.045 0.227 1104 Planarity : 0.004 0.045 1226 Dihedral : 8.793 98.170 1333 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.13 % Allowed : 7.32 % Favored : 91.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.29), residues: 862 helix: 1.41 (0.45), residues: 133 sheet: -0.31 (0.30), residues: 295 loop : -0.92 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 247 HIS 0.004 0.001 HIS B 263 PHE 0.008 0.001 PHE B 164 TYR 0.010 0.001 TYR A 287 ARG 0.010 0.000 ARG A 317 *********************** 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 56 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 1.070 Fit side-chains revert: symmetry clash REVERT: A 123 THR cc_start: 0.7850 (m) cc_final: 0.7134 (p) REVERT: A 269 ASP cc_start: 0.7318 (m-30) cc_final: 0.6800 (m-30) REVERT: A 449 ARG cc_start: 0.3899 (ttt90) cc_final: 0.2178 (mtp85) REVERT: B 185 ASN cc_start: 0.8480 (p0) cc_final: 0.8097 (p0) REVERT: B 200 LYS cc_start: 0.7794 (tttt) cc_final: 0.7309 (ttpt) outliers start: 8 outliers final: 6 residues processed: 53 average time/residue: 0.7593 time to fit residues: 50.1389 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 : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 chunk 33 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 69 optimal weight: 0.4980 chunk 73 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7034 Z= 0.208 Angle : 0.495 5.395 9548 Z= 0.245 Chirality : 0.045 0.235 1104 Planarity : 0.004 0.045 1226 Dihedral : 8.637 99.105 1333 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.85 % Allowed : 7.89 % 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: -0.41 (0.29), residues: 862 helix: 1.56 (0.46), residues: 133 sheet: -0.22 (0.30), residues: 294 loop : -0.85 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 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 0.007 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 52 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 1.051 Fit side-chains REVERT: A 269 ASP cc_start: 0.7324 (m-30) cc_final: 0.6808 (m-30) REVERT: A 449 ARG cc_start: 0.3986 (ttt90) cc_final: 0.2206 (mtp85) REVERT: B 185 ASN cc_start: 0.8465 (p0) cc_final: 0.8099 (p0) REVERT: B 200 LYS cc_start: 0.7782 (tttt) cc_final: 0.7308 (ttpt) REVERT: C 20 ARG cc_start: 0.7749 (ttp80) cc_final: 0.7433 (ttt180) outliers start: 6 outliers final: 3 residues processed: 50 average time/residue: 0.7357 time to fit residues: 44.8387 Evaluate side-chains 46 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER 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 38 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 chunk 20 optimal weight: 0.0970 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.2428 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= 0.173 Angle : 0.483 5.342 9548 Z= 0.238 Chirality : 0.044 0.241 1104 Planarity : 0.003 0.039 1226 Dihedral : 8.441 99.545 1333 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.56 % Allowed : 8.03 % 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: -0.31 (0.29), residues: 862 helix: 1.69 (0.46), residues: 133 sheet: -0.17 (0.30), residues: 294 loop : -0.78 (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 B 325 ARG 0.008 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: 4 poor density : 44 time to evaluate : 0.923 Fit side-chains REVERT: A 269 ASP cc_start: 0.7349 (m-30) cc_final: 0.6844 (m-30) REVERT: A 449 ARG cc_start: 0.3812 (ttt90) cc_final: 0.2199 (mtp85) REVERT: B 185 ASN cc_start: 0.8434 (p0) cc_final: 0.8076 (p0) REVERT: B 200 LYS cc_start: 0.7762 (tttt) cc_final: 0.7294 (ttpt) outliers start: 4 outliers final: 4 residues processed: 46 average time/residue: 0.7790 time to fit residues: 43.1987 Evaluate side-chains 48 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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 32 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 49 optimal weight: 0.0970 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 = 0.3597 r_free = 0.3597 target = 0.118391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.076185 restraints weight = 29179.620| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.99 r_work: 0.2833 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2465 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= 0.202 Angle : 0.487 5.496 9548 Z= 0.240 Chirality : 0.044 0.234 1104 Planarity : 0.004 0.041 1226 Dihedral : 8.403 98.447 1333 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.56 % Allowed : 8.03 % 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: -0.31 (0.29), residues: 862 helix: 1.66 (0.46), residues: 133 sheet: -0.15 (0.30), residues: 294 loop : -0.78 (0.30), residues: 435 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 0.007 0.001 PHE B 164 TYR 0.007 0.001 TYR B 325 ARG 0.009 0.000 ARG A 317 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3631.06 seconds wall clock time: 65 minutes 29.22 seconds (3929.22 seconds total)