Starting phenix.real_space_refine on Sun May 3 11:08:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vuc_65359/05_2026/9vuc_65359_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vuc_65359/05_2026/9vuc_65359.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vuc_65359/05_2026/9vuc_65359.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vuc_65359/05_2026/9vuc_65359.map" model { file = "/net/cci-nas-00/data/ceres_data/9vuc_65359/05_2026/9vuc_65359_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vuc_65359/05_2026/9vuc_65359_trim.cif" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.033 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 K 4 8.98 5 S 89 5.16 5 C 8046 2.51 5 N 2151 2.21 5 O 2182 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12472 Number of models: 1 Model: "" Number of chains: 9 Chain: "E" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 438 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'TRANS': 67} Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 8, 'TYR:plan': 2, 'ARG:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 80 Chain: "F" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 446 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'TRANS': 66} Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 5, 'GLU:plan': 6, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 60 Chain: "G" Number of atoms: 443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 443 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'TRANS': 66} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 4, 'TYR:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 70 Chain: "A" Number of atoms: 2783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2783 Classifications: {'peptide': 356} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 349} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 3, 'PHE:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "B" Number of atoms: 2769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2769 Classifications: {'peptide': 355} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 6, 'TRANS': 348} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TRP:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 2783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2783 Classifications: {'peptide': 356} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 6, 'TRANS': 349} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "D" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2768 Classifications: {'peptide': 356} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 6, 'TRANS': 349} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1, 'PHE:plan': 2, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 28 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' K': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'Y7Z': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.35, per 1000 atoms: 0.27 Number of scatterers: 12472 At special positions: 0 Unit cell: (125.8, 128.35, 99.45, 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) K 4 19.00 S 89 16.00 O 2182 8.00 N 2151 7.00 C 8046 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 332 " - pdb=" SG CYS A 370 " distance=2.03 Simple disulfide: pdb=" SG CYS B 332 " - pdb=" SG CYS B 370 " distance=2.03 Simple disulfide: pdb=" SG CYS C 332 " - pdb=" SG CYS C 370 " distance=2.04 Simple disulfide: pdb=" SG CYS D 332 " - pdb=" SG CYS D 370 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 597.5 milliseconds 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3076 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 4 sheets defined 78.9% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'E' and resid 82 through 91 removed outlier: 3.769A pdb=" N ARG E 90 " --> pdb=" O ARG E 86 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL E 91 " --> pdb=" O GLU E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 111 removed outlier: 3.594A pdb=" N ASN E 111 " --> pdb=" O HIS E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 129 removed outlier: 3.969A pdb=" N VAL E 121 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP E 122 " --> pdb=" O ASP E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 removed outlier: 4.249A pdb=" N PHE E 141 " --> pdb=" O ASN E 137 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL E 142 " --> pdb=" O TYR E 138 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN E 143 " --> pdb=" O GLU E 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 91 removed outlier: 3.511A pdb=" N ARG F 90 " --> pdb=" O ARG F 86 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL F 91 " --> pdb=" O GLU F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 111 Processing helix chain 'F' and resid 117 through 129 removed outlier: 3.977A pdb=" N VAL F 121 " --> pdb=" O THR F 117 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP F 122 " --> pdb=" O ASP F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 146 removed outlier: 4.369A pdb=" N PHE F 141 " --> pdb=" O ASN F 137 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL F 142 " --> pdb=" O TYR F 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 88 Processing helix chain 'G' and resid 101 through 110 Processing helix chain 'G' and resid 117 through 129 removed outlier: 3.890A pdb=" N VAL G 121 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP G 122 " --> pdb=" O ASP G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 146 removed outlier: 4.242A pdb=" N PHE G 141 " --> pdb=" O ASN G 137 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR G 146 " --> pdb=" O VAL G 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 157 removed outlier: 3.768A pdb=" N TRP A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 200 removed outlier: 3.626A pdb=" N LEU A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 208 Processing helix chain 'A' and resid 210 through 224 removed outlier: 3.527A pdb=" N CYS A 224 " --> pdb=" O GLU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 260 Processing helix chain 'A' and resid 261 through 265 Processing helix chain 'A' and resid 266 through 276 removed outlier: 4.121A pdb=" N ALA A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 282 through 292 removed outlier: 3.676A pdb=" N ARG A 286 " --> pdb=" O ASP A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 309 Processing helix chain 'A' and resid 309 through 334 Processing helix chain 'A' and resid 335 through 337 No H-bonds generated for 'chain 'A' and resid 335 through 337' Processing helix chain 'A' and resid 344 through 357 removed outlier: 3.553A pdb=" N LEU A 357 " --> pdb=" O SER A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 397 removed outlier: 3.562A pdb=" N LYS A 372 " --> pdb=" O THR A 368 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 438 removed outlier: 3.536A pdb=" N LYS A 417 " --> pdb=" O THR A 413 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LYS A 438 " --> pdb=" O TYR A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 473 removed outlier: 3.604A pdb=" N ASN A 473 " --> pdb=" O GLN A 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 