Starting phenix.real_space_refine on Sat Feb 7 03:25:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v55_64787/02_2026/9v55_64787.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v55_64787/02_2026/9v55_64787.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9v55_64787/02_2026/9v55_64787.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v55_64787/02_2026/9v55_64787.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9v55_64787/02_2026/9v55_64787.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v55_64787/02_2026/9v55_64787.map" } resolution = 3.26 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= 0.047 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: 4 Type Number sf(0) Gaussians S 39 5.16 5 C 18030 2.51 5 N 5163 2.21 5 O 5829 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29061 Number of models: 1 Model: "" Number of chains: 12 Chain: "C1" Number of atoms: 3331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3331 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 11, 'TRANS': 420} Chain: "C2" Number of atoms: 3331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3331 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 11, 'TRANS': 420} Chain: "C3" Number of atoms: 3331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3331 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 11, 'TRANS': 420} Chain: "P1" Number of atoms: 1182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1182 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 8, 'TRANS': 143} Chain: "P2" Number of atoms: 1182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1182 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 8, 'TRANS': 143} Chain: "P3" Number of atoms: 1182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1182 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 8, 'TRANS': 143} Chain: "A1" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2587 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 16, 'TRANS': 327} Chain: "A2" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2587 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 16, 'TRANS': 327} Chain: "A3" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2587 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 16, 'TRANS': 327} Chain: "a2" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2587 Classifications: {'peptide': 344} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 327} Chain: "a1" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2587 Classifications: {'peptide': 344} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 327} Chain: "a3" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2587 Classifications: {'peptide': 344} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 327} Time building chain proxies: 6.66, per 1000 atoms: 0.23 Number of scatterers: 29061 At special positions: 0 Unit cell: (140.4, 144.45, 290.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 39 16.00 O 5829 8.00 N 5163 7.00 C 18030 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYSP1 36 " - pdb=" SG CYSP1 144 " distance=2.03 Simple disulfide: pdb=" SG CYSP2 36 " - pdb=" SG CYSP2 144 " distance=2.03 Simple disulfide: pdb=" SG CYSP3 36 " - pdb=" SG CYSP3 144 " 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: 2.20 Conformation dependent library (CDL) restraints added in 1.0 seconds 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7140 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 39 sheets defined 42.0% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'C1' and resid 24 through 35 removed outlier: 3.545A pdb=" N LEUC1 34 " --> pdb=" O GLNC1 30 " (cutoff:3.500A) Processing helix chain 'C1' and resid 38 through 58 removed outlier: 3.746A pdb=" N SERC1 42 " --> pdb=" O GLUC1 38 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILEC1 53 " --> pdb=" O ALAC1 49 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ASNC1 54 " --> pdb=" O PHEC1 50 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLUC1 55 " --> pdb=" O GLUC1 51 " (cutoff:3.500A) Processing helix chain 'C1' and resid 99 through 169 removed outlier: 4.025A pdb=" N TRPC1 103 " --> pdb=" O ASPC1 99 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VALC1 138 " --> pdb=" O ALAC1 134 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEUC1 139 " --> pdb=" O TYRC1 135 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALAC1 150 " --> pdb=" O SERC1 146 " (cutoff:3.500A) Processing helix chain 'C1' and resid 172 through 209 removed outlier: 3.830A pdb=" N VALC1 176 " --> pdb=" O ALAC1 172 " (cutoff:3.500A) Processing helix chain 'C1' and resid 230 through 242 removed outlier: 3.933A pdb=" N LYSC1 240 " --> pdb=" O LYSC1 236 " (cutoff:3.500A) Processing helix chain 'C1' and resid 242 through 264 Processing helix chain 'C1' and resid 265 through 267 No H-bonds generated for 'chain 'C1' and resid 265 through 267' Processing helix chain 'C1' and resid 319 through 387 removed outlier: 3.666A pdb=" N ILEC1 356 " --> pdb=" O SERC1 352 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASNC1 357 " --> pdb=" O PHEC1 353 " (cutoff:3.500A) Processing helix chain 'C1' and resid 390 through 426 removed outlier: 3.708A pdb=" N VALC1 394 " --> pdb=" O THRC1 390 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEUC1 420 " --> pdb=" O LEUC1 416 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEUC1 426 " --> pdb=" O ILEC1 422 " (cutoff:3.500A) Processing helix chain 'C1' and resid 430 through 438 removed outlier: 3.914A pdb=" N LEUC1 434 " --> pdb=" O ASNC1 430 " (cutoff:3.500A) Processing helix chain 'C1' and resid 448 through 453 Processing helix chain 'C2' and resid 24 through 35 Processing helix chain 'C2' and resid 38 through 58 removed outlier: 3.704A pdb=" N SERC2 42 " --> pdb=" O GLUC2 38 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILEC2 53 " --> pdb=" O ALAC2 49 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ASNC2 54 " --> pdb=" O PHEC2 50 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLUC2 55 " --> pdb=" O GLUC2 51 " (cutoff:3.500A) Processing helix chain 'C2' and resid 59 through 61 No H-bonds generated for 'chain 'C2' and resid 59 through 61' Processing helix chain 'C2' and resid 99 through 169 removed outlier: 4.140A pdb=" N TRPC2 103 " --> pdb=" O ASPC2 99 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEUC2 139 " --> pdb=" O TYRC2 135 " (cutoff:3.500A) Processing helix chain 'C2' and resid 172 through 209 removed outlier: 3.854A pdb=" N VALC2 176 " --> pdb=" O ALAC2 172 " (cutoff:3.500A) Processing helix chain 'C2' and resid 230 through 242 removed outlier: 3.924A pdb=" N LYSC2 240 " --> pdb=" O LYSC2 236 " (cutoff:3.500A) Processing helix chain 'C2' and resid 242 through 264 Processing helix chain 'C2' and resid 265 through 267 No H-bonds generated for 'chain 'C2' and resid 265 through 267' Processing helix chain 'C2' and resid 319 through 387 removed outlier: 3.722A pdb=" N SERC2 361 " --> pdb=" O ASNC2 357 " (cutoff:3.500A) Processing helix chain 'C2' and resid 390 through 426 removed outlier: 3.755A pdb=" N VALC2 394 " --> pdb=" O THRC2 390 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEUC2 426 " --> pdb=" O ILEC2 422 " (cutoff:3.500A) Processing helix chain 'C2' and resid 430 through 439 removed outlier: 3.945A pdb=" N LEUC2 434 " --> pdb=" O ASNC2 430 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASNC2 439 " --> pdb=" O LEUC2 435 " (cutoff:3.500A) Processing helix chain 'C2' and resid 448 through 453 Processing helix chain 'C3' and resid 24 through 35 Processing helix chain 'C3' and resid 38 through 58 removed outlier: 3.885A pdb=" N SERC3 42 " --> pdb=" O GLUC3 38 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILEC3 53 " --> pdb=" O ALAC3 49 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ASNC3 54 " --> pdb=" O PHEC3 50 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLUC3 55 " --> pdb=" O GLUC3 51 " (cutoff:3.500A) Processing helix chain 'C3' and resid 59 through 61 No H-bonds generated for 'chain 'C3' and resid 59 through 61' Processing helix chain 'C3' and resid 99 through 169 removed outlier: 4.025A pdb=" N TRPC3 103 " --> pdb=" O ASPC3 99 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VALC3 138 " --> pdb=" O ALAC3 134 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEUC3 139 " --> pdb=" O TYRC3 135 " (cutoff:3.500A) Processing helix chain 'C3' and resid 172 through 209 removed outlier: 3.870A pdb=" N VALC3 176 " --> pdb=" O ALAC3 172 " (cutoff:3.500A) Processing helix chain 'C3' and resid 230 through 242 removed outlier: 3.962A pdb=" N LYSC3 240 " --> pdb=" O LYSC3 236 " (cutoff:3.500A) Processing helix chain 'C3' and resid 242 through 264 Processing helix chain 'C3' and resid 319 through 387 removed outlier: 3.600A pdb=" N ALAC3 365 " --> pdb=" O SERC3 361 " (cutoff:3.500A) Processing helix chain 'C3' and resid 390 through 426 removed outlier: 3.790A pdb=" N VALC3 394 " --> pdb=" O THRC3 390 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEUC3 426 " --> pdb=" O ILEC3 422 " (cutoff:3.500A) Processing helix chain 'C3' and resid 430 through 439 removed outlier: 3.922A pdb=" N LEUC3 434 " --> pdb=" O ASNC3 430 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASNC3 439 " --> pdb=" O LEUC3 435 " (cutoff:3.500A) Processing helix chain 'C3' and resid 448 through 453 Processing helix chain 'P1' and resid 40 through 55 Processing helix chain 'P1' and resid 70 through 81 Processing helix chain 'P1' and resid 84 through 91 removed outlier: 3.607A pdb=" N ASPP1 91 " --> pdb=" O LEUP1 87 " (cutoff:3.500A) Processing helix chain 'P1' and resid 163 through 169 Processing helix chain 'P2' and resid 40 through 55 Processing helix chain 'P2' and resid 60 through 64 removed outlier: 3.563A pdb=" N ARGP2 64 " --> pdb=" O THRP2 61 " (cutoff:3.500A) Processing helix chain 'P2' and resid 70 through 81 Processing helix chain 'P2' and resid 84 through 91 removed outlier: 3.575A pdb=" N ASNP2 90 " --> pdb=" O GLUP2 86 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASPP2 91 " --> pdb=" O LEUP2 87 " (cutoff:3.500A) Processing helix chain 'P2' and resid 163 through 169 Processing helix chain 'P3' and resid 40 through 55 removed outlier: 3.587A pdb=" N ILEP3 53 " --> pdb=" O TYRP3 49 " (cutoff:3.500A) Processing helix chain 'P3' and resid 60 through 64 removed outlier: 3.777A pdb=" N ARGP3 64 " --> pdb=" O THRP3 61 " (cutoff:3.500A) Processing helix chain 'P3' and resid 69 through 82 removed outlier: 4.075A pdb=" N THRP3 73 " --> pdb=" O ASPP3 69 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASNP3 82 " --> pdb=" O ALAP3 78 " (cutoff:3.500A) Processing helix chain 'P3' and resid 84 through 91 removed outlier: 3.704A pdb=" N ASPP3 91 " --> pdb=" O LEUP3 87 " (cutoff:3.500A) Processing helix chain 'P3' and resid 163 through 169 Processing helix chain 'A1' and resid 98 through 134 removed outlier: 3.696A pdb=" N LYSA1 131 " --> pdb=" O ASNA1 127 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEUA1 132 " --> pdb=" O ARGA1 128 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLYA1 134 " --> pdb=" O GLNA1 130 " (cutoff:3.500A) Processing helix chain 'A1' and resid 139 through 173 Processing helix chain 'A1' and resid 220 through 232 Processing helix chain 'A1' and resid 311 through 313 No H-bonds generated for 'chain 'A1' and resid 311 through 313' Processing helix chain 'A1' and resid 363 through 367 Processing helix chain 'A2' and resid 98 through 134 removed outlier: 3.978A