Starting phenix.real_space_refine on Sat Sep 12 10:56:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6huk_0280/09_2026/6huk_0280.cif Found real_map, /net/cci-nas-00/data/ceres_data/6huk_0280/09_2026/6huk_0280.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6huk_0280/09_2026/6huk_0280.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6huk_0280/09_2026/6huk_0280.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6huk_0280/09_2026/6huk_0280.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6huk_0280/09_2026/6huk_0280.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6huk_0280/09_2026/6huk_0280.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6huk_0280/09_2026/6huk_0280.map" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 83 5.16 5 C 9892 2.51 5 N 2481 2.21 5 O 2838 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15300 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2809 Classifications: {'peptide': 347} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 332} Chain breaks: 1 Chain: "B" Number of atoms: 2758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2758 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain breaks: 1 Chain: "C" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2720 Classifications: {'peptide': 330} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 316} Chain breaks: 1 Chain: "D" Number of atoms: 2812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2812 Classifications: {'peptide': 347} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 332} Chain breaks: 1 Chain: "E" Number of atoms: 2740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2740 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain breaks: 1 Chain: "G" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 941 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain breaks: 1 Chain: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 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 chiralities: 2 Chain: "I" 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 chiralities: 6 Chain: "J" 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 chiralities: 2 Chain: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "L" 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 chiralities: 2 Chain: "M" 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 chiralities: 6 Chain: "A" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 74 Unusual residues: {'H0Z': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'H0Z': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.76, per 1000 atoms: 0.25 Number of scatterers: 15300 At special positions: 0 Unit cell: (100.58, 124.12, 138.03, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 83 16.00 P 6 15.00 O 2838 8.00 N 2481 7.00 C 9892 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 165 " distance=2.03 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 153 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 150 " distance=2.02 Simple disulfide: pdb=" SG CYS G 428 " - pdb=" SG CYS G 501 " 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=1, symmetry=0 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 7 " " MAN F 4 " - " MAN F 5 " " BMA I 3 " - " MAN I 6 " " MAN I 4 " - " MAN I 5 " " BMA K 3 " - " MAN K 4 " " BMA M 3 " - " MAN M 6 " " MAN M 4 " - " MAN M 5 " ALPHA1-6 " BMA F 3 " - " MAN F 4 " " MAN F 4 " - " MAN F 6 " " BMA I 3 " - " MAN I 4 " " BMA K 3 " - " MAN K 5 " " BMA M 3 " - " MAN M 4 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " NAG-ASN " NAG F 1 " - " ASN A 111 " " NAG H 1 " - " ASN B 80 " " NAG I 1 " - " ASN B 149 " " NAG J 1 " - " ASN C 208 " " NAG K 1 " - " ASN D 111 " " NAG L 1 " - " ASN E 80 " " NAG M 1 " - " ASN E 149 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 775.0 milliseconds 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3436 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 0 sheets defined 36.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 10 through 23 removed outlier: 4.813A pdb=" N LEU A 23 " --> pdb=" O LEU A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 76 removed outlier: 3.555A pdb=" N LYS A 76 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 92 Processing helix chain 'A' and resid 174 through 178 Processing helix chain 'A' and resid 223 through 230 Processing helix chain 'A' and resid 230 through 244 removed outlier: 3.749A pdb=" N CYS A 234 " --> pdb=" O THR A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 247 No H-bonds generated for 'chain 'A' and resid 245 through 247' Processing helix chain 'A' and resid 251 through 276 removed outlier: 4.005A pdb=" N SER A 276 " --> pdb=" O SER A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 309 removed outlier: 3.608A pdb=" N LEU A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 416 removed outlier: 4.013A pdb=" N ILE A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) Proline residue: A 401 - end of helix removed outlier: 3.707A pdb=" N LEU A 416 " --> pdb=" O TRP A 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 20 Processing helix chain 'B' and resid 70 through 73 removed outlier: 3.707A pdb=" N ALA B 73 " --> pdb=" O LYS B 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 70 through 73' Processing helix chain 'B' and resid 84 through 88 Processing helix chain 'B' and resid 218 through 225 removed outlier: 3.613A pdb=" N LEU B 223 " --> pdb=" O GLY B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 236 Processing helix chain 'B' and resid 237 through 242 Processing helix chain 'B' and resid 246 through 272 removed outlier: 3.702A pdb=" N ARG B 250 " --> pdb=" O ALA B 246 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA B 252 " --> pdb=" O ALA B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 307 removed outlier: 3.542A pdb=" N LEU B 296 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N TYR B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 446 Proline residue: B 432 - end of helix Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 85 through 88 removed outlier: 3.938A pdb=" N LYS C 88 " --> pdb=" O ARG C 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 85 through 88' Processing helix chain 'C' and resid 102 through 106 removed outlier: 3.511A pdb=" N ILE C 106 " --> pdb=" O VAL C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 253 Processing helix chain 'C' and resid 254 through 257 Processing helix chain 'C' and resid 261 through 281 Processing helix chain 'C' and resid 282 through 285 Processing helix chain 'C' and resid 294 through 320 removed outlier: 3.579A pdb=" N PHE C 320 " --> pdb=" O THR C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 408 No H-bonds generated for 'chain 'C' and resid 406 through 408' Processing helix chain 'C' and resid 409 through 435 removed outlier: 4.404A pdb=" N ILE C 416 " --> pdb=" O SER C 412 " (cutoff:3.500A) Proline residue: C 419 - end of helix Processing helix chain 'D' and resid 