157 removed outlier: 3.897A pdb=" N TRP B 157 " --> pdb=" O THR B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 200 removed outlier: 3.674A pdb=" N LEU B 168 " --> pdb=" O SER B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 208 Processing helix chain 'B' and resid 210 through 224 Processing helix chain 'B' and resid 254 through 260 Processing helix chain 'B' and resid 261 through 265 removed outlier: 3.623A pdb=" N ARG B 265 " --> pdb=" O MET B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 276 removed outlier: 4.012A pdb=" N ALA B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 282 removed outlier: 3.693A pdb=" N ASP B 282 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 293 Processing helix chain 'B' and resid 297 through 309 removed outlier: 3.780A pdb=" N VAL B 301 " --> pdb=" O ASN B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 334 removed outlier: 3.558A pdb=" N VAL B 313 " --> pdb=" O CYS B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 337 No H-bonds generated for 'chain 'B' and resid 335 through 337' Processing helix chain 'B' and resid 344 through 357 Processing helix chain 'B' and resid 368 through 397 removed outlier: 3.533A pdb=" N ALA B 387 " --> pdb=" O ALA B 383 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG B 395 " --> pdb=" O ALA B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 438 Processing helix chain 'B' and resid 444 through 468 Processing helix chain 'B' and resid 470 through 472 No H-bonds generated for 'chain 'B' and resid 470 through 472' Processing helix chain 'C' and resid 119 through 157 removed outlier: 3.709A pdb=" N TRP C 157 " --> pdb=" O THR C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 200 removed outlier: 3.643A pdb=" N LEU C 168 " --> pdb=" O SER C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 208 Processing helix chain 'C' and resid 210 through 224 removed outlier: 3.513A pdb=" N CYS C 224 " --> pdb=" O GLU C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 260 Processing helix chain 'C' and resid 261 through 265 removed outlier: 3.527A pdb=" N LEU C 264 " --> pdb=" O PRO C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 277 removed outlier: 4.100A pdb=" N ALA C 270 " --> pdb=" O LEU C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 293 removed outlier: 3.522A pdb=" N ARG C 286 " --> pdb=" O ASP C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 309 Processing helix chain 'C' and resid 309 through 334 removed outlier: 3.551A pdb=" N VAL C 313 " --> pdb=" O CYS C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 357 Processing helix chain 'C' and resid 368 through 397 removed outlier: 3.576A pdb=" N ALA C 387 " --> pdb=" O ALA C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 438 removed outlier: 4.144A pdb=" N LYS C 417 " --> pdb=" O THR C 413 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR C 437 " --> pdb=" O ILE C 433 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS C 438 " --> pdb=" O TYR C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 471 removed outlier: 4.193A pdb=" N LYS C 471 " --> pdb=" O MET C 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 156 Processing helix chain 'D' and resid 164 through 200 removed outlier: 3.636A pdb=" N LEU D 168 " --> pdb=" O SER D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 208 Processing helix chain 'D' and resid 210 through 224 Processing helix chain 'D' and resid 254 through 260 Processing helix chain 'D' and resid 261 through 266 removed outlier: 3.552A pdb=" N ARG D 265 " --> pdb=" O MET D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 277 Processing helix chain 'D' and resid 277 through 282 removed outlier: 3.572A pdb=" N ASP D 282 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 293 removed outlier: 3.693A pdb=" N ARG D 286 " --> pdb=" O ASP D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 309 removed outlier: 3.791A pdb=" N VAL D 301 " --> pdb=" O ASN D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 334 removed outlier: 3.611A pdb=" N VAL D 313 " --> pdb=" O CYS D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 337 No H-bonds generated for 'chain 'D' and resid 335 through 337' Processing helix chain 'D' and resid 344 through 357 Processing helix chain 'D' and resid 368 through 397 removed outlier: 3.527A pdb=" N ALA D 387 " --> pdb=" O ALA D 383 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG D 395 " --> pdb=" O ALA D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 438 removed outlier: 3.641A pdb=" N LYS D 438 " --> pdb=" O TYR D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 473 Processing sheet with id=AA1, first strand: chain 'A' and resid 235 through 240 Processing sheet with id=AA2, first strand: chain 'B' and resid 235 through 240 Processing sheet with id=AA3, first strand: chain 'C' and resid 234 through 240 Processing sheet with id=AA4, first strand: chain 'D' and resid 234 through 240 958 hydrogen bonds defined for protein. 2826 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: 2.08 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2779 1.33 - 1.45: 2649 1.45 - 1.57: 7134 1.57 - 1.69: 0 1.69 - 1.81: 146 Bond restraints: 12708 Sorted by residual: bond pdb=" C14 Y7Z D 601 " pdb=" N2 Y7Z D 601 " ideal model delta sigma weight residual 1.349 1.465 -0.116 2.00e-02 2.50e+03 3.34e+01 bond pdb=" C1 Y7Z D 601 " pdb=" C6 Y7Z D 601 " ideal model delta sigma weight residual 1.461 1.358 0.103 2.00e-02 2.50e+03 2.67e+01 bond pdb=" C26 Y7Z D 601 " pdb=" N4 Y7Z D 601 " ideal model delta sigma weight residual 1.452 1.355 0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" C17 Y7Z D 601 " pdb=" C18 Y7Z D 601 " ideal model delta sigma weight residual 1.425 1.351 0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C25 Y7Z D 601 " pdb=" C7 Y7Z D 601 " ideal model delta sigma weight residual 1.431 1.358 0.073 2.00e-02 2.50e+03 1.34e+01 ... (remaining 12703 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 16763 1.81 - 3.61: 417 3.61 - 5.42: 40 5.42 - 7.22: 11 7.22 - 9.03: 5 Bond angle restraints: 17236 Sorted by residual: angle pdb=" N ALA A 159 " pdb=" CA ALA A 159 " pdb=" C ALA A 159 " ideal model delta sigma weight residual 113.55 106.18 7.37 1.26e+00 6.30e-01 3.42e+01 angle pdb=" CA ILE A 260 " pdb=" C ILE A 260 " pdb=" N PRO A 261 " ideal model delta sigma weight residual 120.83 117.86 2.97 5.90e-01 2.87e+00 2.53e+01 angle pdb=" C ILE A 260 " pdb=" CA ILE A 260 " pdb=" CB ILE A 260 " ideal model delta sigma weight residual 113.70 109.21 4.49 9.50e-01 1.11e+00 2.24e+01 angle pdb=" C VAL C 365 " pdb=" N PRO C 366 " pdb=" CA PRO C 366 " ideal model delta sigma weight residual 119.78 123.71 -3.93 1.03e+00 9.43e-01 1.45e+01 angle pdb=" N ASP C 340 " pdb=" CA ASP C 340 " pdb=" C ASP C 340 " ideal model delta sigma weight residual 111.24 116.29 -5.05 1.38e+00 5.25e-01 1.34e+01 ... (remaining 17231 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.75: 7223 30.75 - 61.50: 300 61.50 - 92.26: 9 92.26 - 123.01: 0 123.01 - 153.76: 2 Dihedral angle restraints: 7534 sinusoidal: 2789 harmonic: 4745 Sorted by