pdb=" N GLYA2 134 " --> pdb=" O GLNA2 130 " (cutoff:3.500A) Processing helix chain 'A2' and resid 139 through 174 removed outlier: 3.505A pdb=" N TYRA2 143 " --> pdb=" O SERA2 139 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THRA2 174 " --> pdb=" O ASNA2 170 " (cutoff:3.500A) Processing helix chain 'A2' and resid 220 through 233 Processing helix chain 'A2' and resid 311 through 313 No H-bonds generated for 'chain 'A2' and resid 311 through 313' Processing helix chain 'A2' and resid 363 through 367 Processing helix chain 'A3' and resid 98 through 134 removed outlier: 4.040A pdb=" N GLYA3 134 " --> pdb=" O GLNA3 130 " (cutoff:3.500A) Processing helix chain 'A3' and resid 139 through 174 removed outlier: 3.897A pdb=" N THRA3 174 " --> pdb=" O ASNA3 170 " (cutoff:3.500A) Processing helix chain 'A3' and resid 220 through 232 Processing helix chain 'A3' and resid 363 through 367 removed outlier: 3.527A pdb=" N VALA3 367 " --> pdb=" O LEUA3 364 " (cutoff:3.500A) Processing helix chain 'a2' and resid 98 through 134 removed outlier: 3.804A pdb=" N GLYa2 134 " --> pdb=" O GLNa2 130 " (cutoff:3.500A) Processing helix chain 'a2' and resid 139 through 174 removed outlier: 3.784A pdb=" N THRa2 174 " --> pdb=" O ASNa2 170 " (cutoff:3.500A) Processing helix chain 'a2' and resid 220 through 233 Processing helix chain 'a1' and resid 98 through 134 removed outlier: 3.815A pdb=" N GLYa1 134 " --> pdb=" O GLNa1 130 " (cutoff:3.500A) Processing helix chain 'a1' and resid 139 through 174 removed outlier: 3.771A pdb=" N THRa1 174 " --> pdb=" O ASNa1 170 " (cutoff:3.500A) Processing helix chain 'a1' and resid 220 through 233 Processing helix chain 'a1' and resid 363 through 367 Processing helix chain 'a3' and resid 98 through 134 removed outlier: 3.732A pdb=" N GLYa3 134 " --> pdb=" O GLNa3 130 " (cutoff:3.500A) Processing helix chain 'a3' and resid 139 through 174 removed outlier: 3.766A pdb=" N THRa3 174 " --> pdb=" O ASNa3 170 " (cutoff:3.500A) Processing helix chain 'a3' and resid 220 through 233 Processing helix chain 'a3' and resid 363 through 367 Processing sheet with id=AA1, first strand: chain 'C1' and resid 63 through 77 removed outlier: 6.914A pdb=" N LEUC1 270 " --> pdb=" O ILEC1 97 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASNC3 74 " --> pdb=" O ASNC1 304 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYRC3 70 " --> pdb=" O LEUC1 308 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEUC3 270 " --> pdb=" O ILEC3 97 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYRC2 70 " --> pdb=" O LEUC3 308 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LEUC2 270 " --> pdb=" O ILEC2 97 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C1' and resid 214 through 218 removed outlier: 3.961A pdb=" N LYSC1 443 " --> pdb=" O ALAC1 217 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C2' and resid 214 through 218 removed outlier: 3.811A pdb=" N LYSC2 443 " --> pdb=" O ALAC2 217 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C3' and resid 214 through 218 removed outlier: 3.885A pdb=" N LYSC3 443 " --> pdb=" O ALAC3 217 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'P1' and resid 102 through 104 Processing sheet with id=AA6, first strand: chain 'P1' and resid 119 through 122 Processing sheet with id=AA7, first strand: chain 'P2' and resid 102 through 104 Processing sheet with id=AA8, first strand: chain 'P2' and resid 121 through 122 Processing sheet with id=AA9, first strand: chain 'P3' and resid 102 through 104 Processing sheet with id=AB1, first strand: chain 'P3' and resid 102 through 104 Processing sheet with id=AB2, first strand: chain 'A1' and resid 358 through 362 removed outlier: 6.582A pdb=" N GLYA1 41 " --> pdb=" O ILEA1 361 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A1' and resid 85 through 87 removed outlier: 3.841A pdb=" N SERA1 85 " --> pdb=" O ILEA1 184 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILEA1 184 " --> pdb=" O SERA1 85 " (cutoff:3.500A) removed outlier: 10.993A pdb=" N GLUA1 55 " --> pdb=" O SERA1 219 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N SERA1 219 " --> pdb=" O GLUA1 55 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYRA1 63 " --> pdb=" O PROA1 211 " (cutoff:3.500A) removed outlier: 10.550A pdb=" N ILEA1 65 " --> pdb=" O LEUA1 209 " (cutoff:3.500A) removed outlier: 10.520A pdb=" N LEUA1 209 " --> pdb=" O ILEA1 65 " (cutoff:3.500A) removed outlier: 10.003A pdb=" N GLUA1 67 " --> pdb=" O GLNA1 207 " (cutoff:3.500A) removed outlier: 9.871A pdb=" N GLNA1 207 " --> pdb=" O GLUA1 67 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A1' and resid 94 through 96 removed outlier: 6.817A pdb=" N GLNA1 95 " --> pdb=" O LEUA1 77 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A1' and resid 306 through 309 removed outlier: 3.931A pdb=" N ILEA1 306 " --> pdb=" O VALA1 349 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLNA1 341 " --> pdb=" O LEUA1 348 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A1' and resid 314 through 315 removed outlier: 4.051A pdb=" N ALAA1 321 " --> pdb=" O ILEA1 337 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A2' and resid 358 through 362 removed outlier: 6.554A pdb=" N GLYA2 41 " --> pdb=" O ILEA2 361 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A2' and resid 47 through 48 removed outlier: 3.938A pdb=" N ILEA2 306 " --> pdb=" O VALA2 349 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLNA2 341 " --> pdb=" O LEUA2 348 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A2' and resid 85 through 87 removed outlier: 3.912A pdb=" N SERA2 85 " --> pdb=" O ILEA2 184 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILEA2 184 " --> pdb=" O SERA2 85 " (cutoff:3.500A) removed outlier: 9.846A pdb=" N GLNA2 207 " --> pdb=" O GLUA2 67 " (cutoff:3.500A) removed outlier: 9.983A pdb=" N GLUA2 67 " --> pdb=" O GLNA2 207 " (cutoff:3.500A) removed outlier: 10.512A pdb=" N LEUA2 209 " --> pdb=" O ILEA2 65 " (cutoff:3.500A) removed outlier: 10.597A pdb=" N ILEA2 65 " --> pdb=" O LEUA2 209 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYRA2 63 " --> pdb=" O PROA2 211 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N SERA2 219 " --> pdb=" O GLUA2 55 " (cutoff:3.500A) removed outlier: 11.042A pdb=" N GLUA2 55 " --> pdb=" O SERA2 219 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILEA2 52 " --> pdb=" O GLUA2 299 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THRA2 54 " --> pdb=" O LEUA2 297 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LYSA2 243 " --> pdb=" O GLUA2 298 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A2' and resid 85 through 87 removed outlier: 3.912A pdb=" N SERA2 85 " --> pdb=" O ILEA2 184 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILEA2 184 " --> pdb=" O SERA2 85 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A2' and resid 94 through 96 removed outlier: 6.606A pdb=" N GLNA2 95 " --> pdb=" O LEUA2 77 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A2' and resid 314 through 315 removed outlier: 4.023A pdb=" N ALAA2 321 " --> pdb=" O ILEA2 337 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A3' and resid 358 through 360 Processing sheet with id=AC5, first strand: chain 'A3' and resid 55 through 62 removed outlier: 11.136A pdb=" N GLUA3 55 " --> pdb=" O SERA3 219 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N SERA3 219 " --> pdb=" O GLUA3 55 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A3' and resid 65 through 68 removed outlier: 3.718A pdb=" N ALAA3 204 " --> pdb=" O VALA3 68 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILEA3 184 " --> pdb=" O SERA3 85 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SERA3 85 " --> pdb=" O ILEA3 184 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A3' and resid 94 through 96 removed outlier: 6.831A pdb=" N GLNA3 95 " --> pdb=" O LEUA3 77 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A3' and resid 306 through 309 removed outlier: 3.926A pdb=" N ILEA3 306 " --> pdb=" O VALA3 349 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLNA3 341 " --> pdb=" O LEUA3 348 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A3' and resid 313 through 315 removed outlier: 3.946A pdb=" N ALAA3 321 " --> pdb=" O ILEA3 337 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'a2' and resid 86 through 87 removed outlier: 7.511A pdb=" N THRa2 275 " --> pdb=" O SERa2 263 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N SERa2 263 " --> pdb=" O THRa2 275 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARGa2 277 " --> pdb=" O GLUa2 261 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N LYSa2 243 " --> pdb=" O GLUa2 298 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N PHEa2 292 " --> pdb=" O THRa2 60 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N THRa2 60 " --> pdb=" O PHEa2 292 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ARGa2 294 " --> pdb=" O GLYa2 58 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLYa2 58 " --> pdb=" O ARGa2 294 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ARGa2 296 " --> pdb=" O LEUa2 56 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LEUa2 56 " --> pdb=" O ARGa2 296 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N GLUa2 298 " --> pdb=" O THRa2 54 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N THRa2 54 " --> pdb=" O GLUa2 298 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLYa2 300 " --> pdb=" O ILEa2 52 " (cutoff:3.500A) removed outlier: 11.510A pdb=" N GLUa2 55 " --> pdb=" O SERa2 219 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N SERa2 219 " --> pdb=" O GLUa2 55 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYRa2 63 " --> pdb=" O PROa2 211 " (cutoff:3.500A) removed outlier: 10.721A pdb=" N ILEa2 65 " --> pdb=" O LEUa2 209 " (cutoff:3.500A) removed outlier: 10.562A pdb=" N LEUa2 209 " --> pdb=" O ILEa2 65 " (cutoff:3.500A) removed outlier: 9.964A pdb=" N GLUa2 67 " --> pdb=" O GLNa2 207 " (cutoff:3.500A) removed outlier: 9.601A pdb=" N GLNa2 207 " --> pdb=" O GLUa2 67 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'a2' and resid 94 through 96 removed outlier: 6.867A pdb=" N GLNa2 95 " --> pdb=" O LEUa2 77 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'a2' and resid 306 through 309 removed outlier: 4.323A pdb=" N ILEa2 306 " --> pdb=" O VALa2 349 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLNa2 341 " --> pdb=" O LEUa2 348 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'a2' and resid 313 through 315 removed outlier: 4.385A pdb=" N ALAa2 321 " --> pdb=" O ILEa2 337 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'a1' and resid 358 through 360 removed outlier: 3.829A pdb=" N VALa1 40 " --> pdb=" O LYSa1 374 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'a1' and resid 313 through 315 removed outlier: 4.235A pdb=" N ALAa1 321 " --> pdb=" O ILEa1 337 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N ALAa1 339 " --> pdb=" O THRa1 350 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N THRa1 350 " --> pdb=" O ALAa1 339 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLNa1 341 " --> pdb=" O LEUa1 348 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILEa1 306 " --> pdb=" O VALa1 349 " (cutoff:3.500A) removed outlier: 8.891A pdb=" N GLUa1 351 " --> pdb=" O ASNa1 304 " (cutoff:3.500A) removed outlier: 14.048A pdb=" N ASNa1 304 " --> pdb=" O GLUa1 351 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N LYSa1 243 " --> pdb=" O GLUa1 