10 through 21 Processing helix chain 'D' and resid 72 through 76 removed outlier: 3.694A pdb=" N LEU D 75 " --> pdb=" O ASP D 72 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS D 76 " --> pdb=" O GLU D 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 72 through 76' Processing helix chain 'D' and resid 87 through 92 Processing helix chain 'D' and resid 142 through 146 removed outlier: 4.591A pdb=" N ASP D 145 " --> pdb=" O HIS D 142 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE D 146 " --> pdb=" O LEU D 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 142 through 146' Processing helix chain 'D' and resid 174 through 179 removed outlier: 4.418A pdb=" N VAL D 179 " --> pdb=" O PRO D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 230 Processing helix chain 'D' and resid 230 through 244 removed outlier: 3.948A pdb=" N SER D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 247 No H-bonds generated for 'chain 'D' and resid 245 through 247' Processing helix chain 'D' and resid 251 through 275 removed outlier: 3.875A pdb=" N VAL D 263 " --> pdb=" O GLY D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 309 Processing helix chain 'D' and resid 390 through 415 removed outlier: 3.529A pdb=" N ARG D 397 " --> pdb=" O ASP D 393 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ILE D 398 " --> pdb=" O ARG D 394 " (cutoff:3.500A) Proline residue: D 401 - end of helix Processing helix chain 'E' and resid 9 through 20 Processing helix chain 'E' and resid 84 through 88 Processing helix chain 'E' and resid 139 through 143 removed outlier: 4.349A pdb=" N ARG E 142 " --> pdb=" O ASP E 139 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR E 143 " --> pdb=" O LEU E 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 139 through 143' Processing helix chain 'E' and resid 170 through 174 removed outlier: 4.139A pdb=" N ALA E 174 " --> pdb=" O GLY E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 225 Processing helix chain 'E' and resid 225 through 237 removed outlier: 4.095A pdb=" N SER E 229 " --> pdb=" O THR E 225 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TRP E 237 " --> pdb=" O THR E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 242 Processing helix chain 'E' and resid 246 through 272 removed outlier: 3.685A pdb=" N ARG E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU E 272 " --> pdb=" O LEU E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 308 removed outlier: 3.723A pdb=" N MET E 283 " --> pdb=" O LYS E 279 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR E 284 " --> pdb=" O ALA E 280 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU E 296 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TYR E 299 " --> pdb=" O ALA E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 446 removed outlier: 3.806A pdb=" N ILE E 429 " --> pdb=" O ARG E 425 " (cutoff:3.500A) Proline residue: E 432 - end of helix Processing helix chain 'G' and resid 492 through 496 removed outlier: 3.658A pdb=" N THR G 496 " --> pdb=" O PRO G 493 " (cutoff:3.500A) 423 hydrogen bonds defined for protein. 1224 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.01 Time building geometry restraints manager: 1.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2440 1.32 - 1.45: 4639 1.45 - 1.57: 8461 1.57 - 1.69: 9 1.69 - 1.81: 143 Bond restraints: 15692 Sorted by residual: bond pdb=" O4 PIO A 502 " pdb=" P4 PIO A 502 " ideal model delta sigma weight residual 1.710 1.589 0.121 2.00e-02 2.50e+03 3.68e+01 bond pdb=" O4 PIO D 501 " pdb=" P4 PIO D 501 " ideal model delta sigma weight residual 1.710 1.594 0.116 2.00e-02 2.50e+03 3.34e+01 bond pdb=" O5 PIO A 502 " pdb=" P5 PIO A 502 " ideal model delta sigma weight residual 1.699 1.611 0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" O5 PIO D 501 " pdb=" P5 PIO D 501 " ideal model delta sigma weight residual 1.699 1.613 0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" O13 PIO A 502 " pdb=" P1 PIO A 502 " ideal model delta sigma weight residual 1.651 1.585 0.066 2.00e-02 2.50e+03 1.08e+01 ... (remaining 15687 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 20346 2.22 - 4.45: 876 4.45 - 6.67: 90 6.67 - 8.89: 22 8.89 - 11.12: 4 Bond angle restraints: 21338 Sorted by residual: angle pdb=" C VAL D 64 " pdb=" CA VAL D 64 " pdb=" CB VAL D 64 " ideal model delta sigma weight residual 110.62 99.50 11.12 1.49e+00 4.50e-01 5.57e+01 angle pdb=" N ASN D 417 " pdb=" CA ASN D 417 " pdb=" C ASN D 417 " ideal model delta sigma weight residual 113.50 106.13 7.37 1.23e+00 6.61e-01 3.59e+01 angle pdb=" N VAL E 87 " pdb=" CA VAL E 87 " pdb=" C VAL E 87 " ideal model delta sigma weight residual 113.22 106.14 7.08 1.23e+00 6.61e-01 3.31e+01 angle pdb=" N VAL D 64 " pdb=" CA VAL D 64 " pdb=" C VAL D 64 " ideal model delta sigma weight residual 108.48 116.74 -8.26 1.44e+00 4.82e-01 3.29e+01 angle pdb=" N ASN A 275 " pdb=" CA ASN A 275 " pdb=" C ASN A 275 " ideal model delta sigma weight residual 111.28 116.89 -5.61 1.09e+00 8.42e-01 2.65e+01 ... (remaining 21333 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.00: 8781 22.00 - 43.99: 144 43.99 - 65.99: 15 65.99 - 87.99: 2 87.99 - 109.98: 4 Dihedral angle restraints: 8946 sinusoidal: 3603 harmonic: 5343 Sorted by residual: dihedral pdb=" CB CYS E 136 " pdb=" SG CYS E 136 " pdb=" SG CYS E 150 " pdb=" CB CYS E 150 " ideal model delta sinusoidal sigma weight residual 93.00 143.27 -50.27 1 1.00e+01 1.00e-02 3.46e+01 dihedral pdb=" CA ARG C 231 " pdb=" C ARG C 231 " pdb=" N ARG C 232 " pdb=" CA ARG C 232 " ideal model delta harmonic sigma weight residual 180.00 150.65 29.35 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA VAL A 64 " pdb=" C VAL A 64 " pdb=" N PHE A 65 " pdb=" CA PHE A 65 " ideal model delta harmonic sigma weight residual 180.00 151.05 28.95 0 5.00e+00 4.00e-02 3.35e+01 ... (remaining 8943 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 2339 0.112 - 0.223: 126 0.223 - 0.335: 9 0.335 - 0.447: 3 0.447 - 0.559: 3 Chirality restraints: 2480 Sorted by residual: chirality pdb=" C1 MAN F 4 " pdb=" O6 BMA F 3 " pdb=" C2 MAN F 4 " pdb=" O5 MAN F 4 " both_signs ideal model delta sigma weight residual False 2.40 1.98 0.42 2.00e-02 2.50e+03 4.34e+02 chirality pdb=" C1 BMA M 3 " pdb=" O4 NAG M 2 " pdb=" C2 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-02 2.50e+03 3.12e+02 chirality pdb=" C1 MAN F 7 " pdb=" O3 BMA F 3 " pdb=" C2 MAN F 7 " pdb=" O5 MAN F 7 " both_signs ideal model delta sigma weight residual False 2.40 2.05 0.35 2.00e-02 2.50e+03 3.05e+02 ... (remaining 2477 not shown) Planarity restraints: 2595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C05 H0Z E 501 " 0.098 2.00e-02 2.50e+03 4.91e-02 6.02e+01 pdb=" C06 H0Z E 501 " -0.019 2.00e-02 2.50e+03 pdb=" C07 H0Z E 501 " -0.003 2.00e-02 2.50e+03 pdb=" C08 H0Z E 501 " 0.037 2.00e-02 2.50e+03 pdb=" C09 H0Z E 501 " 0.022 2.00e-02 2.50e+03 pdb=" C13 H0Z E 501 " -0.026 2.00e-02 2.50e+03 pdb=" C14 H0Z E 501 " -0.048 2.00e-02 2.50e+03 pdb=" C15 H0Z E 501 " -0.076 2.00e-02 2.50e+03 pdb=" O10 H0Z E 501 " 0.048 2.00e-02 2.50e+03 pdb=" O12 H0Z E 501 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C05 H0Z A 501 " -0.047 2.00e-02 2.50e+03 3.13e-02 2.46e+01 pdb=" C06 H0Z A 501 " 0.005 2.00e-02 2.50e+03 pdb=" C07 H0Z A 501 " -0.007 2.00e-02 2.50e+03 pdb=" C08 H0Z A 501 " -0.042 2.00e-02 2.50e+03 pdb=" C09 H0Z A 501 " -0.024 2.00e-02 2.50e+03 pdb=" C13 H0Z A 501 " 0.011 2.00e-02 2.50e+03 pdb=" C14 H0Z A 501 " 0.020 2.00e-02 2.50e+03 pdb=" C15 H0Z A 501 " 0.062 2.00e-02 2.50e+03 pdb=" O10 H0Z A 501 " -0.008 2.00e-02 2.50e+03 pdb=" O12 H0Z A 501 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C16 H0Z E 501 " -0.063 2.00e-02 2.50e+03 3.00e-02 2.26e+01 pdb=" C18 H0Z E 501 " 0.058 2.00e-02 2.50e+03 pdb=" C20 H0Z E 501 " 0.004 2.00e-02 2.50e+03 pdb=" C21 H0Z E 501 " -0.006 2.00e-02 2.50e+03 pdb=" C25 H0Z E 501 " 0.001 2.00e-02 2.50e+03 pdb=" C26 H0Z E 501 " 0.018 2.00e-02 2.50e+03 pdb=" C27 H0Z E 501 " 0.020 2.00e-02 2.50e+03 pdb=" C28 H0Z E 501 " 0.006 2.00e-02 2.50e+03 pdb=" O22 H0Z E 501 " -0.029 2.00e-02 2.50e+03 pdb=" O24 H0Z E 501 " -0.009 2.00e-02 2.50e+03 ... (remaining 2592 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2138 2.76 - 3.29: 14062 3.29 - 3.83: 25985 3.83 - 4.36: 30563 4.36 - 4.90: 52354 Nonbonded interactions: 125102 Sorted by model distance: nonbonded pdb=" O LEU B 253 " pdb=" OG1 THR B 257 " model vdw 2.222 3.040 nonbonded pdb=" O LEU E 253 " pdb=" OG1 THR E 257 " model vdw 2.238 3.040 nonbonded pdb=" O LEU C 268 " pdb=" OG1 THR C 272 " model vdw 2.266 3.040 nonbonded pdb=" OD1 ASP D 98 " pdb=" OG SER D 159 " model vdw 2.283 3.040 nonbonded pdb=" O VAL C 248 " pdb=" OG SER C 251 " model vdw 2.309 3.040 ... (remaining 125097 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 'A' and (resid 10 through 320 or resid 384 through 418)) selection = (chain 'D' and resid 10 through 418) } ncs_group { reference = (chain 'B' and (resid 8 through 312 or resid 419 through 447)) selection = (chain 'E' and resid 8 through 447) } ncs_group { reference = (chain 'F' and (resid 2 or resid 5 through 7)) selection = (chain 'I' and (resid 1 or resid 4 through 6)) selection = (chain 'M' and (resid 1 or resid 4 through 6)) } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } 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 group one per residue 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: 0.780 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: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.150 Find NCS groups from input model: 0.190 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 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 : 0.007 0.121 15729 Z= 0.307 Angle : 1.044 18.510 21440 Z= 0.619 Chirality : 0.060 0.559 2480 Planarity : 0.007 0.065 2588 Dihedral : 9.520 109.981 5492 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.20 (0.17), residues: 1791 helix: -1.44 (0.18), residues: 526 sheet: -2.38 (0.22), residues: 449 loop : -2.33 (0.19), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 274 TYR 0.027 0.002 TYR G 479 PHE 0.035 0.004 PHE D 258 TRP 0.026 0.002 TRP A 95 HIS 0.017 0.002 HIS B 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00617 / 0.29 (15692) covalent geometry : angle 1.01954 / 0.62 (21338) SS BOND : bond 0.00351 / 0.24 ( 6) SS BOND : angle 1.23587 / 0.72 ( 12) hydrogen bonds : bond 0.12358 / 8.76 ( 423) hydrogen bonds : angle 6.17971 / 4.29 ( 1224) Misc. bond : bond 0.00274 / 0.14 ( 1) link_ALPHA1-3 : bond 0.05811 / 3.09 ( 7) link_ALPHA1-3 : angle 1.82154 / 1.50 ( 21) link_ALPHA1-6 : bond 0.05868 / 3.27 ( 5) link_ALPHA1-6 : angle 1.55870 / 1.29 ( 15) link_BETA1-4 : bond 0.05711 / 3.41 ( 11) link_BETA1-4 : angle 2.73311 / 1.88 ( 33) link_NAG-ASN : bond 0.00363 / 0.19 ( 7) link_NAG-ASN : angle 6.16732 / 5.49 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 1619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 662 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ARG cc_start: 0.7312 (ttt-90) cc_final: 0.7073 (mtp-110) REVERT: A 112 MET cc_start: 0.8329 (tpp) cc_final: 0.7937 (tpt) REVERT: A 192 ASP cc_start: 0.7936 (t70) cc_final: 0.7586 (t0) REVERT: A 256 THR cc_start: 0.8795 (m) cc_final: 0.8520 (p) REVERT: B 139 ASP cc_start: 0.7434 (t0) cc_final: 0.7078 (t0) REVERT: B 191 HIS cc_start: 0.8463 (p-80) cc_final: 0.8240 (p-80) REVERT: B 226 TYR cc_start: 0.8839 (m-80) cc_final: 0.8559 (m-80) REVERT: B 277 TYR cc_start: 0.8082 (p90) cc_final: 0.7760 (p90) REVERT: C 68 ILE cc_start: 0.9023 (mt) cc_final: 0.8765 (mp) REVERT: C 71 GLU cc_start: 0.7369 (mt-10) cc_final: 0.7161 (mt-10) REVERT: C 86 ARG cc_start: 0.8687 (mtm180) cc_final: 0.8437 (ttp-110) REVERT: C 130 MET cc_start: 0.7763 (ppp) cc_final: 0.7136 (ptm) REVERT: C 300 VAL cc_start: 0.8973 (t) cc_final: 0.8568 (m) REVERT: C 308 PHE cc_start: 0.8544 (t80) cc_final: 0.8201 (t80) REVERT: C 317 LEU cc_start: 0.8896 (tt) cc_final: 0.8676 (tp) REVERT: C 424 LEU cc_start: 0.7978 (mt) cc_final: 0.7746 (mm) REVERT: D 58 MET cc_start: 0.7156 (mtp) cc_final: 0.6715 (mtp) REVERT: D 93 LYS cc_start: 0.8594 (mtmt) cc_final: 0.8352 (mmmm) REVERT: D 103 ASN cc_start: 0.8736 (p0) cc_final: 0.8420 (p0) REVERT: D 117 LYS cc_start: 0.8435 (mttt) cc_final: 0.8184 (mtmm) REVERT: D 138 GLU cc_start: 0.7603 (tt0) cc_final: 0.7335 (tt0) REVERT: D 145 ASP cc_start: 0.8507 (m-30) cc_final: 0.8014 (m-30) REVERT: D 287 ASP cc_start: 0.8579 (m-30) cc_final: 0.8170 (m-30) REVERT: E 187 SER cc_start: 0.8760 (t) cc_final: 0.8485 (p) REVERT: E 199 VAL cc_start: 0.8255 (t) cc_final: 0.8042 (m) REVERT: E 215 LYS cc_start: 0.8916 (tttt) cc_final: 0.8524 (ttpt) REVERT: E 424 ASP cc_start: 0.8519 (m-30) cc_final: 0.8201 (m-30) REVERT: E 425 ARG cc_start: 0.7391 (ttm170) cc_final: 0.7136 (ttp-110) REVERT: G 478 ASP cc_start: 0.8520 (t0) cc_final: 0.8270 (t0) REVERT: G 508 TRP cc_start: 0.8889 (m100) cc_final: 0.8661 (m100) outliers start: 0 outliers final: 0 residues processed: 662 average time/residue: 0.1491 time to fit residues: 138.8918 Evaluate side-chains 409 residues out of total 1619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 409 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.6980 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 87 ASN A 142 HIS A 190 GLN ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN B 267 HIS B 303 ASN C 122 HIS ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 HIS D 142 HIS D 308 ASN E 64 GLN E 90 GLN E 100 ASN ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 267 HIS G 5 GLN G 445 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.126159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.101748 restraints weight = 24565.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.104612 restraints weight = 13809.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.106479 restraints weight = 9741.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.107660 restraints weight = 7875.