residual: dihedral pdb=" CB CYS C 332 " pdb=" SG CYS C 332 " pdb=" SG CYS C 370 " pdb=" CB CYS C 370 " ideal model delta sinusoidal sigma weight residual -86.00 -28.08 -57.92 1 1.00e+01 1.00e-02 4.50e+01 dihedral pdb=" CB CYS A 332 " pdb=" SG CYS A 332 " pdb=" SG CYS A 370 " pdb=" CB CYS A 370 " ideal model delta sinusoidal sigma weight residual -86.00 -124.87 38.87 1 1.00e+01 1.00e-02 2.13e+01 dihedral pdb=" C10 Y7Z D 601 " pdb=" C8 Y7Z D 601 " pdb=" C9 Y7Z D 601 " pdb=" N1 Y7Z D 601 " ideal model delta sinusoidal sigma weight residual 91.84 -61.92 153.76 1 3.00e+01 1.11e-03 2.02e+01 ... (remaining 7531 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1580 0.048 - 0.097: 433 0.097 - 0.145: 32 0.145 - 0.193: 3 0.193 - 0.241: 3 Chirality restraints: 2051 Sorted by residual: chirality pdb=" CA ARG C 265 " pdb=" N ARG C 265 " pdb=" C ARG C 265 " pdb=" CB ARG C 265 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA ARG D 265 " pdb=" N ARG D 265 " pdb=" C ARG D 265 " pdb=" CB ARG D 265 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA VAL A 341 " pdb=" N VAL A 341 " pdb=" C VAL A 341 " pdb=" CB VAL A 341 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.33e-01 ... (remaining 2048 not shown) Planarity restraints: 2123 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 369 " 0.012 2.00e-02 2.50e+03 9.64e-03 1.86e+00 pdb=" CG TYR D 369 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR D 369 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR D 369 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR D 369 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR D 369 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR D 369 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 369 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 356 " -0.011 2.00e-02 2.50e+03 9.72e-03 1.65e+00 pdb=" CG PHE B 356 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE B 356 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE B 356 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE B 356 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 356 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 356 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 356 " 0.011 2.00e-02 2.50e+03 9.52e-03 1.59e+00 pdb=" CG PHE D 356 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE D 356 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 356 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE D 356 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE D 356 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE D 356 " 0.002 2.00e-02 2.50e+03 ... (remaining 2120 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.93: 6009 2.93 - 3.49: 14644 3.49 - 4.04: 20361 4.04 - 4.59: 30960 4.59 - 5.14: 41219 Nonbonded interactions: 113193 Sorted by model distance: nonbonded pdb=" O VAL E 142 " pdb=" OG1 THR E 146 " model vdw 2.382 3.040 nonbonded pdb=" O ASP B 255 " pdb=" OG SER B 259 " model vdw 2.384 3.040 nonbonded pdb=" O VAL E 108 " pdb=" O LEU E 112 " model vdw 2.415 3.040 nonbonded pdb=" O LEU D 357 " pdb=" OG SER D 358 " model vdw 2.423 3.040 nonbonded pdb=" O LEU B 357 " pdb=" OG SER B 358 " model vdw 2.428 3.040 ... (remaining 113188 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 118 through 120 or (resid 121 and (name N or name CA or na \ me C or name O or name CB )) or resid 122 through 203 or (resid 204 and (name N \ or name CA or name C or name O or name CB )) or resid 205 through 206 or (resid \ 207 through 209 and (name N or name CA or name C or name O or name CB )) or resi \ d 210 through 283 or (resid 284 through 285 and (name N or name CA or name C or \ name O or name CB )) or resid 286 through 287 or (resid 288 and (name N or name \ CA or name C or name O or name CB )) or resid 289 through 293 or (resid 294 and \ (name N or name CA or name C or name O or name CB )) or resid 295 through 301 or \ (resid 302 and (name N or name CA or name C or name O or name CB )) or resid 30 \ 3 through 402 or (resid 403 and (name N or name CA or name C or name O or name C \ B )) or resid 404 through 408 or (resid 409 through 410 and (name N or name CA o \ r name C or name O or name CB )) or resid 411 through 415 or (resid 416 through \ 417 and (name N or name CA or name C or name O or name CB )) or resid 418 or (re \ sid 419 through 420 and (name N or name CA or name C or name O or name CB )) or \ resid 421 through 427 or (resid 428 and (name N or name CA or name C or name O o \ r name CB )) or resid 429 through 430 or (resid 431 through 433 and (name N or n \ ame CA or name C or name O or name CB )) or resid 434 or (resid 435 and (name N \ or name CA or name C or name O or name CB )) or resid 436 through 438 or (resid \ 439 and (name N or name CA or name C or name O or name CB )) or resid 440 or (re \ sid 441 and (name N or name CA or name C or name O or name CB )) or resid 442 th \ rough 446 or (resid 447 through 448 and (name N or name CA or name C or name O o \ r name CB )) or resid 449 or (resid 450 through 451 and (name N or name CA or na \ me C or name O or name CB )) or resid 452 through 453 or (resid 454 through 455 \ and (name N or name CA or name C or name O or name CB )) or resid 456 through 45 \ 8 or (resid 459 and (name N or name CA or name C or name O or name CB )) or resi \ d 460 or (resid 461 and (name N or name CA or name C or name O or name CB )) or \ resid 462 through 463 or (resid 464 and (name N or name CA or name C or name O o \ r name CB )) or resid 465 through 466 or (resid 467 and (name N or name CA or na \ me C or name O or name CB )) or resid 468 or (resid 470 through 472 and (name N \ or name CA or name C or name O or name CB )) or resid 473)) selection = (chain 'B' and (resid 118 or (resid 119 and (name N or name CA or name C or name \ O or name CB )) or resid 120 or (resid 121 and (name N or name CA or name C or \ name O or name CB )) or resid 122 through 124 or (resid 125 through 126 and (nam \ e N or name CA or name C or name O or name CB )) or resid 127 through 203 or (re \ sid 204 and (name N or name CA or name C or name O or name CB )) or resid 205 th \ rough 206 or (resid 207 through 209 and (name N or name CA or name C or name O o \ r name CB )) or resid 210 through 278 or (resid 279 through 280 and (name N or n \ ame CA or name C or name O or name CB )) or resid 281 through 283 or (resid 284 \ through 285 and (name N or name CA or name C or name O or name CB )) or resid 28 \ 6 through 293 or (resid 294 and (name N or name CA or name C or name O or name C \ B )) or resid 295 or (resid 296 and (name N or name CA or name C or name O or na \ me CB )) or resid 297 through 301 or (resid 302 and (name N or name CA or name C \ or name O or name CB )) or resid 303 through 402 or (resid 403 and (name N or n \ ame CA or name C or name O or name CB )) or resid 404 through 408 or (resid 409 \ through 410 and (name N or name CA or name C or name O or name CB )) or resid 41 \ 1 through 427 or (resid 428 and (name N or name CA or name C or name O or name C \ B )) or resid 429 through 431 or (resid 432 through 433 and (name N or name CA o \ r name C or name