298 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARGa1 277 " --> pdb=" O GLUa1 261 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N SERa1 263 " --> pdb=" O THRa1 275 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N THRa1 275 " --> pdb=" O SERa1 263 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N SERa1 219 " --> pdb=" O GLUa1 55 " (cutoff:3.500A) removed outlier: 11.439A pdb=" N GLUa1 55 " --> pdb=" O SERa1 219 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N GLUa1 48 " --> pdb=" O PROa1 303 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEUa1 50 " --> pdb=" O LEUa1 301 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N LEUa1 301 " --> pdb=" O LEUa1 50 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILEa1 52 " --> pdb=" O GLUa1 299 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'a1' and resid 65 through 68 removed outlier: 3.901A pdb=" N ALAa1 204 " --> pdb=" O VALa1 68 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SERa1 85 " --> pdb=" O ILEa1 184 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'a1' and resid 94 through 96 removed outlier: 6.900A pdb=" N GLNa1 95 " --> pdb=" O LEUa1 77 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'a3' and resid 358 through 360 removed outlier: 4.115A pdb=" N VALa3 40 " --> pdb=" O LYSa3 374 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLNa3 376 " --> pdb=" O VALa3 40 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'a3' and resid 313 through 315 removed outlier: 4.180A pdb=" N ALAa3 321 " --> pdb=" O ILEa3 337 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ALAa3 339 " --> pdb=" O THRa3 350 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N THRa3 350 " --> pdb=" O ALAa3 339 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLNa3 341 " --> pdb=" O LEUa3 348 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ILEa3 306 " --> pdb=" O VALa3 349 " (cutoff:3.500A) removed outlier: 9.171A pdb=" N GLUa3 351 " --> pdb=" O ASNa3 304 " (cutoff:3.500A) removed outlier: 14.360A pdb=" N ASNa3 304 " --> pdb=" O GLUa3 351 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLUa3 298 " --> pdb=" O LYSa3 243 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N LYSa3 243 " --> pdb=" O GLUa3 298 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALAa3 242 " --> pdb=" O LEUa3 260 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ARGa3 277 " --> pdb=" O GLUa3 261 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N SERa3 263 " --> pdb=" O THRa3 275 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N THRa3 275 " --> pdb=" O SERa3 263 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THRa3 217 " --> pdb=" O PROa3 57 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N SERa3 219 " --> pdb=" O GLUa3 55 " (cutoff:3.500A) removed outlier: 11.469A pdb=" N GLUa3 55 " --> pdb=" O SERa3 219 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLUa3 48 " --> pdb=" O ASNa3 304 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ASNa3 304 " --> pdb=" O GLUa3 48 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLYa3 300 " --> pdb=" O ILEa3 52 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N THRa3 54 " --> pdb=" O GLUa3 298 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N GLUa3 298 " --> pdb=" O THRa3 54 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N LEUa3 56 " --> pdb=" O ARGa3 296 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ARGa3 296 " --> pdb=" O LEUa3 56 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLYa3 58 " --> pdb=" O ARGa3 294 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ARGa3 294 " --> pdb=" O GLYa3 58 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N THRa3 60 " --> pdb=" O PHEa3 292 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N PHEa3 292 " --> pdb=" O THRa3 60 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'a3' and resid 65 through 68 removed outlier: 3.817A pdb=" N ALAa3 204 " --> pdb=" O VALa3 68 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'a3' and resid 94 through 96 removed outlier: 6.878A pdb=" N GLNa3 95 " --> pdb=" O LEUa3 77 " (cutoff:3.500A) 1781 hydrogen bonds defined for protein. 5136 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: 5.55 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6029 1.33 - 1.45: 6422 1.45 - 1.58: 16931 1.58 - 1.70: 0 1.70 - 1.83: 69 Bond restraints: 29451 Sorted by residual: bond pdb=" C PROC3 313 " pdb=" O PROC3 313 " ideal model delta sigma weight residual 1.233 1.203 0.030 1.16e-02 7.43e+03 6.72e+00 bond pdb=" N PROC3 313 " pdb=" CA PROC3 313 " ideal model delta sigma weight residual 1.467 1.442 0.025 1.21e-02 6.83e+03 4.12e+00 bond pdb=" C LEUC3 312 " pdb=" N PROC3 313 " ideal model delta sigma weight residual 1.332 1.352 -0.021 1.30e-02 5.92e+03 2.55e+00 bond pdb=" C ASPA1 210 " pdb=" N PROA1 211 " ideal model delta sigma weight residual 1.330 1.345 -0.015 1.23e-02 6.61e+03 1.47e+00 bond pdb=" CA ASNa2 239 " pdb=" CB ASNa2 239 " ideal model delta sigma weight residual 1.530 1.549 -0.019 1.69e-02 3.50e+03 1.24e+00 ... (remaining 29446 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 39668 2.20 - 4.39: 343 4.39 - 6.59: 28 6.59 - 8.78: 9 8.78 - 10.98: 8 Bond angle restraints: 40056 Sorted by residual: angle pdb=" C THRP1 160 " pdb=" CA THRP1 160 " pdb=" CB THRP1 160 " ideal model delta sigma weight residual 117.23 110.01 7.22 1.36e+00 5.41e-01 2.82e+01 angle pdb=" N ILEa3 361 " pdb=" CA ILEa3 361 " pdb=" C ILEa3 361 " ideal model delta sigma weight residual 113.71 109.96 3.75 9.50e-01 1.11e+00 1.56e+01 angle pdb=" CB METC1 301 " pdb=" CG METC1 301 " pdb=" SD METC1 301 " ideal model delta sigma weight residual 112.70 123.14 -10.44 3.00e+00 1.11e-01 1.21e+01 angle pdb=" CB METC3 301 " pdb=" CG METC3 301 " pdb=" SD METC3 301 " ideal model delta sigma weight residual 112.70 123.14 -10.44 3.00e+00 1.11e-01 1.21e+01 angle pdb=" CB METa1 37 " pdb=" CG METa1 37 " pdb=" SD METa1 37 " ideal model delta sigma weight residual 112.70 122.93 -10.23 3.00e+00 1.11e-01 1.16e+01 ... (remaining 40051 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 15451 17.99 - 35.99: 1936 35.99 - 53.98: 530 53.98 - 71.98: 129 71.98 - 89.97: 35 Dihedral angle restraints: 18081 sinusoidal: 7008 harmonic: 11073 Sorted by residual: dihedral pdb=" CB CYSP1 36 " pdb=" SG CYSP1 36 " pdb=" SG CYSP1 144 " pdb=" CB CYSP1 144 " ideal model delta sinusoidal sigma weight residual -86.00 -132.92 46.92 1 1.00e+01 1.00e-02 3.04e+01 dihedral pdb=" CB CYSP2 36 " pdb=" SG CYSP2 36 " pdb=" SG CYSP2 144 " pdb=" CB CYSP2 144 " ideal model delta sinusoidal sigma weight residual -86.00 -128.11 42.11 1 1.00e+01 1.00e-02 2.48e+01 dihedral pdb=" CA LEUP1 67 " pdb=" C LEUP1 67 " pdb=" N SERP1 68 " pdb=" CA SERP1 68 " ideal model delta harmonic sigma weight residual -180.00 -158.31 -21.69 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 18078 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 3209 0.030 - 0.060: 932 0.060 - 0.090: 335 0.090 - 0.120: 240 0.120 - 0.150: 30 Chirality restraints: 4746 Sorted by residual: chirality pdb=" CA ASPP3 129 " pdb=" N ASPP3 129 " pdb=" C ASPP3 129 " pdb=" CB ASPP3 129 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.63e-01 chirality pdb=" CA VALa2 42 " pdb=" N VALa2 42 " pdb=" C VALa2 42 " pdb=" CB VALa2 42 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CA VALa1 373 " pdb=" N VALa1 373 " pdb=" C VALa1 373 " pdb=" CB VALa1 373 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.91e-01 ... (remaining 4743 not shown) Planarity restraints: 5310 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASNP3 58 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.21e+00 pdb=" C ASNP3 58 " 0.039 2.00e-02 2.50e+03 pdb=" O ASNP3 58 " -0.015 2.00e-02 2.50e+03 pdb=" N ASPP3 59 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THRa2 316 " -0.029 5.00e-02 4.00e+02 4.44e-02 3.15e+00 pdb=" N PROa2 317 " 0.077 5.00e-02 4.00e+02 pdb=" CA PROa2 317 " -0.023 5.00e-02 4.00e+02 pdb=" CD PROa2 317 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARGP3 64 " 0.028 5.00e-02 4.00e+02 4.29e-02 2.95e+00 pdb=" N PROP3 65 " -0.074 5.00e-02 4.00e+02 pdb=" CA PROP3 65 " 0.022 5.00e-02 4.00e+02 pdb=" CD PROP3 65 " 0.024 5.00e-02 4.00e+02 ... (remaining 5307 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1091 2.72 - 3.26: 28579 3.26 - 3.81: 47016 3.81 - 4.35: 52902 4.35 - 4.90: 95318 Nonbonded interactions: 224906 Sorted by model distance: nonbonded pdb=" OD1 ASNa2 239 " pdb=" N GLYa2 240 " model vdw 2.171 3.120 nonbonded pdb=" OG SERa2 187 " pdb=" O VALa2 189 " model vdw 2.199 3.040 nonbonded pdb=" N GLUP1 86 " pdb=" OE1 GLUP1 86 " model vdw 2.224 3.120 nonbonded pdb=" N GLUP3 86 " pdb=" OE1 GLUP3 86 " model vdw 2.225 3.120 nonbonded pdb=" N GLUP2 86 " pdb=" OE1 GLUP2 86 " model vdw 2.237 3.120 ... (remaining 224901 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A1' selection = chain 'A2' selection = chain 'A3' selection = chain 'a1' selection = chain 'a2' selection = chain 'a3' } ncs_group { reference = chain 'C1' selection = chain 'C2' selection = chain 'C3' } ncs_group { reference = chain 'P1' selection = chain 'P2' selection = chain 'P3' } 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: 11.430 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: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 24.200 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 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 : 0.002 0.036 29454 Z= 0.125 Angle : 0.533 10.975 40062 Z= 0.279 Chirality : 0.039 0.150 4746 Planarity : 0.003 0.044 5310 Dihedral : 17.646 89.970 10932 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.19 % Favored : 95.62 % Rotamer: Outliers : 0.25 % Allowed : 27.19 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 2.01 (0.14), residues: 3792 helix: 4.12 (0.12), residues: 1491 sheet: 0.18 (0.19), residues: 717 loop : -0.97 (0.16), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGa2 358 TYR 0.010 0.001 TYRP2 26 PHE 0.018 0.001 PHEa2 262 TRP 0.011 0.001 TRPa3 347 HIS 0.006 0.001 HISP2 158 Details of bonding type rmsd covalent geometry : bond 0.00243 (29451) covalent geometry : angle 0.53347 (40056) SS BOND : bond 0.00116 ( 3) SS BOND : angle 0.29586 ( 6) hydrogen bonds : bond 0.11551 ( 1773) hydrogen bonds : angle 4.90511 ( 5136) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 195 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C2 214 GLU cc_start: 0.8381 (tp30) cc_final: 0.8056 (tp30) REVERT: A1 101 TYR cc_start: 0.9026 (m-80) cc_final: 0.8614 (m-80) REVERT: A1 322 THR cc_start: 0.8851 (p) cc_final: 0.8619 (t) REVERT: a2 101 TYR cc_start: 0.9065 (m-80) cc_final: 0.8804 (m-80) REVERT: a2 137 TYR cc_start: 0.9357 (m-80) cc_final: 0.8893 (m-80) REVERT: a1 37 MET cc_start: 0.4670 (mmm) cc_final: 0.3017 (mmt) REVERT: a1 257 ASP cc_start: 0.8587 (p0) cc_final: 0.8350 (p0) outliers start: 8 outliers final: 6 residues processed: 201 average time/residue: 0.1861 time to fit residues: 59.6328 Evaluate side-chains 191 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 185 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P2 residue 31 THR Chi-restraints excluded: chain P3 residue 58 ASN Chi-restraints excluded: chain A1 residue 158 THR Chi-restraints excluded: chain A2 residue 228 GLN Chi-restraints excluded: chain a2 residue 71 GLN Chi-restraints excluded: chain a3 residue 135 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 0.0270 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C2 