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.108301 restraints weight = 6909.449| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15729 Z= 0.158 Angle : 0.653 11.990 21440 Z= 0.330 Chirality : 0.043 0.257 2480 Planarity : 0.005 0.047 2588 Dihedral : 7.483 92.941 2085 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.24 % Favored : 96.71 % Rotamer: Outliers : 3.40 % Allowed : 11.61 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.19), residues: 1791 helix: 0.28 (0.21), residues: 559 sheet: -2.10 (0.22), residues: 473 loop : -1.71 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 221 TYR 0.016 0.002 TYR B 277 PHE 0.018 0.002 PHE A 407 TRP 0.013 0.001 TRP A 288 HIS 0.011 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (15692) covalent geometry : angle 0.63862 / 0.33 (21338) SS BOND : bond 0.00193 / 0.11 ( 6) SS BOND : angle 0.70312 / 0.38 ( 12) hydrogen bonds : bond 0.04325 / 2.96 ( 423) hydrogen bonds : angle 4.64973 / 3.20 ( 1224) Misc. bond : bond 0.00040 / 0.02 ( 1) link_ALPHA1-3 : bond 0.00486 / 0.24 ( 7) link_ALPHA1-3 : angle 1.50622 / 1.07 ( 21) link_ALPHA1-6 : bond 0.00536 / 0.27 ( 5) link_ALPHA1-6 : angle 1.48799 / 1.01 ( 15) link_BETA1-4 : bond 0.00507 / 0.29 ( 11) link_BETA1-4 : angle 1.53116 / 1.09 ( 33) link_NAG-ASN : bond 0.00365 / 0.21 ( 7) link_NAG-ASN : angle 3.68973 / 3.25 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 1619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 442 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7661 (ttp80) cc_final: 0.7377 (ttp80) REVERT: A 96 THR cc_start: 0.9316 (m) cc_final: 0.9100 (p) REVERT: B 17 ASP cc_start: 0.8424 (OUTLIER) cc_final: 0.8213 (t0) REVERT: B 191 HIS cc_start: 0.8507 (p-80) cc_final: 0.8251 (p-80) REVERT: C 178 GLU cc_start: 0.8361 (mt-10) cc_final: 0.7986 (mt-10) REVERT: C 235 TYR cc_start: 0.7608 (t80) cc_final: 0.6751 (t80) REVERT: C 308 PHE cc_start: 0.8656 (t80) cc_final: 0.8236 (t80) REVERT: D 277 LEU cc_start: 0.8098 (mt) cc_final: 0.7612 (mt) REVERT: E 54 ASN cc_start: 0.8574 (m-40) cc_final: 0.8187 (m-40) REVERT: E 70 LYS cc_start: 0.8574 (mttm) cc_final: 0.8326 (mttp) REVERT: E 182 GLU cc_start: 0.7617 (tp30) cc_final: 0.7404 (tp30) REVERT: E 187 SER cc_start: 0.8843 (t) cc_final: 0.8458 (p) REVERT: E 200 PHE cc_start: 0.7185 (m-80) cc_final: 0.6723 (m-10) REVERT: E 215 LYS cc_start: 0.8883 (tttt) cc_final: 0.8508 (ttpt) REVERT: E 298 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8136 (tm-30) REVERT: E 424 ASP cc_start: 0.8516 (m-30) cc_final: 0.8018 (m-30) REVERT: E 425 ARG cc_start: 0.7544 (ttm170) cc_final: 0.7219 (ttp-110) REVERT: G 478 ASP cc_start: 0.8486 (t0) cc_final: 0.8069 (t0) REVERT: G 524 GLN cc_start: 0.7592 (tp-100) cc_final: 0.7392 (tp-100) outliers start: 55 outliers final: 36 residues processed: 475 average time/residue: 0.1281 time to fit residues: 90.5043 Evaluate side-chains 414 residues out of total 1619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 377 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 275 ASN Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 290 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 59 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 101 optimal weight: 8.9990 chunk 62 optimal weight: 0.6980 chunk 148 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 169 optimal weight: 4.9990 chunk 119 optimal weight: 0.0020 overall best weight: 1.1192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 HIS ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN C 80 GLN D 151 HIS D 218 HIS ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.123125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.099151 restraints weight = 25150.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.102001 restraints weight = 14002.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.103855 restraints weight = 9799.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.105033 restraints weight = 7879.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.105675 restraints weight = 6897.844| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15729 Z= 0.138 Angle : 0.598 11.454 21440 Z= 0.300 Chirality : 0.042 0.244 2480 Planarity : 0.004 0.046 2588 Dihedral : 6.774 92.466 2085 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.77 % Allowed : 13.47 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.20), residues: 1791 helix: 0.89 (0.22), residues: 562 sheet: -2.02 (0.22), residues: 474 loop : -1.47 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 85 TYR 0.017 0.001 TYR D 225 PHE 0.019 0.002 PHE A 407 TRP 0.012 0.001 TRP A 288 HIS 0.006 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (15692) covalent geometry : angle 0.58306 / 0.30 (21338) SS BOND : bond 0.00155 / 0.09 ( 6) SS BOND : angle 0.49229 / 0.27 ( 12) hydrogen bonds : bond 0.03832 / 2.60 ( 423) hydrogen bonds : angle 4.38887 / 3.01 ( 1224) Misc. bond : bond 0.00040 / 0.02 ( 1) link_ALPHA1-3 : bond 0.00548 / 0.28 ( 7) link_ALPHA1-3 : angle 1.48455 / 1.09 ( 21) link_ALPHA1-6 : bond 0.00602 / 0.33 ( 5) link_ALPHA1-6 : angle 1.42327 / 0.98 ( 15) link_BETA1-4 : bond 0.00486 / 0.28 ( 11) link_BETA1-4 : angle 1.41193 / 1.01 ( 33) link_NAG-ASN : bond 0.00367 / 0.20 ( 7) link_NAG-ASN : angle 3.57637 / 3.14 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 1619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 394 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7771 (ttp80) cc_final: 0.7420 (ttp80) REVERT: A 129 TYR cc_start: 0.8528 (t80) cc_final: 0.8292 (t80) REVERT: B 43 ASP cc_start: 0.8335 (t0) cc_final: 0.8129 (t0) REVERT: B 95 ASP cc_start: 0.7903 (p0) cc_final: 0.7639 (p0) REVERT: B 191 HIS cc_start: 0.8475 (p-80) cc_final: 0.8256 (p-80) REVERT: C 178 GLU cc_start: 0.8392 (mt-10) cc_final: 0.7991 (mt-10) REVERT: C 211 GLU cc_start: 0.7577 (tp30) cc_final: 0.7366 (tp30) REVERT: C 308 PHE cc_start: 0.8581 (t80) cc_final: 0.8191 (t80) REVERT: D 108 VAL cc_start: 0.9253 (OUTLIER) cc_final: 0.9050 (m) REVERT: D 258 PHE cc_start: 0.8986 (OUTLIER) cc_final: 0.8585 (t80) REVERT: E 54 ASN cc_start: 0.8538 (m-40) cc_final: 0.8164 (m-40) REVERT: E 70 LYS cc_start: 0.8585 (mttm) cc_final: 0.8336 (mttp) REVERT: E 187 SER cc_start: 0.8737 (t) cc_final: 0.8392 (p) REVERT: E 213 ARG cc_start: 0.7763 (ttm170) cc_final: 0.7539 (tpp-160) REVERT: E 215 LYS cc_start: 0.8861 (tttt) cc_final: 0.8465 (ttpt) REVERT: E 298 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8077 (tm-30) REVERT: E 424 ASP cc_start: 0.8579 (m-30) cc_final: 0.7983 (m-30) REVERT: E 425 ARG cc_start: 0.7682 (ttm170) cc_final: 0.7177 (ttp-110) REVERT: G 478 ASP cc_start: 0.8373 (t0) cc_final: 0.8027 (t0) outliers start: 61 outliers final: 40 residues processed: 424 average time/residue: 0.1127 time to fit residues: 72.8203 Evaluate side-chains 413 residues out of total 1619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 371 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 275 ASN Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 290 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 23 optimal weight: 2.9990 chunk 53 optimal weight: 0.0470 chunk 126 optimal weight: 0.0670 chunk 44 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 166 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 142 HIS ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 ASN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.125330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.101257 restraints weight = 24848.