O or name CB )) or resid 434 through 436 or (resid 437 through \ 439 and (name N or name CA or name C or name O or name CB )) or resid 440 throug \ h 442 or (resid 443 through 444 and (name N or name CA or name C or name O or na \ me CB )) or resid 445 through 446 or (resid 447 through 448 and (name N or name \ CA or name C or name O or name CB )) or resid 449 or (resid 450 through 451 and \ (name N or name CA or name C or name O or name CB )) or resid 452 through 462 or \ (resid 463 through 464 and (name N or name CA or name C or name O or name CB )) \ or resid 465 through 466 or (resid 467 and (name N or name CA or name C or name \ O or name CB )) or resid 468 or (resid 470 through 472 and (name N or name CA o \ r name C or name O or name CB )) or resid 473)) selection = (chain 'C' and (resid 118 through 120 or (resid 121 and (name N or name CA or na \ me C or name O or name CB )) or resid 122 through 203 or (resid 204 and (name N \ or name CA or name C or name O or name CB )) or resid 205 through 206 or (resid \ 207 through 209 and (name N or name CA or name C or name O or name CB )) or resi \ d 210 through 277 or (resid 278 through 280 and (name N or name CA or name C or \ name O or name CB )) or resid 281 through 283 or (resid 284 through 285 and (nam \ e N or name CA or name C or name O or name CB )) or resid 286 through 287 or (re \ sid 288 and (name N or name CA or name C or name O or name CB )) or resid 289 th \ rough 292 or (resid 293 through 294 and (name N or name CA or name C or name O o \ r name CB )) or resid 295 through 402 or (resid 403 and (name N or name CA or na \ me C or name O or name CB )) or resid 404 through 408 or (resid 409 through 410 \ and (name N or name CA or name C or name O or name CB )) or resid 411 through 41 \ 5 or (resid 416 through 417 and (name N or name CA or name C or name O or name C \ B )) or resid 418 or (resid 419 through 420 and (name N or name CA or name C or \ name O or name CB )) or resid 421 through 430 or (resid 431 through 433 and (nam \ e N or name CA or name C or name O or name CB )) or resid 434 through 436 or (re \ sid 437 through 439 and (name N or name CA or name C or name O or name CB )) or \ resid 440 through 442 or (resid 443 through 444 and (name N or name CA or name C \ or name O or name CB )) or resid 445 through 447 or (resid 448 and (name N or n \ ame CA or name C or name O or name CB )) or resid 449 or (resid 450 through 451 \ and (name N or name CA or name C or name O or name CB )) or resid 452 through 45 \ 3 or (resid 454 through 455 and (name N or name CA or name C or name O or name C \ B )) or resid 456 through 458 or (resid 459 and (name N or name CA or name C or \ name O or name CB )) or resid 460 or (resid 461 and (name N or name CA or name C \ or name O or name CB )) or resid 462 or (resid 463 through 464 and (name N or n \ ame CA or name C or name O or name CB )) or resid 465 through 466 or (resid 467 \ and (name N or name CA or name C or name O or name CB )) or resid 468 or resid 4 \ 70 through 473)) selection = (chain 'D' and (resid 118 or (resid 119 and (name N or name CA or name C or name \ O or name CB )) or resid 120 through 124 or (resid 125 through 126 and (name N \ or name CA or name C or name O or name CB )) or resid 127 through 278 or (resid \ 279 through 280 and (name N or name CA or name C or name O or name CB )) or resi \ d 281 through 284 or (resid 285 and (name N or name CA or name C or name O or na \ me CB )) or resid 286 through 292 or (resid 293 through 294 and (name N or name \ CA or name C or name O or name CB )) or resid 295 or (resid 296 and (name N or n \ ame CA or name C or name O or name CB )) or resid 297 through 301 or (resid 302 \ and (name N or name CA or name C or name O or name CB )) or resid 303 through 41 \ 5 or (resid 416 through 417 and (name N or name CA or name C or name O or name C \ B )) or resid 418 through 427 or (resid 428 and (name N or name CA or name C or \ name O or name CB )) or resid 429 through 430 or (resid 431 through 433 and (nam \ e N or name CA or name C or name O or name CB )) or resid 434 through 436 or (re \ sid 437 through 439 and (name N or name CA or name C or name O or name CB )) or \ resid 440 through 442 or (resid 443 through 444 and (name N or name CA or name C \ or name O or name CB )) or resid 445 through 446 or (resid 447 through 448 and \ (name N or name CA or name C or name O or name CB )) or resid 449 through 453 or \ (resid 454 through 455 and (name N or name CA or name C or name O or name CB )) \ or resid 456 through 462 or (resid 463 through 464 and (name N or name CA or na \ me C or name O or name CB )) or resid 465 through 468 or (resid 470 through 472 \ and (name N or name CA or name C or name O or name CB )) or resid 473)) } ncs_group { reference = (chain 'E' and (resid 81 or (resid 82 and (name N or name CA or name C or name O \ or name CB )) or resid 83 through 84 or (resid 85 through 88 and (name N or nam \ e CA or name C or name O or name CB )) or resid 89 or (resid 90 and (name N or n \ ame CA or name C or name O or name CB )) or resid 91 through 108 or (resid 109 a \ nd (name N or name CA or name C or name O or name CB )) or resid 110 through 142 \ or (resid 143 through 145 and (name N or name CA or name C or name O or name CB \ )) or resid 146 through 147)) selection = (chain 'F' and (resid 81 or (resid 82 and (name N or name CA or name C or name O \ or name CB )) or resid 83 or (resid 84 through 88 and (name N or name CA or nam \ e C or name O or name CB )) or resid 89 or (resid 90 and (name N or name CA or n \ ame C or name O or name CB )) or resid 91 through 98 or (resid 99 and (name N or \ name CA or name C or name O or name CB )) or resid 100 through 135 or (resid 13 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 137 through \ 140 or (resid 141 through 145 and (name N or name CA or name C or name O or name \ CB )) or resid 146 through 147)) selection = (chain 'G' and (resid 81 through 83 or (resid 84 through 88 and (name N or name \ CA or name C or name O or name CB )) or resid 89 through 108 or (resid 109 and ( \ name N or name CA or name C or name O or name CB )) or resid 110 through 135 or \ (resid 136 and (name N or name CA or name C or name O or name CB )) or resid 137 \ or (resid 138 through 145 and (name N or name CA or name C or name O or name CB \ )) or resid 146 through 147)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.930 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: 0.020 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.020 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 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 0.116 12712 Z= 0.319 Angle : 0.721 9.025 17244 Z= 0.457 Chirality : 0.041 0.241 2051 Planarity : 0.003 0.032 2123 Dihedral : 15.666 153.761 4446 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.48 % Allowed : 22.59 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.21), residues: 1609 helix: 1.79 (0.15), residues: 1173 sheet: 0.61 (0.69), residues: 56 loop : -1.88 (0.27), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 449 TYR 0.023 0.002 TYR D 