85 ASN P2 55 HIS P2 166 GLN A1 237 GLN A2 228 GLN a2 304 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.097379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.073964 restraints weight = 57117.537| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.58 r_work: 0.2892 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.0655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 29454 Z= 0.111 Angle : 0.482 10.807 40062 Z= 0.249 Chirality : 0.039 0.147 4746 Planarity : 0.003 0.049 5310 Dihedral : 3.960 68.830 4136 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.80 % Favored : 96.02 % Rotamer: Outliers : 2.16 % Allowed : 24.65 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 2.08 (0.14), residues: 3792 helix: 4.15 (0.12), residues: 1509 sheet: 0.36 (0.19), residues: 684 loop : -1.02 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGC3 40 TYR 0.011 0.001 TYRa3 137 PHE 0.021 0.001 PHEa2 262 TRP 0.008 0.001 TRPa3 347 HIS 0.006 0.001 HISP2 158 Details of bonding type rmsd covalent geometry : bond 0.00225 (29451) covalent geometry : angle 0.48178 (40056) SS BOND : bond 0.00069 ( 3) SS BOND : angle 0.30400 ( 6) hydrogen bonds : bond 0.05111 ( 1773) hydrogen bonds : angle 4.13815 ( 5136) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 212 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C2 301 MET cc_start: 0.7767 (mmm) cc_final: 0.7121 (tpp) REVERT: P3 149 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7813 (t0) REVERT: P3 164 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8329 (tt) REVERT: A1 365 GLN cc_start: 0.9189 (OUTLIER) cc_final: 0.7161 (mt0) REVERT: a2 333 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7304 (mm-30) REVERT: a1 257 ASP cc_start: 0.8788 (p0) cc_final: 0.8579 (p0) REVERT: a1 259 THR cc_start: 0.8723 (OUTLIER) cc_final: 0.8475 (p) REVERT: a1 358 ARG cc_start: 0.6030 (ttt90) cc_final: 0.5724 (ttt90) REVERT: a3 142 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7908 (mp0) outliers start: 68 outliers final: 28 residues processed: 264 average time/residue: 0.1833 time to fit residues: 77.7027 Evaluate side-chains 213 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 180 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C1 residue 76 TYR Chi-restraints excluded: chain C1 residue 259 ILE Chi-restraints excluded: chain C2 residue 76 TYR Chi-restraints excluded: chain C2 residue 186 VAL Chi-restraints excluded: chain C3 residue 422 ILE Chi-restraints excluded: chain P2 residue 67 LEU Chi-restraints excluded: chain P2 residue 147 ILE Chi-restraints excluded: chain P3 residue 149 ASP Chi-restraints excluded: chain P3 residue 157 VAL Chi-restraints excluded: chain P3 residue 164 LEU Chi-restraints excluded: chain A1 residue 37 MET Chi-restraints excluded: chain A1 residue 126 VAL Chi-restraints excluded: chain A1 residue 217 THR Chi-restraints excluded: chain A1 residue 230 LEU Chi-restraints excluded: chain A1 residue 249 SER Chi-restraints excluded: chain A1 residue 365 GLN Chi-restraints excluded: chain A2 residue 126 VAL Chi-restraints excluded: chain A2 residue 249 SER Chi-restraints excluded: chain A2 residue 338 VAL Chi-restraints excluded: chain A2 residue 359 VAL Chi-restraints excluded: chain A2 residue 364 LEU Chi-restraints excluded: chain A3 residue 249 SER Chi-restraints excluded: chain A3 residue 325 VAL Chi-restraints excluded: chain A3 residue 338 VAL Chi-restraints excluded: chain A3 residue 378 VAL Chi-restraints excluded: chain a2 residue 65 ILE Chi-restraints excluded: chain a2 residue 248 THR Chi-restraints excluded: chain a1 residue 212 ILE Chi-restraints excluded: chain a1 residue 248 THR Chi-restraints excluded: chain a1 residue 259 THR Chi-restraints excluded: chain a3 residue 142 GLU Chi-restraints excluded: chain a3 residue 248 THR Chi-restraints excluded: chain a3 residue 361 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 276 optimal weight: 0.0070 chunk 210 optimal weight: 4.9990 chunk 297 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 349 optimal weight: 0.1980 chunk 311 optimal weight: 5.9990 chunk 314 optimal weight: 0.0980 chunk 377 optimal weight: 0.9980 chunk 332 optimal weight: 0.5980 chunk 308 optimal weight: 5.9990 chunk 136 optimal weight: 5.9990 overall best weight: 0.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1 43 ASN P1 166 GLN ** P2 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a2 304 ASN ** a1 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.099485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.076198 restraints weight = 57590.282| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.58 r_work: 0.2932 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 29454 Z= 0.098 Angle : 0.455 9.495 40062 Z= 0.235 Chirality : 0.039 0.147 4746 Planarity : 0.003 0.044 5310 Dihedral : 3.513 20.344 4125 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.77 % Favored : 96.02 % Rotamer: Outliers : 2.04 % Allowed : 24.90 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 2.20 (0.14), residues: 3792 helix: 4.29 (0.12), residues: 1509 sheet: 0.43 (0.19), residues: 684 loop : -1.01 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGC2 46 TYR 0.010 0.001 TYRa3 137 PHE 0.020 0.001 PHEa2 262 TRP 0.008 0.001 TRPa3 347 HIS 0.006 0.001 HISP2 158 Details of bonding type rmsd covalent geometry : bond 0.00193 (29451) covalent geometry : angle 0.45522 (40056) SS BOND : bond 0.00077 ( 3) SS BOND : angle 0.28711 ( 6) hydrogen bonds : bond 0.04534 ( 1773) hydrogen bonds : angle 3.86458 ( 5136) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 216 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C1 301 MET cc_start: 0.7892 (tpp) cc_final: 0.7648 (mmm) REVERT: C2 212 TYR cc_start: 0.8712 (m-80) cc_final: 0.8146 (m-80) REVERT: C2 301 MET cc_start: 0.7704 (mmm) cc_final: 0.6938 (tpp) REVERT: C3 100 MET cc_start: 0.7716 (mmm) cc_final: 0.7357 (mtp) REVERT: P1 138 MET cc_start: 0.9308 (mmm) cc_final: 0.8975 (mmm) REVERT: P2 138 MET cc_start: 0.8488 (mmm) cc_final: 0.8251 (mmt) REVERT: P3 47 GLN cc_start: 0.8745 (mt0) cc_final: 0.8539 (mt0) REVERT: P3 91 ASP cc_start: 0.8293 (t0) cc_final: 0.7433 (t0) REVERT: P3 149 ASP cc_start: 0.7881 (OUTLIER) cc_final: 0.7444 (t0) REVERT: P3 164 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8232 (tt) REVERT: P3 169 GLU cc_start: 0.8117 (tt0) cc_final: 0.7884 (tt0) REVERT: A1 101 TYR cc_start: 0.8626 (m-80) cc_final: 0.8397 (m-80) REVERT: A1 322 THR cc_start: 0.8709 (p) cc_final: 0.8421 (p) REVERT: A1 365 GLN cc_start: 0.9177 (OUTLIER) cc_final: 0.7121 (mt0) REVERT: A1 376 GLN cc_start: 0.6843 (mp10) cc_final: 0.6465 (pm20) REVERT: a2 333 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7202 (mm-30) REVERT: a1 259 THR cc_start: 0.8409 (OUTLIER) cc_final: 0.8189 (t) REVERT: a3 78 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8680 (ttpp) outliers start: 64 outliers final: 31 residues processed: 264 average time/residue: 0.1832 time to fit residues: 79.1960 Evaluate side-chains 232 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 196 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C1 residue 69 ASP Chi-restraints excluded: chain C1 residue 76 TYR Chi-restraints excluded: chain C1 residue 288 THR Chi-restraints excluded: chain C2 residue 76 TYR Chi-restraints excluded: chain C2 residue 186 VAL Chi-restraints excluded: chain C2 residue 372 SER Chi-restraints excluded: chain C3 residue 76 TYR Chi-restraints excluded: chain C3 residue 422 ILE Chi-restraints excluded: chain P2 residue 31 THR Chi-restraints excluded: chain P2 residue 67 LEU Chi-restraints excluded: chain P2 residue 136 VAL Chi-restraints excluded: chain P2 residue 147 ILE Chi-restraints excluded: chain P3 residue 139 ILE Chi-restraints excluded: chain P3 residue 147 ILE Chi-restraints excluded: chain P3 residue 149 ASP Chi-restraints excluded: chain P3 residue 157 VAL Chi-restraints excluded: chain P3 residue 164 LEU Chi-restraints excluded: chain A1 residue 126 VAL Chi-restraints excluded: chain A1 residue 365 GLN Chi-restraints excluded: chain A2 residue 126 VAL Chi-restraints excluded: chain A2 residue 164 VAL Chi-restraints excluded: chain A2 residue 249 SER Chi-restraints excluded: chain A2 residue 338 VAL Chi-restraints excluded: chain A2 residue 340 SER Chi-restraints excluded: chain A2 residue 364 LEU Chi-restraints excluded: chain A3 residue 249 SER Chi-restraints excluded: chain A3 residue 325 VAL Chi-restraints excluded: chain A3 residue 338 VAL Chi-restraints excluded: chain a2 residue 65 ILE Chi-restraints excluded: chain a2 residue 248 THR Chi-restraints excluded: chain a1 residue 50 LEU Chi-restraints excluded: chain a1 residue 212 ILE Chi-restraints excluded: chain a1 residue 248 THR Chi-restraints excluded: chain a1 residue 259 THR Chi-restraints excluded: chain a3 residue 78 LYS Chi-restraints excluded: chain a3 residue 248 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 150 optimal weight: 10.0000 chunk 216 optimal weight: 0.9980 chunk 170 optimal weight: 5.9990 chunk 258 optimal weight: 4.9990 chunk 366 optimal weight: 4.9990 chunk 220 optimal weight: 0.7980 chunk 231 optimal weight: 0.9990 chunk 361 optimal weight: 3.9990 chunk 340 optimal weight: 10.0000 chunk 130 optimal weight: 0.0470 chunk 61 optimal weight: 4.9990 overall best weight: 1.3682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1 438 ASN P2 90 ASN P2 158 HIS a2 71 GLN ** a1 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.095959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.072289 restraints weight = 57468.486| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.57 r_work: 0.2866 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29454 Z= 0.145 Angle : 0.498 10.226 40062 Z= 0.255 Chirality : 0.040 0.187 4746 Planarity : 0.003 0.045 5310 Dihedral : 3.616 20.140 4125 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.88 % Favored : 95.91 % Rotamer: Outliers : 2.58 % Allowed : 25.10 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 2.10 (0.14), residues: 3792 helix: 4.16 (0.12), residues: 1509 sheet: 0.44 (0.19), residues: 684 loop : -1.04 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGC3 40 TYR 0.014 0.001 TYRa3 137 PHE 0.022 0.001 PHEa2 262 TRP 0.010 0.001 TRPa3 347 HIS 0.006 0.001 HISP2 158 Details of bonding type rmsd covalent geometry : bond 0.00330 (29451) covalent geometry : angle 0.49756 (40056) SS BOND : bond 0.00105 ( 3) SS BOND : angle 0.37952 ( 6) hydrogen bonds : bond 0.05379 ( 1773) hydrogen bonds : angle 4.03053 ( 5136) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 194 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C1 272 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7838 (pp) REVERT: C2 212 TYR cc_start: 0.8772 (m-80) cc_final: 0.8332 (m-80) REVERT: C3 100 MET cc_start: 0.7886 (mmm) cc_final: 0.7445 (mtp) REVERT: P1 138 MET cc_start: 0.9295 (mmm) cc_final: 0.8969 (mmm) REVERT: P2 138 MET cc_start: 0.8646 (mmm) cc_final: 0.8201 (mmt) REVERT: P3 149 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7781 (t0) REVERT: P3 169 GLU cc_start: 0.8124 (tt0) cc_final: 0.7848 (tt0) REVERT: A1 365 GLN cc_start: 0.9169 (OUTLIER) cc_final: 0.7165 (mt0) REVERT: A2 75 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8749 (mt) REVERT: a2 333 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7249 (mm-30) outliers start: 81 outliers final: 52 residues processed: 261 average time/residue: 0.1844 time to fit residues: 