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.104178 restraints weight = 13567.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.106080 restraints weight = 9407.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.107314 restraints weight = 7538.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.107949 restraints weight = 6570.574| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15729 Z= 0.108 Angle : 0.568 10.969 21440 Z= 0.282 Chirality : 0.041 0.239 2480 Planarity : 0.004 0.044 2588 Dihedral : 6.174 87.925 2085 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.09 % Allowed : 14.95 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.20), residues: 1791 helix: 1.23 (0.22), residues: 565 sheet: -1.84 (0.22), residues: 474 loop : -1.34 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 85 TYR 0.024 0.001 TYR C 235 PHE 0.017 0.001 PHE A 407 TRP 0.009 0.001 TRP A 288 HIS 0.007 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (15692) covalent geometry : angle 0.55317 / 0.28 (21338) SS BOND : bond 0.00202 / 0.11 ( 6) SS BOND : angle 0.68420 / 0.37 ( 12) hydrogen bonds : bond 0.03559 / 2.39 ( 423) hydrogen bonds : angle 4.20014 / 2.88 ( 1224) Misc. bond : bond 0.00032 / 0.02 ( 1) link_ALPHA1-3 : bond 0.00540 / 0.29 ( 7) link_ALPHA1-3 : angle 1.43081 / 1.06 ( 21) link_ALPHA1-6 : bond 0.00612 / 0.34 ( 5) link_ALPHA1-6 : angle 1.37691 / 0.96 ( 15) link_BETA1-4 : bond 0.00490 / 0.28 ( 11) link_BETA1-4 : angle 1.35592 / 0.96 ( 33) link_NAG-ASN : bond 0.00401 / 0.22 ( 7) link_NAG-ASN : angle 3.40041 / 2.99 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 402 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7840 (ttp80) cc_final: 0.7478 (ttp80) REVERT: A 192 ASP cc_start: 0.8072 (t0) cc_final: 0.7844 (t0) REVERT: B 43 ASP cc_start: 0.8404 (t0) cc_final: 0.8143 (t0) REVERT: B 95 ASP cc_start: 0.8051 (p0) cc_final: 0.7753 (p0) REVERT: B 191 HIS cc_start: 0.8495 (p-80) cc_final: 0.8255 (p-80) REVERT: B 303 ASN cc_start: 0.8782 (OUTLIER) cc_final: 0.8578 (t0) REVERT: C 49 LYS cc_start: 0.8907 (ptmm) cc_final: 0.8625 (ptpp) REVERT: C 178 GLU cc_start: 0.8401 (mt-10) cc_final: 0.7942 (mt-10) REVERT: C 211 GLU cc_start: 0.7513 (tp30) cc_final: 0.7200 (tp30) REVERT: C 308 PHE cc_start: 0.8485 (t80) cc_final: 0.8179 (t80) REVERT: D 108 VAL cc_start: 0.9191 (OUTLIER) cc_final: 0.8968 (m) REVERT: D 258 PHE cc_start: 0.8910 (OUTLIER) cc_final: 0.8710 (t80) REVERT: D 392 ILE cc_start: 0.7112 (pt) cc_final: 0.6804 (pt) REVERT: D 415 TYR cc_start: 0.8155 (m-10) cc_final: 0.7258 (m-10) REVERT: E 54 ASN cc_start: 0.8414 (m-40) cc_final: 0.7935 (m110) REVERT: E 215 LYS cc_start: 0.8831 (tttt) cc_final: 0.8427 (ttpt) REVERT: E 298 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8069 (tm-30) REVERT: E 424 ASP cc_start: 0.8592 (m-30) cc_final: 0.8043 (m-30) REVERT: E 425 ARG cc_start: 0.7714 (ttm170) cc_final: 0.7130 (ttp-110) REVERT: G 478 ASP cc_start: 0.8355 (t0) cc_final: 0.8034 (t0) outliers start: 50 outliers final: 33 residues processed: 427 average time/residue: 0.1153 time to fit residues: 74.3263 Evaluate side-chains 399 residues out of total 1619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 363 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 266 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 63 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 116 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 129 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 GLN D 242 GLN ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.122207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.098637 restraints weight = 24952.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.101459 restraints weight = 13725.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.103275 restraints weight = 9550.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.104435 restraints weight = 7681.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.105051 restraints weight = 6713.507| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15729 Z= 0.121 Angle : 0.578 10.680 21440 Z= 0.283 Chirality : 0.042 0.241 2480 Planarity : 0.004 0.044 2588 Dihedral : 6.075 89.531 2085 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.27 % Allowed : 16.37 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.20), residues: 1791 helix: 1.36 (0.22), residues: 564 sheet: -1.77 (0.23), residues: 469 loop : -1.25 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 31 TYR 0.021 0.001 TYR E 220 PHE 0.024 0.001 PHE A 304 TRP 0.009 0.001 TRP A 288 HIS 0.006 0.001 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (15692) covalent geometry : angle 0.56411 / 0.28 (21338) SS BOND : bond 0.00217 / 0.12 ( 6) SS BOND : angle 0.70030 / 0.38 ( 12) hydrogen bonds : bond 0.03520 / 2.36 ( 423) hydrogen bonds : angle 4.16262 / 2.85 ( 1224) Misc. bond : bond 0.00036 / 0.02 ( 1) link_ALPHA1-3 : bond 0.00552 / 0.28 ( 7) link_ALPHA1-3 : angle 1.46780 / 1.08 ( 21) link_ALPHA1-6 : bond 0.00581 / 0.31 ( 5) link_ALPHA1-6 : angle 1.39925 / 0.98 ( 15) link_BETA1-4 : bond 0.00486 / 0.28 ( 11) link_BETA1-4 : angle 1.33751 / 0.96 ( 33) link_NAG-ASN : bond 0.00381 / 0.22 ( 7) link_NAG-ASN : angle 3.35317 / 2.93 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 380 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7787 (ttp80) cc_final: 0.7528 (ttp80) REVERT: A 192 ASP cc_start: 0.8110 (t0) cc_final: 0.7831 (t0) REVERT: A 199 ASP cc_start: 0.7947 (t0) cc_final: 0.7626 (t0) REVERT: B 43 ASP cc_start: 0.8400 (t0) cc_final: 0.8119 (t0) REVERT: B 95 ASP cc_start: 0.8020 (p0) cc_final: 0.7758 (p0) REVERT: B 191 HIS cc_start: 0.8491 (p-80) cc_final: 0.8241 (p-80) REVERT: C 49 LYS cc_start: 0.8889 (ptmm) cc_final: 0.8643 (ptpp) REVERT: C 178 GLU cc_start: 0.8351 (mt-10) cc_final: 0.7920 (mt-10) REVERT: C 211 GLU cc_start: 0.7463 (tp30) cc_final: 0.7189 (tp30) REVERT: C 223 MET cc_start: 0.8464 (mmt) cc_final: 0.7959 (mmm) REVERT: C 308 PHE cc_start: 0.8466 (t80) cc_final: 0.8197 (t80) REVERT: D 57 ASP cc_start: 0.8447 (m-30) cc_final: 0.8191 (m-30) REVERT: D 90 MET cc_start: 0.7479 (OUTLIER) cc_final: 0.7275 (ttm) REVERT: D 108 VAL cc_start: 0.9144 (OUTLIER) cc_final: 0.8942 (m) REVERT: D 148 MET cc_start: 0.7293 (mpp) cc_final: 0.6643 (mtm) REVERT: D 392 ILE cc_start: 0.7159 (pt) cc_final: 0.6859 (pt) REVERT: E 14 GLU cc_start: 0.8566 (tp30) cc_final: 0.8336 (tp30) REVERT: E 173 LYS cc_start: 0.8561 (mmtm) cc_final: 0.8293 (tptp) REVERT: E 215 LYS cc_start: 0.8867 (tttt) cc_final: 0.8467 (ttpt) REVERT: E 298 GLU cc_start: 0.8683 (tm-30) cc_final: 0.8106 (tm-30) REVERT: E 424 ASP cc_start: 0.8502 (m-30) cc_final: 0.7909 (m-30) REVERT: E 425 ARG cc_start: 0.7672 (ttm170) cc_final: 0.7086 (ttp-110) REVERT: G 478 ASP cc_start: 0.8358 (t0) cc_final: 0.8087 (t0) outliers start: 53 outliers final: 40 residues processed: 409 average time/residue: 0.1225 time to fit residues: 75.3008 Evaluate side-chains 406 residues out of total 1619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 364 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 213 ARG Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 525 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 10 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 117 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 ASN D 242 GLN ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.117560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.093483 restraints weight = 25185.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.096235 restraints weight = 13971.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.098042 restraints weight = 9786.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.099179 restraints weight = 7902.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.099809 restraints weight = 6938.385| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 15729 Z= 0.252 Angle : 0.676 10.747 21440 Z= 0.334 Chirality : 0.045 0.250 2480 Planarity : 0.005 0.047 2588 Dihedral : 6.599 108.447 2085 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.95 % Allowed : 16.86 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.20), residues: 1791 helix: 1.22 (0.22), residues: 572 sheet: -1.91 (0.23), residues: 466 loop : -1.27 (0.22), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 85 TYR 0.024 0.002 TYR D 225 PHE 0.030 0.002 PHE G 453 TRP 0.016 0.001 TRP D 412 HIS 0.008 0.002 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.25 (15692) covalent geometry : angle 0.66377 / 0.33 (21338) SS BOND : bond 0.00357 / 0.19 ( 6) SS BOND : angle 0.93318 / 0.53 ( 12) hydrogen bonds : bond 0.04024 / 2.74 ( 423) hydrogen bonds : angle 4.37845 / 3.01 ( 1224) Misc. bond : bond 0.00086 / 0.05 ( 1) link_ALPHA1-3 : bond 0.00520 / 0.26 ( 7) link_ALPHA1-3 : angle 1.67612 / 1.22 ( 21) link_ALPHA1-6 : bond 0.00397 / 0.23 ( 5) link_ALPHA1-6 : angle 1.49681 / 1.03 ( 15) link_BETA1-4 : bond 0.00510 / 0.29 ( 11) link_BETA1-4 : angle 1.38774 / 1.00 ( 33) link_NAG-ASN : bond 0.00332 / 0.21 ( 7) link_NAG-ASN : angle 3.38868 / 2.97 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 343 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 ASP cc_start: 0.8228 (t0) cc_final: 0.8007 (t0) REVERT: A 199 ASP cc_start: 0.8011 (t0) cc_final: 0.7717 (t0) REVERT: B 43 ASP cc_start: 0.8402 (t0) cc_final: 0.8107 (t0) REVERT: B 191 HIS cc_start: 0.8599 (p-80) cc_final: 0.8258 (p-80) REVERT: C 233 MET cc_start: 0.8059 (tmm) cc_final: 0.7606 (tmm) REVERT: C 308 PHE cc_start: 0.8614 (t80) cc_final: 0.8375 (t80) REVERT: C 410 MET cc_start: 0.7811 (ttt) cc_final: 0.7454 (tpp) REVERT: D 288 TRP cc_start: 0.7075 (OUTLIER) cc_final: 0.6739 (m-10) REVERT: E 14 GLU cc_start: 0.8556 (tp30) cc_final: 0.8338 (tp30) REVERT: E 215 LYS cc_start: 0.8905 (tttt) cc_final: 0.8530 (ttpt) REVERT: E 227 MET cc_start: 0.8680 (ttp) cc_final: 0.8447 (ttt) REVERT: E 298 GLU cc_start: 0.8713 (tm-30) cc_final: 0.8182 (tm-30) REVERT: E 424 ASP cc_start: 0.8548 (m-30) cc_final: 0.8043 (m-30) REVERT: G 478 ASP cc_start: 0.8468 (t0) cc_final: 0.8171 (t0) outliers start: 64 outliers final: 52 residues processed: 380 average time/residue: 0.1171 time to fit residues: 67.7057 Evaluate side-chains 373 residues out of total 1619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 320 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 288 TRP Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 525 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 163 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 chunk 147 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 170 optimal weight: 7.9990 chunk 102 optimal weight: 0.8980 chunk 157 optimal weight: 2.9990 chunk 56 optimal weight: 0.0970 chunk 96 optimal weight: 0.9990 chunk 150 optimal weight: 4.9990 chunk 125 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 142 HIS ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 ASN D 242 GLN ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.120777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.097377 restraints weight = 24786.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.100166 restraints weight = 13714.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.101968 restraints weight = 9576.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.103118 restraints weight = 7718.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.103819 restraints weight = 6758.865| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15729 Z= 0.116 Angle : 0.593 11.080 21440 Z= 0.289 Chirality : 0.042 0.248 2480 Planarity : 0.004 0.043 2588 Dihedral : 6.059 90.094 2085 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.46 % Allowed : 17.91 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.20), residues: 1791 helix: 1.42 (0.22), residues: 572 sheet: -1.81 (0.23), residues: 468 loop : -1.10 (0.23), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 85 TYR 0.020 0.001 TYR D 225 PHE 0.025 0.002 PHE A 304 TRP 0.013 0.001 TRP D 412 HIS 0.007 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (15692) covalent geometry : angle 0.57970 / 0.29 (21338) SS BOND : bond 0.00191 / 0.10 ( 6) SS BOND : angle 0.64816 / 0.35 ( 12) hydrogen bonds : bond 0.03623 / 2.44 ( 423) hydrogen bonds : angle 4.21607 / 2.90 ( 1224) Misc. bond : bond 0.00034 / 0.02 ( 1) link_ALPHA1-3 : bond 0.00590 / 0.30 ( 7) link_ALPHA1-3 : angle 1.46003 / 1.09 ( 21) link_ALPHA1-6 : bond 0.00615 / 0.33 ( 5) link_ALPHA1-6 : angle 1.35275 / 0.94 ( 15) link_BETA1-4 : bond 0.00489 / 0.28 ( 11) link_BETA1-4 : angle 1.30333 / 0.92 ( 33) link_NAG-ASN : bond 0.00377 / 0.23 ( 7) link_NAG-ASN : angle 3.31324 / 2.91 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 364 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7143 (ttp80) cc_final: 0.6681 (ttp80) REVERT: A 192 ASP cc_start: 0.8170 (t0) cc_final: 0.7956 (t0) REVERT: A 199 ASP cc_start: 0.7997 (t0) cc_final: 0.7723 (t70) REVERT: B 28 ARG cc_start: 0.8254 (ttp-110) cc_final: 0.8002 (ttp-170) REVERT: B 43 ASP cc_start: 0.8415 (t0) cc_final: 0.8121 (t0) REVERT: B 191 HIS cc_start: 0.8511 (p-80) cc_final: 0.8185 (p-80) REVERT: C 223 MET cc_start: 0.8373 (mmt) cc_final: 0.7998 (mmm) REVERT: C 308 PHE cc_start: 0.8466 (t80) cc_final: 0.8230 (t80) REVERT: C 410 MET cc_start: 0.7637 (ttt) cc_final: 0.7359 (tpp) REVERT: D 288 TRP cc_start: 0.7096 (OUTLIER) cc_final: 0.6667 (m-10) REVERT: E 14 GLU cc_start: 0.8482 (tp30) cc_final: 0.8220 (tp30) REVERT: E 18 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7895 (ttmt) REVERT: E 215 LYS cc_start: 0.8862 (tttt) cc_final: 0.8498 (ttpt) REVERT: E 227 MET cc_start: 0.8608 (ttp) cc_final: 0.8402 (ttt) REVERT: E 298 GLU cc_start: 0.8686 (tm-30) cc_final: 0.8149 (tm-30) REVERT: E 440 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8845 (tp) REVERT: G 443 PHE cc_start: 0.7428 (OUTLIER) cc_final: 0.7092 (m-10) REVERT: G 478 ASP cc_start: 0.8403 (t0) cc_final: 0.8147 (t0) outliers start: 56 outliers final: 39 residues processed: 399 average time/residue: 0.1125 time to fit residues: 68.3569 Evaluate side-chains 387 residues out of total 1619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 344 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 288 TRP Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 443 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 134 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 169 optimal weight: 0.9980 chunk 38 optimal weight: 0.1980 chunk 167 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 117 optimal weight: 0.0270 chunk 73 optimal weight: 8.9990 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 142 HIS A 190 GLN ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 ASN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.122284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.098614 restraints weight = 24908.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.101486 restraints weight = 13757.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.103327 restraints weight = 9583.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.104521 restraints weight = 7716.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.105139 restraints weight = 6738.104| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15729 Z= 0.108 Angle : 0.591 11.079 21440 Z= 0.286 Chirality : 0.042 0.325 2480 Planarity : 0.004 0.044 2588 Dihedral : 5.834 85.966 2085 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.09 % Allowed : 18.65 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.20), residues: 1791 helix: 1.59 (0.22), residues: 570 sheet: -1.67 (0.23), residues: 469 loop : -0.96 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 425 TYR 0.017 0.001 TYR D 225 PHE 0.023 0.001 PHE A 304 TRP 0.012 0.001 TRP D 412 HIS 0.007 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (15692) covalent geometry : angle 0.57688 / 0.28 (21338) SS BOND : bond 0.00160 / 0.09 ( 6) SS BOND : angle 0.64536 / 0.41 ( 12) hydrogen bonds : bond 0.03461 / 2.35 ( 423) hydrogen bonds : angle 4.13642 / 2.84 ( 1224) Misc. bond : bond 0.00027 / 0.01 ( 1) link_ALPHA1-3 : bond 0.00601 / 0.31 ( 7) link_ALPHA1-3 : angle 1.46672 / 1.10 ( 21) link_ALPHA1-6 : bond 0.00612 / 0.32 ( 5) link_ALPHA1-6 : angle 1.37441 / 0.97 ( 15) link_BETA1-4 : bond 0.00495 / 0.28 ( 11) link_BETA1-4 : angle 1.32246 / 0.95 ( 33) link_NAG-ASN : bond 0.00366 / 0.22 ( 7) link_NAG-ASN : angle 3.37417 / 2.97 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 370 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 ASP cc_start: 0.8222 (t0) cc_final: 0.7974 (t0) REVERT: A 199 ASP cc_start: 0.8007 (t0) cc_final: 0.7745 (t70) REVERT: B 43 ASP cc_start: 0.8507 (t0) cc_final: 0.8209 (t0) REVERT: B 191 HIS cc_start: 0.8543 (p-80) cc_final: 0.8236 (p-80) REVERT: B 261 MET cc_start: 0.8826 (mmt) cc_final: 0.8624 (mmm) REVERT: C 136 ASP cc_start: 0.8855 (p0) cc_final: 0.8565 (p0) REVERT: C 211 GLU cc_start: 0.7506 (tp30) cc_final: 0.7121 (tp30) REVERT: C 223 MET cc_start: 0.8367 (mmt) cc_final: 0.7985 (mmm) REVERT: C 308 PHE cc_start: 0.8401 (t80) cc_final: 0.8192 (t80) REVERT: C 410 MET cc_start: 0.7652 (ttt) cc_final: 0.7402 (tpp) REVERT: D 63 ASP cc_start: 0.8213 (OUTLIER) cc_final: 0.7982 (m-30) REVERT: D 288 TRP cc_start: 0.7181 (OUTLIER) cc_final: 0.6691 (m-10) REVERT: E 14 GLU cc_start: 0.8405 (tp30) cc_final: 0.8147 (tp30) REVERT: E 18 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.8127 (ttmt) REVERT: E 215 LYS cc_start: 0.8834 (tttt) cc_final: 0.8453 (ttpt) REVERT: E 227 MET cc_start: 0.8560 (ttp) cc_final: 0.8350 (ttt) REVERT: E 424 ASP cc_start: 0.8388 (m-30) cc_final: 0.7771 (m-30) REVERT: E 425 ARG cc_start: 0.8049 (mtm-85) cc_final: 0.7780 (ptt-90) REVERT: G 443 PHE cc_start: 0.7450 (OUTLIER) cc_final: 0.7138 (m-10) REVERT: G 478 ASP cc_start: 0.8373 (t0) cc_final: 0.8122 (t0) outliers start: 50 outliers final: 41 residues processed: 402 average time/residue: 0.1194 time to fit residues: 72.1182 Evaluate side-chains 392 residues out of total 1619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 347 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 288 TRP Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 443 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 160 optimal weight: 0.3980 chunk 72 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 142 HIS ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN ** C 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.120561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.096575 restraints weight = 25021.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.099423 restraints weight = 13805.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.101316 restraints weight = 9632.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.102446 restraints weight = 7722.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.103071 restraints weight = 6785.085| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15729 Z= 0.152 Angle : 0.612 10.974 21440 Z= 0.297 Chirality : 0.043 0.301 2480 Planarity : 0.004 0.046 2588 Dihedral : 5.991 94.873 2085 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.52 % Allowed : 18.47 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.20), residues: 1791 helix: 1.64 (0.22), residues: 567 sheet: -1.63 (0.23), residues: 458 loop : -0.99 (0.23), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 85 TYR 0.018 0.001 TYR D 225 PHE 0.023 0.002 PHE A 304 TRP 0.014 0.001 TRP C 183 HIS 0.008 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (15692) covalent geometry : angle 0.59969 / 0.29 (21338) SS BOND : bond 0.00207 / 0.11 ( 6) SS BOND : angle 0.65130 / 0.37 ( 12) hydrogen bonds : bond 0.03526 / 2.40 ( 423) hydrogen bonds : angle 4.17663 / 2.88 ( 1224) Misc. bond : bond 0.00045 / 0.02 ( 1) link_ALPHA1-3 : bond 0.00551 / 0.28 ( 7) link_ALPHA1-3 : angle 1.52173 / 1.13 ( 21) link_ALPHA1-6 : bond 0.00537 / 0.29 ( 5) link_ALPHA1-6 : angle 1.41970 / 1.00 ( 15) link_BETA1-4 : bond 0.00492 / 0.29 ( 11) link_BETA1-4 : angle 1.31090 / 0.94 ( 33) link_NAG-ASN : bond 0.00380 / 0.23 ( 7) link_NAG-ASN : angle 3.28604 / 2.87 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 346 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 ASP cc_start: 0.8236 (t0) cc_final: 0.8002 (t0) REVERT: B 43 ASP cc_start: 0.8496 (t0) cc_final: 0.8236 (t0) REVERT: B 103 LYS cc_start: 0.8729 (ttmt) cc_final: 0.8482 (ttmt) REVERT: B 191 HIS cc_start: 0.8516 (p-80) cc_final: 0.8223 (p-80) REVERT: C 136 ASP cc_start: 0.8825 (p0) cc_final: 0.8518 (p0) REVERT: C 211 GLU cc_start: 0.7543 (tp30) cc_final: 0.7252 (tp30) REVERT: C 223 MET cc_start: 0.8409 (mmt) cc_final: 0.8069 (mmm) REVERT: C 308 PHE cc_start: 0.8393 (t80) cc_final: 0.8186 (t80) REVERT: D 63 ASP cc_start: 0.8246 (OUTLIER) cc_final: 0.8023 (m-30) REVERT: D 288 TRP cc_start: 0.7133 (OUTLIER) cc_final: 0.6633 (m-10) REVERT: E 14 GLU cc_start: 0.8402 (tp30) cc_final: 0.8146 (tp30) REVERT: E 215 LYS cc_start: 0.8877 (tttt) cc_final: 0.8470 (ttpt) REVERT: E 298 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8096 (tm-30) REVERT: E 424 ASP cc_start: 0.8353 (m-30) cc_final: 0.7658 (m-30) REVERT: E 440 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8790 (tp) REVERT: G 443 PHE cc_start: 0.7472 (OUTLIER) cc_final: 0.7176 (m-10) REVERT: G 478 ASP cc_start: 0.8405 (t0) cc_final: 0.8156 (t0) outliers start: 57 outliers final: 48 residues processed: 383 average time/residue: 0.1197 time to fit residues: 69.3297 Evaluate side-chains 385 residues out of total 1619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 333 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 288 TRP Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 443 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 51 optimal weight: 0.0970 chunk 104 optimal weight: 0.5980 chunk 164 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 142 HIS ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN ** C 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.120820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.096764 restraints weight = 25193.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.099660 restraints weight = 13750.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.101532 restraints weight = 9571.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.102711 restraints weight = 7684.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.103333 restraints weight = 6731.406| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 15729 Z= 0.132 Angle : 0.603 11.137 21440 Z= 0.292 Chirality : 0.043 0.313 2480 Planarity : 0.004 0.055 2588 Dihedral : 5.940 94.297 2085 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.21 % Allowed : 18.72 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.20), residues: 1791 helix: 1.64 (0.22), residues: 572 sheet: -1.62 (0.23), residues: 458 loop : -0.93 (0.23), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 425 TYR 0.019 0.001 TYR B 299 PHE 0.024 0.002 PHE A 304 TRP 0.011 0.001 TRP C 123 HIS 0.008 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (15692) covalent geometry : angle 0.58954 / 0.29 (21338) SS BOND : bond 0.00180 / 0.09 ( 6) SS BOND : angle 0.61110 / 0.36 ( 12) hydrogen bonds : bond 0.03478 / 2.37 ( 423) hydrogen bonds : angle 4.15773 / 2.85 ( 1224) Misc. bond : bond 0.00039 / 0.02 ( 1) link_ALPHA1-3 : bond 0.00580 / 0.30 ( 7) link_ALPHA1-3 : angle 1.50072 / 1.12 ( 21) link_ALPHA1-6 : bond 0.00553 / 0.29 ( 5) link_ALPHA1-6 : angle 1.38711 / 0.98 ( 15) link_BETA1-4 : bond 0.00481 / 0.28 ( 11) link_BETA1-4 : angle 1.30638 / 0.94 ( 33) link_NAG-ASN : bond 0.00388 / 0.23 ( 7) link_NAG-ASN : angle 3.34005 / 2.92 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 339 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 ASP cc_start: 0.8203 (t0) cc_final: 0.7960 (t0) REVERT: B 43 ASP cc_start: 0.8510 (t0) cc_final: 0.8241 (t0) REVERT: B 103 LYS cc_start: 0.8735 (ttmt) cc_final: 0.8486 (ttmt) REVERT: B 138 MET cc_start: 0.7934 (mtt) cc_final: 0.7640 (mtt) REVERT: B 191 HIS cc_start: 0.8533 (p-80) cc_final: 0.8196 (p-80) REVERT: C 136 ASP cc_start: 0.8821 (p0) cc_final: 0.8533 (p0) REVERT: C 211 GLU cc_start: 0.7540 (tp30) cc_final: 0.7260 (tp30) REVERT: C 223 MET cc_start: 0.8397 (mmt) cc_final: 0.8054 (mmm) REVERT: C 313 GLU cc_start: 0.8908 (tm-30) cc_final: 0.7059 (mm-30) REVERT: D 63 ASP cc_start: 0.8272 (OUTLIER) cc_final: 0.8057 (m-30) REVERT: E 14 GLU cc_start: 0.8352 (tp30) cc_final: 0.8111 (tp30) REVERT: E 215 LYS cc_start: 0.8863 (tttt) cc_final: 0.8501 (ttpt) REVERT: E 424 ASP cc_start: 0.8373 (m-30) cc_final: 0.7681 (m-30) REVERT: E 440 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8779 (tt) REVERT: G 443 PHE cc_start: 0.7469 (OUTLIER) cc_final: 0.7166 (m-10) REVERT: G 478 ASP cc_start: 0.8392 (t0) cc_final: 0.8140 (t0) outliers start: 52 outliers final: 45 residues processed: 374 average time/residue: 0.1165 time to fit residues: 66.6067 Evaluate side-chains 382 residues out of total 1619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 334 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 418 PHE Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 443 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 85 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 51 optimal weight: 0.2980 chunk 122 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 120 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 167 optimal weight: 5.9990 chunk 172 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 142 HIS ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.121440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.097574 restraints weight = 25040.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.100477 restraints weight = 13642.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.102390 restraints weight = 9449.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.103605 restraints weight = 7558.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.104195 restraints weight = 6580.841| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15729 Z= 0.115 Angle : 0.594 11.165 21440 Z= 0.288 Chirality : 0.042 0.321 2480 Planarity : 0.004 0.062 2588 Dihedral : 5.755 89.469 2085 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.15 % Allowed : 18.96 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.20), residues: 1791 helix: 1.70 (0.22), residues: 570 sheet: -1.55 (0.24), residues: 453 loop : -0.90 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 425 TYR 0.016 0.001 TYR E 299 PHE 0.023 0.002 PHE A 304 TRP 0.011 0.001 TRP B 237 HIS 0.008 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 (15692) covalent geometry : angle 0.58074 / 0.28 (21338) SS BOND : bond 0.00148 / 0.08 ( 6) SS BOND : angle 0.52726 / 0.29 ( 12) hydrogen bonds : bond 0.03411 / 2.32 ( 423) hydrogen bonds : angle 4.13354 / 2.83 ( 1224) Misc. bond : bond 0.00036 / 0.02 ( 1) link_ALPHA1-3 : bond 0.00596 / 0.31 ( 7) link_ALPHA1-3 : angle 1.47769 / 1.11 ( 21) link_ALPHA1-6 : bond 0.00556 / 0.29 ( 5) link_ALPHA1-6 : angle 1.36327 / 0.96 ( 15) link_BETA1-4 : bond 0.00485 / 0.28 ( 11) link_BETA1-4 : angle 1.30417 / 0.94 ( 33) link_NAG-ASN : bond 0.00392 / 0.23 ( 7) link_NAG-ASN : angle 3.25513 / 2.84 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2765.47 seconds wall clock time: 48 minutes 38.42 seconds (2918.42 seconds total)