369 PHE 0.023 0.002 PHE B 356 TRP 0.012 0.002 TRP D 350 HIS 0.006 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00664 (12708) covalent geometry : angle 0.72012 (17236) SS BOND : bond 0.00580 ( 4) SS BOND : angle 1.47568 ( 8) hydrogen bonds : bond 0.14234 ( 958) hydrogen bonds : angle 4.97722 ( 2826) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 209 time to evaluate : 0.471 Fit side-chains revert: symmetry clash REVERT: G 84 GLU cc_start: 0.6802 (mp0) cc_final: 0.5751 (pp20) REVERT: A 398 GLU cc_start: 0.8290 (mm-30) cc_final: 0.8054 (mm-30) REVERT: A 436 ASN cc_start: 0.7030 (m-40) cc_final: 0.6535 (m-40) REVERT: B 274 LEU cc_start: 0.7186 (OUTLIER) cc_final: 0.6910 (tp) REVERT: B 299 ARG cc_start: 0.7617 (mtm-85) cc_final: 0.5943 (ttt180) REVERT: B 340 ASP cc_start: 0.8053 (t0) cc_final: 0.7746 (t70) REVERT: B 408 ASN cc_start: 0.5605 (m110) cc_final: 0.5383 (m-40) REVERT: B 450 LYS cc_start: 0.6738 (tttt) cc_final: 0.6410 (tmtt) REVERT: C 206 ARG cc_start: 0.7910 (mtm180) cc_final: 0.7591 (mpp80) REVERT: C 209 MET cc_start: 0.7826 (mmt) cc_final: 0.7421 (mmt) REVERT: C 338 GLN cc_start: 0.8078 (mt0) cc_final: 0.7658 (pm20) REVERT: D 299 ARG cc_start: 0.7481 (mtm-85) cc_final: 0.5836 (ttt180) outliers start: 6 outliers final: 3 residues processed: 212 average time/residue: 0.5966 time to fit residues: 136.5926 Evaluate side-chains 170 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 166 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain D residue 161 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.2980 chunk 149 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN A 339 GLN A 344 ASN A 425 ASN A 461 GLN B 339 GLN B 451 HIS C 232 ASN C 338 GLN C 421 ASN C 425 ASN C 473 ASN D 473 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.212305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.146392 restraints weight = 13324.751| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.26 r_work: 0.3042 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12712 Z= 0.130 Angle : 0.472 9.045 17244 Z= 0.259 Chirality : 0.036 0.215 2051 Planarity : 0.003 0.033 2123 Dihedral : 6.408 129.755 1774 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.34 % Allowed : 21.08 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.03 (0.21), residues: 1609 helix: 3.12 (0.15), residues: 1165 sheet: -0.49 (0.72), residues: 60 loop : -1.32 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 418 TYR 0.009 0.001 TYR B 361 PHE 0.010 0.001 PHE C 128 TRP 0.011 0.001 TRP D 350 HIS 0.003 0.001 HIS A 405 Details of bonding type rmsd covalent geometry : bond 0.00258 (12708) covalent geometry : angle 0.47062 (17236) SS BOND : bond 0.00341 ( 4) SS BOND : angle 1.43755 ( 8) hydrogen bonds : bond 0.05912 ( 958) hydrogen bonds : angle 3.39891 ( 2826) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 161 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 199 ASP cc_start: 0.8067 (t0) cc_final: 0.7570 (m-30) REVERT: A 398 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7650 (mm-30) REVERT: A 460 HIS cc_start: 0.7910 (m90) cc_final: 0.7033 (t70) REVERT: B 340 ASP cc_start: 0.8084 (t0) cc_final: 0.7729 (t70) REVERT: C 206 ARG cc_start: 0.8047 (mtm180) cc_final: 0.7657 (mpp80) REVERT: C 299 ARG cc_start: 0.6359 (mtm180) cc_final: 0.5657 (ptp-170) REVERT: C 338 GLN cc_start: 0.8129 (mt0) cc_final: 0.7498 (pm20) REVERT: C 460 HIS cc_start: 0.7840 (m-70) cc_final: 0.6999 (t70) outliers start: 42 outliers final: 15 residues processed: 188 average time/residue: 0.5424 time to fit residues: 111.6680 Evaluate side-chains 170 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 443 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 96 optimal weight: 10.0000 chunk 120 optimal weight: 8.9990 chunk 154 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 121 optimal weight: 0.9980 chunk 105 optimal weight: 6.9990 chunk 67 optimal weight: 0.3980 chunk 55 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN A 452 GLN C 425 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.207005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.143592 restraints weight = 13547.810| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.45 r_work: 0.3023 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12712 Z= 0.156 Angle : 0.498 8.863 17244 Z= 0.268 Chirality : 0.038 0.247 2051 Planarity : 0.003 0.039 2123 Dihedral : 6.268 121.706 1769 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.30 % Allowed : 20.21 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.19 (0.21), residues: 1609 helix: 3.18 (0.14), residues: 1169 sheet: 1.17 (0.76), residues: 50 loop : -1.36 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 449 TYR 0.019 0.001 TYR B 361 PHE 0.014 0.002 PHE A 356 TRP 0.010 0.001 TRP D 350 HIS 0.003 0.001 HIS C 276 Details of bonding type rmsd covalent geometry : bond 0.00361 (12708) covalent geometry : angle 0.49761 (17236) SS BOND : bond 0.00325 ( 4) SS BOND : angle 1.41847 ( 8) hydrogen bonds : bond 0.06305 ( 958) hydrogen bonds : angle 3.24742 ( 2826) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 160 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 100 ILE cc_start: 0.2985 (OUTLIER) cc_final: 0.2711 (pt) REVERT: A 199 ASP cc_start: 0.8069 (t0) cc_final: 0.7587 (t0) REVERT: A 212 GLU cc_start: 0.6752 (OUTLIER) cc_final: 0.6441 (tt0) REVERT: A 248 SER cc_start: 0.8923 (t) cc_final: 0.8554 (p) REVERT: A 427 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7189 (mp) REVERT: A 460 HIS cc_start: 0.7937 (m90) cc_final: 0.7066 (t70) REVERT: B 248 SER cc_start: 0.8595 (t) cc_final: 0.8163 (p) REVERT: B 302 MET cc_start: 0.7131 (OUTLIER) cc_final: 0.6897 (tpt) REVERT: B 340 ASP cc_start: 0.8234 (t0) cc_final: 0.7899 (t70) REVERT: C 206 ARG cc_start: 0.8129 (mtm180) cc_final: 0.7921 (mpp80) REVERT: C 248 SER cc_start: 0.8961 (t) cc_final: 0.8603 (p) REVERT: C 299 ARG cc_start: 0.6501 (mtm180) cc_final: 0.5760 (ptp-170) REVERT: C 340 ASP cc_start: 0.8117 (t0) cc_final: 0.7901 (t0) REVERT: C 460 HIS cc_start: 0.7856 (m-70) cc_final: 0.7121 (t70) outliers start: 54 outliers final: 24 residues processed: 199 average time/residue: 0.5358 time to fit residues: 116.0986 Evaluate side-chains 184 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 443 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 76 optimal weight: 0.9990 chunk 152 optimal weight: 6.9990 chunk 91 optimal weight: 0.6980 chunk 133 optimal weight: 3.9990 chunk 67 optimal weight: 0.4980 chunk 144 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 118 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 ASN A 425 ASN A 436 ASN C 425 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.211377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.155827 restraints weight = 13450.926| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.18 r_work: 0.3234 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12712 Z= 0.113 Angle : 0.429 7.002 17244 Z= 0.233 Chirality : 0.035 0.186 2051 Planarity : 0.003 0.037 2123 Dihedral : 6.100 126.271 1769 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.42 % Allowed : 