77.6872 Evaluate side-chains 239 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 183 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C1 residue 64 LEU Chi-restraints excluded: chain C1 residue 69 ASP Chi-restraints excluded: chain C1 residue 76 TYR Chi-restraints excluded: chain C1 residue 259 ILE Chi-restraints excluded: chain C1 residue 272 LEU Chi-restraints excluded: chain C1 residue 288 THR Chi-restraints excluded: chain C2 residue 76 TYR Chi-restraints excluded: chain C2 residue 186 VAL Chi-restraints excluded: chain C2 residue 270 LEU Chi-restraints excluded: chain C2 residue 372 SER Chi-restraints excluded: chain C3 residue 76 TYR Chi-restraints excluded: chain C3 residue 269 THR Chi-restraints excluded: chain C3 residue 390 THR Chi-restraints excluded: chain P1 residue 23 THR Chi-restraints excluded: chain P1 residue 149 ASP Chi-restraints excluded: chain P2 residue 31 THR Chi-restraints excluded: chain P2 residue 67 LEU Chi-restraints excluded: chain P2 residue 147 ILE Chi-restraints excluded: chain P3 residue 147 ILE Chi-restraints excluded: chain P3 residue 149 ASP Chi-restraints excluded: chain P3 residue 157 VAL Chi-restraints excluded: chain A1 residue 37 MET Chi-restraints excluded: chain A1 residue 73 SER Chi-restraints excluded: chain A1 residue 126 VAL Chi-restraints excluded: chain A1 residue 217 THR Chi-restraints excluded: chain A1 residue 230 LEU Chi-restraints excluded: chain A1 residue 234 THR Chi-restraints excluded: chain A1 residue 249 SER Chi-restraints excluded: chain A1 residue 365 GLN Chi-restraints excluded: chain A2 residue 75 ILE Chi-restraints excluded: chain A2 residue 126 VAL Chi-restraints excluded: chain A2 residue 157 VAL Chi-restraints excluded: chain A2 residue 164 VAL Chi-restraints excluded: chain A2 residue 249 SER Chi-restraints excluded: chain A2 residue 325 VAL Chi-restraints excluded: chain A2 residue 338 VAL Chi-restraints excluded: chain A2 residue 340 SER Chi-restraints excluded: chain A2 residue 359 VAL Chi-restraints excluded: chain A3 residue 234 THR Chi-restraints excluded: chain A3 residue 249 SER Chi-restraints excluded: chain A3 residue 325 VAL Chi-restraints excluded: chain A3 residue 338 VAL Chi-restraints excluded: chain A3 residue 378 VAL Chi-restraints excluded: chain a2 residue 37 MET Chi-restraints excluded: chain a2 residue 65 ILE Chi-restraints excluded: chain a2 residue 71 GLN Chi-restraints excluded: chain a2 residue 248 THR Chi-restraints excluded: chain a2 residue 275 THR Chi-restraints excluded: chain a1 residue 50 LEU Chi-restraints excluded: chain a1 residue 65 ILE Chi-restraints excluded: chain a1 residue 212 ILE Chi-restraints excluded: chain a1 residue 248 THR Chi-restraints excluded: chain a1 residue 361 ILE Chi-restraints excluded: chain a3 residue 65 ILE Chi-restraints excluded: chain a3 residue 248 THR Chi-restraints excluded: chain a3 residue 361 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 377 optimal weight: 10.0000 chunk 167 optimal weight: 10.0000 chunk 342 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 130 optimal weight: 0.0370 chunk 171 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 83 optimal weight: 0.6980 chunk 278 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 243 optimal weight: 5.9990 overall best weight: 0.8460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P2 158 HIS a2 304 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.097190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.073775 restraints weight = 57080.142| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.56 r_work: 0.2890 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 29454 Z= 0.113 Angle : 0.477 9.749 40062 Z= 0.245 Chirality : 0.039 0.177 4746 Planarity : 0.003 0.045 5310 Dihedral : 3.562 20.007 4125 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.85 % Favored : 95.97 % Rotamer: Outliers : 2.89 % Allowed : 24.87 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 2.16 (0.14), residues: 3792 helix: 4.23 (0.12), residues: 1512 sheet: 0.44 (0.19), residues: 684 loop : -1.03 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGA2 368 TYR 0.012 0.001 TYRa3 137 PHE 0.021 0.001 PHEa2 262 TRP 0.010 0.001 TRPa3 347 HIS 0.006 0.001 HISP2 158 Details of bonding type rmsd covalent geometry : bond 0.00242 (29451) covalent geometry : angle 0.47674 (40056) SS BOND : bond 0.00027 ( 3) SS BOND : angle 0.32416 ( 6) hydrogen bonds : bond 0.04993 ( 1773) hydrogen bonds : angle 3.92212 ( 5136) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 205 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C1 272 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.7859 (pp) REVERT: C2 98 PHE cc_start: 0.8921 (t80) cc_final: 0.8649 (t80) REVERT: C2 212 TYR cc_start: 0.8698 (m-80) cc_final: 0.8269 (m-80) REVERT: C2 301 MET cc_start: 0.7259 (mmp) cc_final: 0.6762 (tmm) REVERT: C3 100 MET cc_start: 0.7910 (mmm) cc_final: 0.7463 (mtp) REVERT: P1 138 MET cc_start: 0.9321 (mmm) cc_final: 0.9003 (mmm) REVERT: P2 138 MET cc_start: 0.8699 (mmm) cc_final: 0.8365 (mmt) REVERT: P3 91 ASP cc_start: 0.8380 (t0) cc_final: 0.7635 (t0) REVERT: P3 149 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7667 (t0) REVERT: P3 153 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7674 (tt) REVERT: P3 164 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8532 (tp) REVERT: P3 169 GLU cc_start: 0.8138 (tt0) cc_final: 0.7825 (tt0) REVERT: A1 365 GLN cc_start: 0.9119 (OUTLIER) cc_final: 0.6957 (mt0) REVERT: a2 333 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7202 (mm-30) REVERT: a1 225 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.8063 (ttp80) outliers start: 91 outliers final: 63 residues processed: 282 average time/residue: 0.1768 time to fit residues: 81.5830 Evaluate side-chains 261 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 192 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C1 residue 64 LEU Chi-restraints excluded: chain C1 residue 69 ASP Chi-restraints excluded: chain C1 residue 76 TYR Chi-restraints excluded: chain C1 residue 259 ILE Chi-restraints excluded: chain C1 residue 272 LEU Chi-restraints excluded: chain C1 residue 288 THR Chi-restraints excluded: chain C2 residue 64 LEU Chi-restraints excluded: chain C2 residue 76 TYR Chi-restraints excluded: chain C2 residue 186 VAL Chi-restraints excluded: chain C2 residue 270 LEU Chi-restraints excluded: chain C2 residue 372 SER Chi-restraints excluded: chain C3 residue 76 TYR Chi-restraints excluded: chain C3 residue 278 ILE Chi-restraints excluded: chain C3 residue 390 THR Chi-restraints excluded: chain C3 residue 422 ILE Chi-restraints excluded: chain P1 residue 23 THR Chi-restraints excluded: chain P1 residue 74 LEU Chi-restraints excluded: chain P2 residue 31 THR Chi-restraints excluded: chain P2 residue 61 THR Chi-restraints excluded: chain P2 residue 67 LEU Chi-restraints excluded: chain P2 residue 74 LEU Chi-restraints excluded: chain P2 residue 136 VAL Chi-restraints excluded: chain P2 residue 147 ILE Chi-restraints excluded: chain P3 residue 132 TRP Chi-restraints excluded: chain P3 residue 149 ASP Chi-restraints excluded: chain P3 residue 153 LEU Chi-restraints excluded: chain P3 residue 157 VAL Chi-restraints excluded: chain P3 residue 164 LEU Chi-restraints excluded: chain A1 residue 37 MET Chi-restraints excluded: chain A1 residue 73 SER Chi-restraints excluded: chain A1 residue 126 VAL Chi-restraints excluded: chain A1 residue 217 THR Chi-restraints excluded: chain A1 residue 226 LEU Chi-restraints excluded: chain A1 residue 230 LEU Chi-restraints excluded: chain A1 residue 234 THR Chi-restraints excluded: chain A1 residue 249 SER Chi-restraints excluded: chain A1 residue 365 GLN Chi-restraints excluded: chain A2 residue 126 VAL Chi-restraints excluded: chain A2 residue 157 VAL Chi-restraints excluded: chain A2 residue 164 VAL Chi-restraints excluded: chain A2 residue 249 SER Chi-restraints excluded: chain A2 residue 324 LEU Chi-restraints excluded: chain A2 residue 325 VAL Chi-restraints excluded: chain A2 residue 338 VAL Chi-restraints excluded: chain A2 residue 340 SER Chi-restraints excluded: chain A2 residue 359 VAL Chi-restraints excluded: chain A2 residue 364 LEU Chi-restraints excluded: chain A3 residue 56 LEU Chi-restraints excluded: chain A3 residue 65 ILE Chi-restraints excluded: chain A3 residue 234 THR Chi-restraints excluded: chain A3 residue 249 SER Chi-restraints excluded: chain A3 residue 265 VAL Chi-restraints excluded: chain A3 residue 325 VAL Chi-restraints excluded: chain A3 residue 338 VAL Chi-restraints excluded: chain A3 residue 378 VAL Chi-restraints excluded: chain a2 residue 37 MET Chi-restraints excluded: chain a2 residue 65 ILE Chi-restraints excluded: chain a2 residue 75 ILE Chi-restraints excluded: chain a2 residue 248 THR Chi-restraints excluded: chain a2 residue 275 THR Chi-restraints excluded: chain a1 residue 50 LEU Chi-restraints excluded: chain a1 residue 65 ILE Chi-restraints excluded: chain a1 residue 212 ILE Chi-restraints excluded: chain a1 residue 225 ARG Chi-restraints excluded: chain a1 residue 248 THR Chi-restraints excluded: chain a3 residue 212 ILE Chi-restraints excluded: chain a3 residue 232 ASN Chi-restraints excluded: chain a3 residue 248 THR Chi-restraints excluded: chain a3 residue 260 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 352 optimal weight: 0.9990 chunk 249 optimal weight: 0.9990 chunk 218 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 308 optimal weight: 0.0980 chunk 283 optimal weight: 3.9990 chunk 63 optimal weight: 0.0670 chunk 325 optimal weight: 5.9990 chunk 178 optimal weight: 0.8980 chunk 257 optimal weight: 6.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P2 158 HIS P2 166 GLN P3 55 HIS a2 304 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.098961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.075603 restraints weight = 57145.282| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.55 r_work: 0.2923 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 29454 Z= 0.101 Angle : 0.471 9.173 40062 Z= 0.239 Chirality : 0.039 0.214 4746 Planarity : 0.003 0.045 5310 Dihedral : 3.457 20.649 4125 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.61 % Favored : 96.20 % Rotamer: Outliers : 2.77 % Allowed : 25.54 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 2.23 (0.14), residues: 3792 helix: 4.31 (0.12), residues: 1512 sheet: 0.48 (0.19), residues: 684 loop : -1.01 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGA1 368 TYR 0.012 0.001 TYRa3 137 PHE 0.019 0.001 PHEa2 262 TRP 0.011 0.001 TRPa3 347 HIS 0.006 0.001 HISP2 158 Details of bonding type rmsd covalent geometry : bond 0.00208 (29451) covalent geometry : angle 0.47076 (40056) SS BOND : bond 0.00024 ( 3) SS BOND : angle 0.29631 ( 6) hydrogen bonds : bond 0.04550 ( 1773) hydrogen bonds : angle 3.77609 ( 5136) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 217 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C1 272 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7815 (pp) REVERT: C2 98 PHE cc_start: 0.8920 (t80) cc_final: 0.8592 (t80) REVERT: C2 212 TYR cc_start: 0.8759 (m-80) cc_final: 0.8229 (m-80) REVERT: C2 301 MET cc_start: 0.7442 (mmp) cc_final: 0.7080 (mmm) REVERT: C3 100 MET cc_start: 0.7737 (mmm) cc_final: 0.7236 (mtp) REVERT: P1 138 MET cc_start: 0.9300 (mmm) cc_final: 0.8972 (mmm) REVERT: P1 170 ASN cc_start: 0.8399 (m-40) cc_final: 0.8026 (p0) REVERT: P2 138 MET