21.24 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.61 (0.21), residues: 1609 helix: 3.51 (0.14), residues: 1171 sheet: 0.40 (0.74), residues: 56 loop : -1.17 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 131 TYR 0.013 0.001 TYR B 361 PHE 0.009 0.001 PHE C 455 TRP 0.012 0.001 TRP D 350 HIS 0.003 0.001 HIS A 405 Details of bonding type rmsd covalent geometry : bond 0.00228 (12708) covalent geometry : angle 0.42825 (17236) SS BOND : bond 0.00297 ( 4) SS BOND : angle 1.27601 ( 8) hydrogen bonds : bond 0.05100 ( 958) hydrogen bonds : angle 3.03084 ( 2826) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 163 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 199 ASP cc_start: 0.7937 (t0) cc_final: 0.7466 (t0) REVERT: A 206 ARG cc_start: 0.8256 (mpp80) cc_final: 0.8031 (mpp80) REVERT: A 248 SER cc_start: 0.8966 (t) cc_final: 0.8644 (p) REVERT: A 460 HIS cc_start: 0.8091 (m90) cc_final: 0.7238 (t70) REVERT: B 248 SER cc_start: 0.8628 (t) cc_final: 0.8276 (p) REVERT: B 340 ASP cc_start: 0.8205 (t0) cc_final: 0.7944 (t70) REVERT: C 192 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7721 (tp30) REVERT: C 206 ARG cc_start: 0.8180 (mtm180) cc_final: 0.7818 (mpp80) REVERT: C 248 SER cc_start: 0.9011 (t) cc_final: 0.8681 (p) REVERT: C 338 GLN cc_start: 0.7660 (OUTLIER) cc_final: 0.7207 (mt0) REVERT: C 340 ASP cc_start: 0.8217 (t0) cc_final: 0.7961 (t0) REVERT: C 460 HIS cc_start: 0.8040 (m-70) cc_final: 0.7357 (t70) outliers start: 43 outliers final: 21 residues processed: 192 average time/residue: 0.5221 time to fit residues: 109.5776 Evaluate side-chains 180 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 157 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 338 GLN Chi-restraints excluded: chain C residue 467 MET Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 443 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 118 optimal weight: 0.9990 chunk 11 optimal weight: 0.0030 chunk 134 optimal weight: 0.9980 chunk 104 optimal weight: 8.9990 chunk 58 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 50 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 30 optimal weight: 0.5980 chunk 153 optimal weight: 10.0000 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN A 436 ASN A 452 GLN C 425 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.212509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.154860 restraints weight = 13551.034| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.33 r_work: 0.3028 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12712 Z= 0.105 Angle : 0.413 7.240 17244 Z= 0.223 Chirality : 0.035 0.122 2051 Planarity : 0.003 0.035 2123 Dihedral : 6.061 133.321 1769 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.26 % Allowed : 21.96 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.87 (0.21), residues: 1609 helix: 3.68 (0.14), residues: 1174 sheet: 0.55 (0.76), residues: 56 loop : -1.07 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 449 TYR 0.010 0.001 TYR B 361 PHE 0.010 0.001 PHE B 243 TRP 0.011 0.001 TRP D 350 HIS 0.003 0.000 HIS A 405 Details of bonding type rmsd covalent geometry : bond 0.00212 (12708) covalent geometry : angle 0.41213 (17236) SS BOND : bond 0.00283 ( 4) SS BOND : angle 1.24386 ( 8) hydrogen bonds : bond 0.04619 ( 958) hydrogen bonds : angle 2.88188 ( 2826) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 158 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 ASP cc_start: 0.7651 (t0) cc_final: 0.7193 (t0) REVERT: A 212 GLU cc_start: 0.6735 (OUTLIER) cc_final: 0.6388 (tt0) REVERT: A 248 SER cc_start: 0.8810 (t) cc_final: 0.8430 (p) REVERT: A 299 ARG cc_start: 0.6361 (mpp-170) cc_final: 0.5964 (ptp-170) REVERT: A 460 HIS cc_start: 0.8007 (m90) cc_final: 0.7093 (t70) REVERT: B 248 SER cc_start: 0.8441 (t) cc_final: 0.8079 (p) REVERT: B 340 ASP cc_start: 0.8244 (t0) cc_final: 0.7954 (t70) REVERT: C 192 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7513 (tp30) REVERT: C 248 SER cc_start: 0.8887 (t) cc_final: 0.8506 (p) REVERT: C 338 GLN cc_start: 0.7606 (OUTLIER) cc_final: 0.7163 (mt0) REVERT: C 340 ASP cc_start: 0.8273 (t0) cc_final: 0.8053 (t0) REVERT: C 414 GLN cc_start: 0.8046 (tt0) cc_final: 0.7781 (mt0) REVERT: C 460 HIS cc_start: 0.7935 (m-70) cc_final: 0.7195 (t70) REVERT: D 294 ILE cc_start: 0.7615 (OUTLIER) cc_final: 0.7140 (mt) outliers start: 41 outliers final: 25 residues processed: 187 average time/residue: 0.5286 time to fit residues: 108.2858 Evaluate side-chains 182 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 338 GLN Chi-restraints excluded: chain C residue 467 MET Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 443 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 19 optimal weight: 0.9990 chunk 131 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 122 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 132 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 425 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.212177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.154310 restraints weight = 13513.835| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.10 r_work: 0.3044 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12712 Z= 0.109 Angle : 0.426 6.897 17244 Z= 0.229 Chirality : 0.035 0.122 2051 Planarity : 0.003 0.034 2123 Dihedral : 6.078 135.572 1769 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.34 % Allowed : 21.64 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.89 (0.21), residues: 1609 helix: 3.70 (0.14), residues: 1174 sheet: 0.60 (0.77), residues: 56 loop : -1.09 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 449 TYR 0.011 0.001 TYR B 361 PHE 0.009 0.001 PHE B 356 TRP 0.010 0.001 TRP D 350 HIS 0.002 0.001 HIS A 405 Details of bonding type rmsd covalent geometry : bond 0.00227 (12708) covalent geometry : angle 0.42571 (17236) SS BOND : bond 0.00281 ( 4) SS BOND : angle 1.25643 ( 8) hydrogen bonds : bond 0.04733 ( 958) hydrogen bonds : angle 2.87342 ( 2826) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 163 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 ASP cc_start: 0.7605 (t0) cc_final: 0.7160 (t0) REVERT: A 212 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.6388 (tt0) REVERT: A 248 SER cc_start: 0.8801 (t) cc_final: 0.8423 (p) REVERT: A 299 ARG cc_start: 0.6378 (mpp-170) cc_final: 0.5976 (ptp-170) REVERT: A 337 ASP cc_start: 0.7974 (t0) cc_final: 0.7440 (t70) REVERT: A 460 HIS cc_start: 0.7989 (m90) cc_final: 0.7088 (t70) REVERT: B 248 SER cc_start: 0.8388 (t) cc_final: 0.8026 (p) REVERT: B 340 ASP cc_start: 0.8246 (t0) cc_final: 0.7923 (t70) REVERT: C 192 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7481 (tp30) REVERT: C 248 SER cc_start: 0.8850 (t) cc_final: 0.8465 (p) REVERT: C 338 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.7201 (mt0) REVERT: C 340 ASP cc_start: 0.8259 (t0) cc_final: 0.8049 (t0) REVERT: C 414 GLN cc_start: 0.8092 (tt0) cc_final: 0.7863 (mt0) REVERT: C 460 HIS cc_start: 0.7838 (m-70) cc_final: 0.7143 (t70) REVERT: D 294 ILE cc_start: 0.7586 (OUTLIER) cc_final: 0.7110 (mt) outliers start: 42 outliers final: 28 residues processed: 193 average time/residue: 0.5236 time to fit residues: 110.5258 Evaluate side-chains 189 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 338 GLN Chi-restraints excluded: chain C residue 467 MET Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 416 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 150 optimal weight: 0.8980 chunk 15 optimal weight: 0.0470 chunk 50 optimal weight: 9.9990 chunk 153 optimal weight: 10.0000 chunk 13 optimal weight: 0.6980 chunk 144 optimal weight: 1.9990 chunk 22 optimal weight: 0.0170 chunk 154 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 85 optimal weight: 8.9990 chunk 79 optimal weight: 4.