cc_start: 0.8656 (mmm) cc_final: 0.8406 (mmt) REVERT: P2 141 GLU cc_start: 0.8280 (tt0) cc_final: 0.7977 (tt0) REVERT: P3 91 ASP cc_start: 0.8314 (t0) cc_final: 0.7560 (t0) REVERT: P3 149 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.7553 (t0) REVERT: P3 153 LEU cc_start: 0.8075 (tt) cc_final: 0.7689 (tt) REVERT: P3 164 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8291 (tt) REVERT: P3 169 GLU cc_start: 0.8100 (tt0) cc_final: 0.7774 (tt0) REVERT: A1 101 TYR cc_start: 0.8703 (m-80) cc_final: 0.8417 (m-80) REVERT: A1 322 THR cc_start: 0.8625 (p) cc_final: 0.8327 (p) REVERT: A1 361 ILE cc_start: 0.8421 (tp) cc_final: 0.8104 (tp) REVERT: A1 365 GLN cc_start: 0.9076 (OUTLIER) cc_final: 0.6889 (mt0) REVERT: a2 37 MET cc_start: 0.4361 (OUTLIER) cc_final: 0.3892 (tpt) outliers start: 87 outliers final: 57 residues processed: 290 average time/residue: 0.1811 time to fit residues: 86.1183 Evaluate side-chains 256 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 194 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C1 residue 69 ASP Chi-restraints excluded: chain C1 residue 76 TYR Chi-restraints excluded: chain C1 residue 186 VAL Chi-restraints excluded: chain C1 residue 259 ILE Chi-restraints excluded: chain C1 residue 272 LEU Chi-restraints excluded: chain C1 residue 288 THR Chi-restraints excluded: chain C2 residue 64 LEU Chi-restraints excluded: chain C2 residue 76 TYR Chi-restraints excluded: chain C2 residue 186 VAL Chi-restraints excluded: chain C2 residue 270 LEU Chi-restraints excluded: chain C2 residue 372 SER Chi-restraints excluded: chain C3 residue 76 TYR Chi-restraints excluded: chain C3 residue 269 THR Chi-restraints excluded: chain C3 residue 422 ILE Chi-restraints excluded: chain P1 residue 23 THR Chi-restraints excluded: chain P1 residue 149 ASP Chi-restraints excluded: chain P2 residue 31 THR Chi-restraints excluded: chain P2 residue 61 THR Chi-restraints excluded: chain P2 residue 67 LEU Chi-restraints excluded: chain P2 residue 74 LEU Chi-restraints excluded: chain P2 residue 136 VAL Chi-restraints excluded: chain P2 residue 147 ILE Chi-restraints excluded: chain P2 residue 163 THR Chi-restraints excluded: chain P3 residue 132 TRP Chi-restraints excluded: chain P3 residue 149 ASP Chi-restraints excluded: chain P3 residue 157 VAL Chi-restraints excluded: chain P3 residue 164 LEU Chi-restraints excluded: chain A1 residue 126 VAL Chi-restraints excluded: chain A1 residue 226 LEU Chi-restraints excluded: chain A1 residue 230 LEU Chi-restraints excluded: chain A1 residue 234 THR Chi-restraints excluded: chain A1 residue 249 SER Chi-restraints excluded: chain A1 residue 365 GLN Chi-restraints excluded: chain A2 residue 126 VAL Chi-restraints excluded: chain A2 residue 157 VAL Chi-restraints excluded: chain A2 residue 164 VAL Chi-restraints excluded: chain A2 residue 249 SER Chi-restraints excluded: chain A2 residue 324 LEU Chi-restraints excluded: chain A2 residue 325 VAL Chi-restraints excluded: chain A2 residue 338 VAL Chi-restraints excluded: chain A2 residue 359 VAL Chi-restraints excluded: chain A2 residue 364 LEU Chi-restraints excluded: chain A3 residue 56 LEU Chi-restraints excluded: chain A3 residue 65 ILE Chi-restraints excluded: chain A3 residue 234 THR Chi-restraints excluded: chain A3 residue 249 SER Chi-restraints excluded: chain A3 residue 265 VAL Chi-restraints excluded: chain A3 residue 325 VAL Chi-restraints excluded: chain A3 residue 338 VAL Chi-restraints excluded: chain A3 residue 378 VAL Chi-restraints excluded: chain a2 residue 37 MET Chi-restraints excluded: chain a2 residue 65 ILE Chi-restraints excluded: chain a2 residue 75 ILE Chi-restraints excluded: chain a2 residue 212 ILE Chi-restraints excluded: chain a2 residue 248 THR Chi-restraints excluded: chain a2 residue 275 THR Chi-restraints excluded: chain a1 residue 65 ILE Chi-restraints excluded: chain a1 residue 212 ILE Chi-restraints excluded: chain a1 residue 248 THR Chi-restraints excluded: chain a3 residue 37 MET Chi-restraints excluded: chain a3 residue 212 ILE Chi-restraints excluded: chain a3 residue 248 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 125 optimal weight: 0.9990 chunk 264 optimal weight: 0.6980 chunk 275 optimal weight: 4.9990 chunk 297 optimal weight: 2.9990 chunk 220 optimal weight: 2.9990 chunk 272 optimal weight: 0.0010 chunk 227 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 336 optimal weight: 0.9990 chunk 233 optimal weight: 0.0070 chunk 263 optimal weight: 3.9990 overall best weight: 0.5408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C3 229 GLN P1 47 GLN P2 130 GLN P2 158 HIS a3 256 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.099339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.076211 restraints weight = 57062.975| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.55 r_work: 0.2934 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 29454 Z= 0.099 Angle : 0.469 10.273 40062 Z= 0.237 Chirality : 0.039 0.162 4746 Planarity : 0.003 0.045 5310 Dihedral : 3.410 19.817 4125 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.74 % Favored : 96.04 % Rotamer: Outliers : 2.77 % Allowed : 25.45 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 2.25 (0.14), residues: 3792 helix: 4.35 (0.12), residues: 1509 sheet: 0.45 (0.20), residues: 654 loop : -0.98 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGA1 368 TYR 0.011 0.001 TYRa3 137 PHE 0.020 0.001 PHEa2 262 TRP 0.011 0.001 TRPa3 347 HIS 0.006 0.001 HISP2 158 Details of bonding type rmsd covalent geometry : bond 0.00203 (29451) covalent geometry : angle 0.46876 (40056) SS BOND : bond 0.00031 ( 3) SS BOND : angle 0.27476 ( 6) hydrogen bonds : bond 0.04424 ( 1773) hydrogen bonds : angle 3.72481 ( 5136) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 217 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C1 272 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7816 (pp) REVERT: C2 98 PHE cc_start: 0.8947 (t80) cc_final: 0.8628 (t80) REVERT: C2 301 MET cc_start: 0.7497 (mmp) cc_final: 0.7136 (mmm) REVERT: C3 100 MET cc_start: 0.7671 (mmm) cc_final: 0.7165 (mtp) REVERT: C3 126 THR cc_start: 0.9326 (t) cc_final: 0.9087 (p) REVERT: C3 229 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.8353 (pt0) REVERT: P1 138 MET cc_start: 0.9308 (mmm) cc_final: 0.8965 (mmm) REVERT: P1 170 ASN cc_start: 0.8393 (m-40) cc_final: 0.8034 (p0) REVERT: P2 69 ASP cc_start: 0.7710 (t0) cc_final: 0.7369 (m-30) REVERT: P2 138 MET cc_start: 0.8618 (mmm) cc_final: 0.8405 (mmt) REVERT: P3 91 ASP cc_start: 0.8266 (t0) cc_final: 0.7560 (t0) REVERT: P3 149 ASP cc_start: 0.7772 (OUTLIER) cc_final: 0.7367 (t0) REVERT: P3 153 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7601 (tt) REVERT: P3 164 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8308 (tt) REVERT: P3 169 GLU cc_start: 0.8028 (tt0) cc_final: 0.7743 (tt0) REVERT: A1 361 ILE cc_start: 0.8417 (tp) cc_final: 0.8095 (tp) REVERT: A1 365 GLN cc_start: 0.9074 (OUTLIER) cc_final: 0.7095 (mt0) REVERT: A2 376 GLN cc_start: 0.7801 (tp-100) cc_final: 0.7443 (mp10) REVERT: a2 37 MET cc_start: 0.4377 (tpt) cc_final: 0.3959 (tpt) REVERT: a1 358 ARG cc_start: 0.5509 (ttt90) cc_final: 0.5124 (ttt90) outliers start: 87 outliers final: 67 residues processed: 288 average time/residue: 0.1640 time to fit residues: 78.4131 Evaluate side-chains 278 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 205 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C1 residue 64 LEU Chi-restraints excluded: chain C1 residue 69 ASP Chi-restraints excluded: chain C1 residue 76 TYR Chi-restraints excluded: chain C1 residue 186 VAL Chi-restraints excluded: chain C1 residue 259 ILE Chi-restraints excluded: chain C1 residue 272 LEU Chi-restraints excluded: chain C1 residue 288 THR Chi-restraints excluded: chain C2 residue 64 LEU Chi-restraints excluded: chain C2 residue 76 TYR Chi-restraints excluded: chain C2 residue 186 VAL Chi-restraints excluded: chain C2 residue 270 LEU Chi-restraints excluded: chain C2 residue 372 SER Chi-restraints excluded: chain C3 residue 76 TYR Chi-restraints excluded: chain C3 residue 226 ASP Chi-restraints excluded: chain C3 residue 229 GLN Chi-restraints excluded: chain C3 residue 269 THR Chi-restraints excluded: chain C3 residue 422 ILE Chi-restraints excluded: chain P1 residue 23 THR Chi-restraints excluded: chain P1 residue 149 ASP Chi-restraints excluded: chain P2 residue 31 THR Chi-restraints excluded: chain P2 residue 61 THR Chi-restraints excluded: chain P2 residue 67 LEU Chi-restraints excluded: chain P2 residue 136 VAL Chi-restraints excluded: chain P2 residue 147 ILE Chi-restraints excluded: chain P2 residue 163 THR Chi-restraints excluded: chain P3 residue 132 TRP Chi-restraints excluded: chain P3 residue 149 ASP Chi-restraints excluded: chain P3 residue 153 LEU Chi-restraints excluded: chain P3 residue 157 VAL Chi-restraints excluded: chain P3 residue 164 LEU Chi-restraints excluded: chain A1 residue 37 MET Chi-restraints excluded: chain A1 residue 73 SER Chi-restraints excluded: chain A1 residue 126 VAL Chi-restraints excluded: chain A1 residue 217 THR Chi-restraints excluded: chain A1 residue 226 LEU Chi-restraints excluded: chain A1 residue 230 LEU Chi-restraints excluded: chain A1 residue 234 THR Chi-restraints excluded: chain A1 residue 249 SER Chi-restraints excluded: chain A1 residue 365 GLN Chi-restraints excluded: chain A1 residue 367 VAL Chi-restraints excluded: chain A2 residue 126 VAL Chi-restraints excluded: chain A2 residue 157 VAL Chi-restraints excluded: chain A2 residue 164 VAL Chi-restraints excluded: chain A2 residue 249 SER Chi-restraints excluded: chain A2 residue 324 LEU Chi-restraints excluded: chain A2 residue 325 VAL Chi-restraints excluded: chain A2 residue 338 VAL Chi-restraints excluded: chain A2 residue 340 SER Chi-restraints excluded: chain A2 residue 359 VAL Chi-restraints excluded: chain A2 residue 364 LEU Chi-restraints excluded: chain A3 residue 56 LEU Chi-restraints excluded: chain A3 residue 65 ILE Chi-restraints excluded: chain A3 residue 234 THR Chi-restraints excluded: chain A3 residue 249 SER Chi-restraints excluded: chain A3 residue 265 VAL Chi-restraints excluded: chain A3 residue 325 VAL Chi-restraints excluded: chain A3 residue 338 VAL Chi-restraints excluded: chain A3 residue 378 VAL Chi-restraints excluded: chain a2 residue 65 ILE Chi-restraints excluded: chain a2 residue 73 SER Chi-restraints excluded: chain a2 residue 75 ILE Chi-restraints excluded: chain a2 residue 212 ILE Chi-restraints excluded: chain a2 residue 248 THR Chi-restraints excluded: chain a2 residue 275 THR Chi-restraints excluded: chain a1 residue 65 ILE Chi-restraints excluded: chain a1 residue 212 ILE Chi-restraints excluded: chain a1 residue 248 THR Chi-restraints excluded: chain a3 residue 37 MET Chi-restraints excluded: chain a3 residue 65 ILE Chi-restraints excluded: chain a3 residue 73 SER Chi-restraints excluded: chain a3 residue 212 ILE Chi-restraints excluded: chain a3 residue 248 THR Chi-restraints excluded: chain a3 residue 256 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 38 optimal weight: 1.9990 chunk 234 optimal weight: 1.9990 chunk 364 optimal weight: 5.9990 chunk 372 optimal weight: 3.9990 chunk 181 optimal weight: 0.6980 chunk 305 optimal weight: 9.9990 chunk 249 optimal weight: 0.8980 chunk 341 optimal weight: 0.8980 chunk 265 optimal weight: 0.0970 chunk 239 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C2 