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN A 452 GLN C 425 ASN D 336 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.215217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.146792 restraints weight = 13395.641| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.81 r_work: 0.3074 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12712 Z= 0.096 Angle : 0.407 7.854 17244 Z= 0.220 Chirality : 0.034 0.121 2051 Planarity : 0.003 0.032 2123 Dihedral : 6.097 143.502 1769 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.02 % Allowed : 22.04 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.11 (0.21), residues: 1609 helix: 3.85 (0.14), residues: 1176 sheet: 0.65 (0.78), residues: 56 loop : -0.98 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 449 TYR 0.008 0.001 TYR B 361 PHE 0.007 0.001 PHE C 280 TRP 0.011 0.001 TRP D 350 HIS 0.003 0.000 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00189 (12708) covalent geometry : angle 0.40652 (17236) SS BOND : bond 0.00260 ( 4) SS BOND : angle 1.17865 ( 8) hydrogen bonds : bond 0.04080 ( 958) hydrogen bonds : angle 2.78076 ( 2826) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 163 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 95 ASP cc_start: 0.4463 (OUTLIER) cc_final: 0.3295 (p0) REVERT: A 199 ASP cc_start: 0.7495 (t0) cc_final: 0.7053 (t0) REVERT: A 248 SER cc_start: 0.8719 (t) cc_final: 0.8342 (p) REVERT: A 299 ARG cc_start: 0.6302 (mpp-170) cc_final: 0.5925 (ptp-170) REVERT: A 337 ASP cc_start: 0.7950 (t0) cc_final: 0.7407 (t70) REVERT: A 414 GLN cc_start: 0.7969 (mt0) cc_final: 0.7697 (mt0) REVERT: A 460 HIS cc_start: 0.7823 (m90) cc_final: 0.6925 (t70) REVERT: B 248 SER cc_start: 0.8359 (t) cc_final: 0.8053 (p) REVERT: B 340 ASP cc_start: 0.8255 (t0) cc_final: 0.7955 (t70) REVERT: B 450 LYS cc_start: 0.6366 (OUTLIER) cc_final: 0.4527 (tptp) REVERT: C 152 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8246 (tp30) REVERT: C 192 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7323 (tp30) REVERT: C 248 SER cc_start: 0.8817 (t) cc_final: 0.8436 (p) REVERT: C 338 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.7205 (mt0) REVERT: C 340 ASP cc_start: 0.8258 (t0) cc_final: 0.8055 (t0) REVERT: C 414 GLN cc_start: 0.8000 (tt0) cc_final: 0.7790 (mt0) REVERT: C 460 HIS cc_start: 0.7700 (m-70) cc_final: 0.6944 (t70) REVERT: D 294 ILE cc_start: 0.7509 (OUTLIER) cc_final: 0.7017 (mt) outliers start: 38 outliers final: 19 residues processed: 188 average time/residue: 0.5466 time to fit residues: 111.8242 Evaluate side-chains 181 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain G residue 95 ASP Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 450 LYS Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 338 GLN Chi-restraints excluded: chain C residue 467 MET Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 443 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 7 optimal weight: 10.0000 chunk 116 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 129 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 154 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 425 ASN D 344 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.204199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.139724 restraints weight = 13439.923| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.82 r_work: 0.2912 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 12712 Z= 0.274 Angle : 0.619 8.460 17244 Z= 0.331 Chirality : 0.043 0.140 2051 Planarity : 0.004 0.045 2123 Dihedral : 6.423 135.656 1767 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 4.06 % Allowed : 21.08 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.80 (0.21), residues: 1609 helix: 2.70 (0.14), residues: 1202 sheet: 1.82 (0.82), residues: 50 loop : -1.30 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 449 TYR 0.023 0.002 TYR B 361 PHE 0.018 0.002 PHE B 356 TRP 0.009 0.002 TRP B 205 HIS 0.006 0.002 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00699 (12708) covalent geometry : angle 0.61817 (17236) SS BOND : bond 0.00412 ( 4) SS BOND : angle 1.76260 ( 8) hydrogen bonds : bond 0.07988 ( 958) hydrogen bonds : angle 3.28287 ( 2826) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 170 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 95 ASP cc_start: 0.4885 (OUTLIER) cc_final: 0.3922 (p0) REVERT: A 192 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7598 (tp30) REVERT: A 199 ASP cc_start: 0.8149 (t0) cc_final: 0.7695 (t0) REVERT: A 212 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6617 (tt0) REVERT: A 248 SER cc_start: 0.8903 (t) cc_final: 0.8506 (p) REVERT: A 427 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7233 (mp) REVERT: A 439 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6461 (mt) REVERT: A 460 HIS cc_start: 0.8098 (m90) cc_final: 0.7300 (t70) REVERT: B 299 ARG cc_start: 0.7439 (mtm-85) cc_final: 0.5946 (ttt180) REVERT: B 340 ASP cc_start: 0.8284 (t0) cc_final: 0.8000 (t70) REVERT: C 192 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7535 (tp30) REVERT: C 206 ARG cc_start: 0.8136 (mtm180) cc_final: 0.7924 (mpp80) REVERT: C 338 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.7696 (mp10) REVERT: C 340 ASP cc_start: 0.8357 (t0) cc_final: 0.8142 (t0) REVERT: C 450 LYS cc_start: 0.7583 (tttt) cc_final: 0.6849 (tptt) REVERT: C 460 HIS cc_start: 0.8049 (m-70) cc_final: 0.7263 (t70) REVERT: D 294 ILE cc_start: 0.7707 (OUTLIER) cc_final: 0.7263 (mt) REVERT: D 299 ARG cc_start: 0.7507 (mtm-85) cc_final: 0.5939 (ttt180) outliers start: 51 outliers final: 25 residues processed: 210 average time/residue: 0.5068 time to fit residues: 116.3762 Evaluate side-chains 195 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 162 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain G residue 95 ASP Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 338 GLN Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 467 MET Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 416 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 101 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 129 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 144 optimal weight: 0.9980 chunk 83 optimal weight: 8.9990 chunk 125 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 150 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 ASN A 425 ASN C 425 ASN C 452 GLN D 338 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.203434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.135737 restraints weight = 13544.707| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.90 r_work: 0.3007 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12712 Z= 0.121 Angle : 0.457 7.756 17244 Z= 0.249 Chirality : 0.035 0.123 2051 Planarity : 0.003 0.036 2123 Dihedral : 6.150 140.849 1767 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.78 % Allowed : 23.07 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.50 (0.21), residues: 1609 helix: 3.38 (0.14), residues: 1178 sheet: 0.86 (0.78), residues: 56 loop : -1.20 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 449 TYR 0.010 0.001 TYR B 361 PHE 0.011 0.001 PHE B 356 TRP 0.010 0.001 TRP B 350 HIS 0.003 0.001 HIS C 451 Details of bonding type rmsd covalent geometry : bond 0.00248 (12708) covalent geometry : angle 0.45675 (17236) SS BOND : bond 0.00316 ( 4) SS BOND : angle 1.28599 ( 8) hydrogen bonds : bond 0.05389 ( 958) hydrogen bonds : angle 3.01680 ( 2826) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 165 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 95 ASP cc_start: 0.4522 (OUTLIER) cc_final: 0.3580 (p0) REVERT: A 192 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7418 (tp30) REVERT: A 199 ASP cc_start: 0.7749 (t0) cc_final: 0.7248 (m-30) REVERT: A 248 SER cc_start: 0.8866 (t) cc_final: 0.8502 (p) REVERT: A 439 LEU cc_start: 0.7254 (OUTLIER) cc_final: 0.6438 (mt) REVERT: A 460 HIS cc_start: 0.7937 (m90) cc_final: 0.7143 (t70) REVERT: B 248 SER cc_start: 0.8551 (t) cc_final: 0.8164 (m) REVERT: B 340 ASP cc_start: 0.8146 (t0) cc_final: 0.7905 (t70) REVERT: B 450 LYS cc_start: 0.6407 (OUTLIER) cc_final: 0.4484 (tptp) REVERT: C 192 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7474 (tp30) REVERT: C 338 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7642 (mp10) REVERT: C 450 LYS cc_start: 0.7468 (tttt) cc_final: 0.6771 (tptp) REVERT: C 460 HIS cc_start: 0.7799 (m-70) cc_final: 0.7041 (t70) REVERT: D 294 ILE cc_start: 0.7625 (OUTLIER) cc_final: 0.7191 (mt) outliers start: 35 outliers final: 23 residues processed: 190 average time/residue: 0.5392 time to fit residues: 111.7826 Evaluate side-chains 188 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 158 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain G residue 95 ASP Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 450 LYS Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 338 GLN Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 467 MET Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 416 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 101 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 72 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 145 optimal weight: 0.4980 chunk 89 optimal weight: 2.9990 chunk 147 optimal weight: 0.0470 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN B 451 HIS C 425 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.211498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.149838 restraints weight = 13522.817| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.50 r_work: 0.3028 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12712 Z= 0.107 Angle : 0.433 7.094 17244 Z= 0.236 Chirality : 0.035 0.122 2051 Planarity : 0.003 0.034 2123 Dihedral : 6.220 151.740 1767 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.55 % Allowed : 23.55 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.95 (0.21), residues: 1609 helix: 3.69 (0.14), residues: 1178 sheet: 1.49 (0.83), residues: 50 loop : -1.04 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 449 TYR 0.010 0.001 TYR B 361 PHE 0.008 0.001 PHE B 356 TRP 0.011 0.001 TRP B 350 HIS 0.006 0.001 HIS D 405 Details of bonding type rmsd covalent geometry : bond 0.00216 (12708) covalent geometry : angle 0.43209 (17236) SS BOND : bond 0.00297 ( 4) SS BOND : angle 1.22429 ( 8) hydrogen bonds : bond 0.04421 ( 958) hydrogen bonds : angle 2.88147 ( 2826) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 159 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: G 95 ASP cc_start: 0.4548 (OUTLIER) cc_final: 0.3566 (p0) REVERT: A 192 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7145 (tp30) REVERT: A 199 ASP cc_start: 0.7612 (t0) cc_final: 0.7032 (m-30) REVERT: A 248 SER cc_start: 0.8820 (t) cc_final: 0.8452 (p) REVERT: A 299 ARG cc_start: 0.6364 (mpp-170) cc_final: 0.5990 (ptp-170) REVERT: A 439 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.6452 (mt) REVERT: A 460 HIS cc_start: 0.7877 (m90) cc_final: 0.7060 (t70) REVERT: B 248 SER cc_start: 0.8452 (t) cc_final: 0.8119 (m) REVERT: B 340 ASP cc_start: 0.8245 (t0) cc_final: 0.7990 (t70) REVERT: B 450 LYS cc_start: 0.6492 (OUTLIER) cc_final: 0.4575 (tptp) REVERT: C 192 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7348 (tp30) REVERT: C 206 ARG cc_start: 0.8056 (mtm180) cc_final: 0.7804 (mpp80) REVERT: C 338 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.7566 (mp10) REVERT: C 414 GLN cc_start: 0.7997 (mt0) cc_final: 0.7737 (mt0) REVERT: C 450 LYS cc_start: 0.7377 (tttt) cc_final: 0.6720 (tptp) REVERT: C 460 HIS cc_start: 0.7741 (m-70) cc_final: 0.7031 (t70) REVERT: D 294 ILE cc_start: 0.7614 (OUTLIER) cc_final: 0.7131 (mt) outliers start: 32 outliers final: 18 residues processed: 180 average time/residue: 0.5688 time to fit residues: 111.2885 Evaluate side-chains 180 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain G residue 95 ASP Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 450 LYS Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain C residue 338 GLN Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 416 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 132 optimal weight: 0.1980 chunk 1 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 104 optimal weight: 0.9980 chunk 123 optimal weight: 20.0000 chunk 8 optimal weight: 9.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 425 ASN C 452 GLN D 344 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.207401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.150734 restraints weight = 13507.637| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.15 r_work: 0.2992 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12712 Z= 0.161 Angle : 0.495 7.112 17244 Z= 0.270 Chirality : 0.037 0.134 2051 Planarity : 0.003 0.039 2123 Dihedral : 6.346 152.813 1767 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.70 % Allowed : 23.63 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.55 (0.21), residues: 1609 helix: 3.39 (0.14), residues: 1175 sheet: 1.66 (0.82), residues: 50 loop : -1.16 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 449 TYR 0.016 0.001 TYR B 361 PHE 0.013 0.001 PHE B 356 TRP 0.010 0.001 TRP A 350 HIS 0.004 0.001 HIS C 123 Details of bonding type rmsd covalent geometry : bond 0.00390 (12708) covalent geometry : angle 0.49458 (17236) SS BOND : bond 0.00323 ( 4) SS BOND : angle 1.47125 ( 8) hydrogen bonds : bond 0.05927 ( 958) hydrogen bonds : angle 3.02754 ( 2826) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5151.95 seconds wall clock time: 88 minutes 18.56 seconds (5298.56 seconds total)