30 GLN C3 229 GLN P2 158 HIS a3 256 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.098132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.074682 restraints weight = 57474.198| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.57 r_work: 0.2908 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29454 Z= 0.116 Angle : 0.481 9.384 40062 Z= 0.244 Chirality : 0.039 0.188 4746 Planarity : 0.003 0.045 5310 Dihedral : 3.442 19.595 4125 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.69 % Favored : 96.10 % Rotamer: Outliers : 2.70 % Allowed : 25.54 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 2.25 (0.14), residues: 3792 helix: 4.30 (0.12), residues: 1509 sheet: 0.51 (0.19), residues: 684 loop : -0.98 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGA1 368 TYR 0.011 0.001 TYRa2 101 PHE 0.022 0.001 PHEa2 262 TRP 0.011 0.001 TRPa3 347 HIS 0.006 0.001 HISP1 158 Details of bonding type rmsd covalent geometry : bond 0.00255 (29451) covalent geometry : angle 0.48063 (40056) SS BOND : bond 0.00038 ( 3) SS BOND : angle 0.30167 ( 6) hydrogen bonds : bond 0.04710 ( 1773) hydrogen bonds : angle 3.79680 ( 5136) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 203 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C1 272 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7812 (pp) REVERT: C2 98 PHE cc_start: 0.8954 (t80) cc_final: 0.8637 (t80) REVERT: C2 301 MET cc_start: 0.7471 (mmp) cc_final: 0.7228 (mmm) REVERT: C3 100 MET cc_start: 0.7735 (mmm) cc_final: 0.7213 (mtp) REVERT: C3 229 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8365 (pt0) REVERT: C3 301 MET cc_start: 0.7878 (tpp) cc_final: 0.7676 (mmp) REVERT: P1 138 MET cc_start: 0.9359 (mmm) cc_final: 0.9015 (mmm) REVERT: P1 170 ASN cc_start: 0.8393 (m-40) cc_final: 0.8044 (p0) REVERT: P2 69 ASP cc_start: 0.7676 (t0) cc_final: 0.7335 (m-30) REVERT: P2 138 MET cc_start: 0.8641 (mmm) cc_final: 0.8438 (mmt) REVERT: P3 91 ASP cc_start: 0.8344 (t0) cc_final: 0.7697 (t0) REVERT: P3 149 ASP cc_start: 0.8009 (OUTLIER) cc_final: 0.7582 (t0) REVERT: P3 153 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7730 (tt) REVERT: P3 164 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8311 (tt) REVERT: A1 361 ILE cc_start: 0.8446 (tp) cc_final: 0.8122 (tp) REVERT: A1 365 GLN cc_start: 0.9076 (OUTLIER) cc_final: 0.7104 (mt0) REVERT: A2 376 GLN cc_start: 0.7805 (tp-100) cc_final: 0.7335 (mp10) REVERT: a2 37 MET cc_start: 0.4308 (OUTLIER) cc_final: 0.3830 (tpt) outliers start: 85 outliers final: 69 residues processed: 274 average time/residue: 0.1656 time to fit residues: 75.3436 Evaluate side-chains 271 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 195 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C1 residue 64 LEU Chi-restraints excluded: chain C1 residue 69 ASP Chi-restraints excluded: chain C1 residue 76 TYR Chi-restraints excluded: chain C1 residue 186 VAL Chi-restraints excluded: chain C1 residue 259 ILE Chi-restraints excluded: chain C1 residue 272 LEU Chi-restraints excluded: chain C1 residue 288 THR Chi-restraints excluded: chain C1 residue 394 VAL Chi-restraints excluded: chain C2 residue 64 LEU Chi-restraints excluded: chain C2 residue 76 TYR Chi-restraints excluded: chain C2 residue 186 VAL Chi-restraints excluded: chain C2 residue 270 LEU Chi-restraints excluded: chain C2 residue 372 SER Chi-restraints excluded: chain C3 residue 76 TYR Chi-restraints excluded: chain C3 residue 229 GLN Chi-restraints excluded: chain C3 residue 269 THR Chi-restraints excluded: chain C3 residue 385 SER Chi-restraints excluded: chain C3 residue 390 THR Chi-restraints excluded: chain C3 residue 422 ILE Chi-restraints excluded: chain P1 residue 23 THR Chi-restraints excluded: chain P1 residue 149 ASP Chi-restraints excluded: chain P2 residue 31 THR Chi-restraints excluded: chain P2 residue 61 THR Chi-restraints excluded: chain P2 residue 67 LEU Chi-restraints excluded: chain P2 residue 136 VAL Chi-restraints excluded: chain P2 residue 147 ILE Chi-restraints excluded: chain P3 residue 132 TRP Chi-restraints excluded: chain P3 residue 149 ASP Chi-restraints excluded: chain P3 residue 153 LEU Chi-restraints excluded: chain P3 residue 157 VAL Chi-restraints excluded: chain P3 residue 164 LEU Chi-restraints excluded: chain A1 residue 37 MET Chi-restraints excluded: chain A1 residue 73 SER Chi-restraints excluded: chain A1 residue 126 VAL Chi-restraints excluded: chain A1 residue 217 THR Chi-restraints excluded: chain A1 residue 226 LEU Chi-restraints excluded: chain A1 residue 230 LEU Chi-restraints excluded: chain A1 residue 234 THR Chi-restraints excluded: chain A1 residue 235 LEU Chi-restraints excluded: chain A1 residue 249 SER Chi-restraints excluded: chain A1 residue 365 GLN Chi-restraints excluded: chain A1 residue 367 VAL Chi-restraints excluded: chain A2 residue 126 VAL Chi-restraints excluded: chain A2 residue 157 VAL Chi-restraints excluded: chain A2 residue 164 VAL Chi-restraints excluded: chain A2 residue 249 SER Chi-restraints excluded: chain A2 residue 324 LEU Chi-restraints excluded: chain A2 residue 325 VAL Chi-restraints excluded: chain A2 residue 338 VAL Chi-restraints excluded: chain A2 residue 340 SER Chi-restraints excluded: chain A2 residue 359 VAL Chi-restraints excluded: chain A2 residue 364 LEU Chi-restraints excluded: chain A3 residue 56 LEU Chi-restraints excluded: chain A3 residue 65 ILE Chi-restraints excluded: chain A3 residue 234 THR Chi-restraints excluded: chain A3 residue 249 SER Chi-restraints excluded: chain A3 residue 265 VAL Chi-restraints excluded: chain A3 residue 325 VAL Chi-restraints excluded: chain A3 residue 338 VAL Chi-restraints excluded: chain A3 residue 378 VAL Chi-restraints excluded: chain a2 residue 37 MET Chi-restraints excluded: chain a2 residue 65 ILE Chi-restraints excluded: chain a2 residue 73 SER Chi-restraints excluded: chain a2 residue 75 ILE Chi-restraints excluded: chain a2 residue 248 THR Chi-restraints excluded: chain a2 residue 275 THR Chi-restraints excluded: chain a1 residue 65 ILE Chi-restraints excluded: chain a1 residue 212 ILE Chi-restraints excluded: chain a1 residue 248 THR Chi-restraints excluded: chain a3 residue 37 MET Chi-restraints excluded: chain a3 residue 65 ILE Chi-restraints excluded: chain a3 residue 73 SER Chi-restraints excluded: chain a3 residue 212 ILE Chi-restraints excluded: chain a3 residue 232 ASN Chi-restraints excluded: chain a3 residue 248 THR Chi-restraints excluded: chain a3 residue 256 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 160 optimal weight: 0.0980 chunk 60 optimal weight: 0.9980 chunk 171 optimal weight: 0.8980 chunk 179 optimal weight: 1.9990 chunk 142 optimal weight: 7.9990 chunk 256 optimal weight: 4.9990 chunk 305 optimal weight: 5.9990 chunk 133 optimal weight: 8.9990 chunk 51 optimal weight: 0.9990 chunk 134 optimal weight: 0.8980 chunk 336 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P2 158 HIS A3 376 GLN a3 256 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.098428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.074989 restraints weight = 57308.362| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.57 r_work: 0.2913 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 29454 Z= 0.108 Angle : 0.474 10.256 40062 Z= 0.240 Chirality : 0.039 0.160 4746 Planarity : 0.003 0.045 5310 Dihedral : 3.426 19.588 4125 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.74 % Favored : 96.04 % Rotamer: Outliers : 2.83 % Allowed : 25.38 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 2.27 (0.14), residues: 3792 helix: 4.33 (0.12), residues: 1509 sheet: 0.54 (0.19), residues: 684 loop : -0.97 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGA2 368 TYR 0.011 0.001 TYRa2 101 PHE 0.020 0.001 PHEa2 262 TRP 0.011 0.001 TRPP3 132 HIS 0.006 0.001 HISP2 158 Details of bonding type rmsd covalent geometry : bond 0.00234 (29451) covalent geometry : angle 0.47414 (40056) SS BOND : bond 0.00036 ( 3) SS BOND : angle 0.27814 ( 6) hydrogen bonds : bond 0.04652 ( 1773) hydrogen bonds : angle 3.77135 ( 5136) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 204 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C1 272 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7792 (pp) REVERT: C2 98 PHE cc_start: 0.8962 (t80) cc_final: 0.8608 (t80) REVERT: C2 301 MET cc_start: 0.7470 (mmp) cc_final: 0.7227 (mmm) REVERT: C3 100 MET cc_start: 0.7734 (mmm) cc_final: 0.7195 (mtp) REVERT: C3 229 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8508 (pt0) REVERT: C3 301 MET cc_start: 0.8057 (tpp) cc_final: 0.7811 (mmp) REVERT: P1 138 MET cc_start: 0.9359 (mmm) cc_final: 0.9012 (mmm) REVERT: P1 170 ASN cc_start: 0.8558 (m-40) cc_final: 0.8046 (p0) REVERT: P2 69 ASP cc_start: 0.7642 (t0) cc_final: 0.7302 (m-30) REVERT: P3 91 ASP cc_start: 0.8318 (t0) cc_final: 0.7663 (t0) REVERT: P3 149 ASP cc_start: 0.7969 (OUTLIER) cc_final: 0.7544 (t0) REVERT: P3 153 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7671 (tt) REVERT: P3 164 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8300 (tt) REVERT: A1 322 THR cc_start: 0.8634 (p) cc_final: 0.8309 (p) REVERT: A1 361 ILE cc_start: 0.8433 (tp) cc_final: 0.8110 (tp) REVERT: A1 365 GLN cc_start: 0.9070 (OUTLIER) cc_final: 0.7101 (mt0) REVERT: A2 376 GLN cc_start: 0.7803 (tp-100) cc_final: 0.7289 (mp10) REVERT: a2 37 MET cc_start: 0.4343 (OUTLIER) cc_final: 0.3919 (tpt) outliers start: 89 outliers final: 78 residues processed: 279 average time/residue: 0.1661 time to fit residues: 77.3282 Evaluate side-chains 284 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 199 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C1 residue 64 LEU Chi-restraints excluded: chain C1 residue 69 ASP Chi-restraints excluded: chain C1 residue 76 TYR Chi-restraints excluded: chain C1 residue 186 VAL Chi-restraints excluded: chain C1 residue 259 ILE Chi-restraints excluded: chain C1 residue 272 LEU Chi-restraints excluded: chain C1 residue 288 THR Chi-restraints excluded: chain C1 residue 394 VAL Chi-restraints excluded: chain C2 residue 64 LEU Chi-restraints excluded: chain C2 residue 76 TYR Chi-restraints excluded: chain C2 residue 186 VAL Chi-restraints excluded: chain C2 residue 270 LEU Chi-restraints excluded: chain C2 residue 372 SER Chi-restraints excluded: chain C2 residue 390 THR Chi-restraints excluded: chain C3 residue 64 LEU Chi-restraints excluded: chain C3 residue 76 TYR Chi-restraints excluded: chain C3 residue 229 GLN Chi-restraints excluded: chain C3 residue 259 ILE Chi-restraints excluded: chain C3 residue 269 THR Chi-restraints excluded: chain C3 residue 385 SER Chi-restraints excluded: chain C3 residue 390 THR Chi-restraints excluded: chain C3 residue 422 ILE Chi-restraints excluded: chain P1 residue 23 THR Chi-restraints excluded: chain P1 residue 149 ASP Chi-restraints excluded: chain P2 residue 31 THR Chi-restraints excluded: chain P2 residue 61 THR Chi-restraints excluded: chain P2 residue 67 LEU Chi-restraints excluded: chain P2 residue 74 LEU Chi-restraints excluded: chain P2 residue 136 VAL Chi-restraints excluded: chain P2 residue 147 ILE Chi-restraints excluded: chain P2 residue 163 THR Chi-restraints excluded: chain P3 residue 132 TRP Chi-restraints excluded: chain P3 residue 149 ASP Chi-restraints excluded: chain P3 residue 153 LEU Chi-restraints excluded: chain P3 residue 157 VAL Chi-restraints excluded: chain P3 residue 164 LEU Chi-restraints excluded: chain A1 residue 37 MET Chi-restraints excluded: chain A1 residue 73 SER Chi-restraints excluded: chain A1 residue 126 VAL Chi-restraints excluded: chain A1 residue 217 THR Chi-restraints excluded: chain A1 residue 226 LEU Chi-restraints excluded: chain A1 residue 230 LEU Chi-restraints excluded: chain A1 residue 234 THR Chi-restraints excluded: chain A1 residue 235 LEU Chi-restraints excluded: chain A1 residue 249 SER Chi-restraints excluded: chain A1 residue 365 GLN Chi-restraints excluded: chain A1 residue 367 VAL Chi-restraints excluded: chain A2 residue 126 VAL Chi-restraints excluded: chain A2 residue 157 VAL Chi-restraints excluded: chain A2 residue 164 VAL Chi-restraints excluded: chain A2 residue 249 SER Chi-restraints excluded: chain A2 residue 324 LEU Chi-restraints excluded: chain A2 residue 325 VAL Chi-restraints excluded: chain A2 residue 338 VAL Chi-restraints excluded: chain A2 residue 340 SER Chi-restraints excluded: chain A2 residue 359 VAL Chi-restraints excluded: chain A2 residue 364 LEU Chi-restraints excluded: chain A3 residue 56 LEU Chi-restraints excluded: chain A3 residue 65 ILE Chi-restraints excluded: chain A3 residue 234 THR Chi-restraints excluded: chain A3 residue 249 SER Chi-restraints excluded: chain A3 residue 265 VAL Chi-restraints excluded: chain A3 residue 325 VAL Chi-restraints excluded: chain A3 residue 338 VAL Chi-restraints excluded: chain A3 residue 378 VAL Chi-restraints excluded: chain a2 residue 37 MET Chi-restraints excluded: chain a2 residue 65 ILE Chi-restraints excluded: chain a2 residue 73 SER Chi-restraints excluded: chain a2 residue 75 ILE Chi-restraints excluded: chain a2 residue 212 ILE Chi-restraints excluded: chain a2 residue 217 THR Chi-restraints excluded: chain a2 residue 248 THR Chi-restraints excluded: chain a2 residue 275 THR Chi-restraints excluded: chain a1 residue 65 ILE Chi-restraints excluded: chain a1 residue 212 ILE Chi-restraints excluded: chain a1 residue 248 THR Chi-restraints excluded: chain a1 residue 260 LEU Chi-restraints excluded: chain a3 residue 37 MET Chi-restraints excluded: chain a3 residue 65 ILE Chi-restraints excluded: chain a3 residue 73 SER Chi-restraints excluded: chain a3 residue 212 ILE Chi-restraints excluded: chain a3 residue 217 THR Chi-restraints excluded: chain a3 residue 232 ASN Chi-restraints excluded: chain a3 residue 248 THR Chi-restraints excluded: chain a3 residue 256 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 210 optimal weight: 1.9990 chunk 288 optimal weight: 4.9990 chunk 371 optimal weight: 3.9990 chunk 264 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 344 optimal weight: 0.0570 chunk 91 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 110 optimal weight: 0.7980 chunk 113 optimal weight: 8.9990 chunk 219 optimal weight: 2.9990 overall best weight: 0.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P2 158 HIS a3 256 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.097839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.074357 restraints weight = 57253.846| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.57 r_work: 0.2904 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29454 Z= 0.117 Angle : 0.484 10.430 40062 Z= 0.246 Chirality : 0.039 0.183 4746 Planarity : 0.003 0.045 5310 Dihedral : 3.445 19.483 4125 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.72 % Favored : 96.07 % Rotamer: Outliers : 2.80 % Allowed : 25.35 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 2.25 (0.14), residues: 3792 helix: 4.31 (0.12), residues: 1509 sheet: 0.49 (0.19), residues: 687 loop : -0.97 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGA2 368 TYR 0.012 0.001 TYRa3 137 PHE 0.021 0.001 PHEa2 262 TRP 0.012 0.001 TRPP3 132 HIS 0.006 0.001 HISP2 158 Details of bonding type rmsd covalent geometry : bond 0.00260 (29451) covalent geometry : angle 0.48362 (40056) SS BOND : bond 0.00045 ( 3) SS BOND : angle 0.30523 ( 6) hydrogen bonds : bond 0.04777 ( 1773) hydrogen bonds : angle 3.80216 ( 5136) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 196 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C1 272 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7814 (pp) REVERT: C2 98 PHE cc_start: 0.8968 (t80) cc_final: 0.8622 (t80) REVERT: C2 212 TYR cc_start: 0.8596 (m-80) cc_final: 0.8286 (m-80) REVERT: C2 301 MET cc_start: 0.7483 (mmp) cc_final: 0.7238 (mmm) REVERT: C3 100 MET cc_start: 0.7771 (mmm) cc_final: 0.7213 (mtp) REVERT: C3 229 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8475 (pt0) REVERT: C3 301 MET cc_start: 0.8066 (tpp) cc_final: 0.7825 (mmp) REVERT: P1 138 MET cc_start: 0.9358 (mmm) cc_final: 0.9008 (mmm) REVERT: P1 170 ASN cc_start: 0.8543 (m-40) cc_final: 0.8045 (p0) REVERT: P2 69 ASP cc_start: 0.7650 (t0) cc_final: 0.7313 (m-30) REVERT: P2 138 MET cc_start: 0.8797 (mmt) cc_final: 0.8518 (mmt) REVERT: P3 91 ASP cc_start: 0.8345 (t0) cc_final: 0.7688 (t0) REVERT: P3 149 ASP cc_start: 0.7999 (OUTLIER) cc_final: 0.7564 (t0) REVERT: P3 153 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7727 (tt) REVERT: A1 322 THR cc_start: 0.8695 (p) cc_final: 0.8362 (p) REVERT: A1 361 ILE cc_start: 0.8449 (tp) cc_final: 0.8121 (tp) REVERT: A1 365 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.7204 (mt0) REVERT: A2 376 GLN cc_start: 0.7760 (tp-100) cc_final: 0.7273 (mp10) REVERT: a2 37 MET cc_start: 0.4135 (OUTLIER) cc_final: 0.3524 (tpt) outliers start: 88 outliers final: 77 residues processed: 271 average time/residue: 0.1658 time to fit residues: 74.3646 Evaluate side-chains 279 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 196 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C1 residue 64 LEU Chi-restraints excluded: chain C1 residue 69 ASP Chi-restraints excluded: chain C1 residue 76 TYR Chi-restraints excluded: chain C1 residue 186 VAL Chi-restraints excluded: chain C1 residue 259 ILE Chi-restraints excluded: chain C1 residue 272 LEU Chi-restraints excluded: chain C1 residue 288 THR Chi-restraints excluded: chain C1 residue 394 VAL Chi-restraints excluded: chain C2 residue 64 LEU Chi-restraints excluded: chain C2 residue 76 TYR Chi-restraints excluded: chain C2 residue 186 VAL Chi-restraints excluded: chain C2 residue 270 LEU Chi-restraints excluded: chain C2 residue 372 SER Chi-restraints excluded: chain C2 residue 390 THR Chi-restraints excluded: chain C3 residue 64 LEU Chi-restraints excluded: chain C3 residue 76 TYR Chi-restraints excluded: chain C3 residue 229 GLN Chi-restraints excluded: chain C3 residue 259 ILE Chi-restraints excluded: chain C3 residue 269 THR Chi-restraints excluded: chain C3 residue 385 SER Chi-restraints excluded: chain C3 residue 390 THR Chi-restraints excluded: chain C3 residue 422 ILE Chi-restraints excluded: chain P1 residue 23 THR Chi-restraints excluded: chain P1 residue 149 ASP Chi-restraints excluded: chain P2 residue 31 THR Chi-restraints excluded: chain P2 residue 61 THR Chi-restraints excluded: chain P2 residue 67 LEU Chi-restraints excluded: chain P2 residue 74 LEU Chi-restraints excluded: chain P2 residue 136 VAL Chi-restraints excluded: chain P2 residue 147 ILE Chi-restraints excluded: chain P3 residue 132 TRP Chi-restraints excluded: chain P3 residue 149 ASP Chi-restraints excluded: chain P3 residue 153 LEU Chi-restraints excluded: chain P3 residue 157 VAL Chi-restraints excluded: chain A1 residue 37 MET Chi-restraints excluded: chain A1 residue 73 SER Chi-restraints excluded: chain A1 residue 126 VAL Chi-restraints excluded: chain A1 residue 217 THR Chi-restraints excluded: chain A1 residue 226 LEU Chi-restraints excluded: chain A1 residue 230 LEU Chi-restraints excluded: chain A1 residue 234 THR Chi-restraints excluded: chain A1 residue 235 LEU Chi-restraints excluded: chain A1 residue 249 SER Chi-restraints excluded: chain A1 residue 365 GLN Chi-restraints excluded: chain A1 residue 367 VAL Chi-restraints excluded: chain A2 residue 126 VAL Chi-restraints excluded: chain A2 residue 157 VAL Chi-restraints excluded: chain A2 residue 164 VAL Chi-restraints excluded: chain A2 residue 249 SER Chi-restraints excluded: chain A2 residue 324 LEU Chi-restraints excluded: chain A2 residue 325 VAL Chi-restraints excluded: chain A2 residue 338 VAL Chi-restraints excluded: chain A2 residue 340 SER Chi-restraints excluded: chain A2 residue 359 VAL Chi-restraints excluded: chain A2 residue 364 LEU Chi-restraints excluded: chain A3 residue 56 LEU Chi-restraints excluded: chain A3 residue 65 ILE Chi-restraints excluded: chain A3 residue 234 THR Chi-restraints excluded: chain A3 residue 265 VAL Chi-restraints excluded: chain A3 residue 325 VAL Chi-restraints excluded: chain A3 residue 338 VAL Chi-restraints excluded: chain A3 residue 378 VAL Chi-restraints excluded: chain a2 residue 37 MET Chi-restraints excluded: chain a2 residue 65 ILE Chi-restraints excluded: chain a2 residue 73 SER Chi-restraints excluded: chain a2 residue 75 ILE Chi-restraints excluded: chain a2 residue 217 THR Chi-restraints excluded: chain a2 residue 226 LEU Chi-restraints excluded: chain a2 residue 248 THR Chi-restraints excluded: chain a2 residue 275 THR Chi-restraints excluded: chain a2 residue 304 ASN Chi-restraints excluded: chain a1 residue 65 ILE Chi-restraints excluded: chain a1 residue 212 ILE Chi-restraints excluded: chain a1 residue 248 THR Chi-restraints excluded: chain a1 residue 260 LEU Chi-restraints excluded: chain a3 residue 37 MET Chi-restraints excluded: chain a3 residue 65 ILE Chi-restraints excluded: chain a3 residue 73 SER Chi-restraints excluded: chain a3 residue 212 ILE Chi-restraints excluded: chain a3 residue 217 THR Chi-restraints excluded: chain a3 residue 232 ASN Chi-restraints excluded: chain a3 residue 248 THR Chi-restraints excluded: chain a3 residue 256 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 191 optimal weight: 3.9990 chunk 311 optimal weight: 4.9990 chunk 281 optimal weight: 4.9990 chunk 225 optimal weight: 3.9990 chunk 275 optimal weight: 0.5980 chunk 117 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 145 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 197 optimal weight: 0.9990 chunk 315 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P2 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3 376 GLN a3 256 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.092622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.068880 restraints weight = 58267.445| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.58 r_work: 0.2802 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 29454 Z= 0.234 Angle : 0.582 10.782 40062 Z= 0.301 Chirality : 0.042 0.161 4746 Planarity : 0.004 0.044 5310 Dihedral : 3.887 21.583 4125 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.22 % Favored : 95.57 % Rotamer: Outliers : 2.83 % Allowed : 25.25 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 1.83 (0.14), residues: 3792 helix: 3.80 (0.12), residues: 1518 sheet: 0.30 (0.19), residues: 714 loop : -1.07 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGC3 343 TYR 0.020 0.002 TYRa3 137 PHE 0.028 0.002 PHEa2 262 TRP 0.016 0.002 TRPP3 132 HIS 0.008 0.001 HISP3 158 Details of bonding type rmsd covalent geometry : bond 0.00556 (29451) covalent geometry : angle 0.58215 (40056) SS BOND : bond 0.00196 ( 3) SS BOND : angle 0.56206 ( 6) hydrogen bonds : bond 0.06480 ( 1773) hydrogen bonds : angle 4.32115 ( 5136) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6842.09 seconds wall clock time: 117 minutes 47.76 seconds (7067.76 seconds total)