Starting phenix.real_space_refine on Mon Aug 25 15:20:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g1u_29677/08_2025/8g1u_29677_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g1u_29677/08_2025/8g1u_29677.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8g1u_29677/08_2025/8g1u_29677_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g1u_29677/08_2025/8g1u_29677_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g1u_29677/08_2025/8g1u_29677.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g1u_29677/08_2025/8g1u_29677.map" } resolution = 2.83 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= 0.003 sd= 0.233 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 140 5.16 5 C 18457 2.51 5 N 5013 2.21 5 O 5438 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 202 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29048 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 4930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 609, 4930 Classifications: {'peptide': 609} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 35, 'TRANS': 569} Chain breaks: 3 Chain: "B" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2240 Classifications: {'peptide': 295} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 282} Chain breaks: 2 Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Chain: "E" Number of atoms: 4933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4933 Classifications: {'peptide': 610} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 36, 'TRANS': 569} Chain breaks: 3 Chain: "F" Number of atoms: 2233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2233 Classifications: {'peptide': 294} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 282} Chain breaks: 2 Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Chain: "I" Number of atoms: 4931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 609, 4931 Classifications: {'peptide': 609} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 36, 'TRANS': 568} Chain breaks: 3 Chain: "J" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2240 Classifications: {'peptide': 295} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 282} Chain breaks: 2 Chain: "K" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 37 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Chain: "M" Number of atoms: 4930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 609, 4930 Classifications: {'peptide': 609} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 35, 'TRANS': 569} Chain breaks: 3 Chain: "N" Number of atoms: 2223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2223 Classifications: {'peptide': 292} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 280} Chain breaks: 2 Chain: "O" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 37 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Chain: "D" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 45 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "H" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 45 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "L" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 45 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "P" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 45 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'ADN%rna2p': 1} Classifications: {'undetermined': 1} Modifications used: {'rna2p': 1} Chain: "E" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'ADN%rna2p': 1} Classifications: {'undetermined': 1} Modifications used: {'rna2p': 1} Chain: "I" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'ADN%rna2p': 1} Classifications: {'undetermined': 1} Modifications used: {'rna2p': 1} Chain: "M" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'ADN%rna2p': 1} Classifications: {'undetermined': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 6.52, per 1000 atoms: 0.22 Number of scatterers: 29048 At special positions: 0 Unit cell: (146.91, 151.89, 159.36, 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 140 16.00 O 5438 8.00 N 5013 7.00 C 18457 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.32 Conformation dependent library (CDL) restraints added in 862.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6910 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 55 sheets defined 25.6% alpha, 31.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 25 through 37 Processing helix chain 'A' and resid 58 through 62 removed outlier: 3.503A pdb=" N ARG A 62 " --> pdb=" O ALA A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 73 removed outlier: 3.730A pdb=" N LEU A 72 " --> pdb=" O SER A 69 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 73 " --> pdb=" O ASP A 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 69 through 73' Processing helix chain 'A' and resid 74 through 81 Processing helix chain 'A' and resid 96 through 118 Processing helix chain 'A' and resid 131 through 143 Processing helix chain 'A' and resid 183 through 196 removed outlier: 3.702A pdb=" N MET A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 224 Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 247 through 260 removed outlier: 3.831A pdb=" N LEU A 260 " --> pdb=" O ARG A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 289 removed outlier: 4.112A pdb=" N LEU A 281 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 284 " --> pdb=" O TYR A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 320 through 329 Processing helix chain 'A' and resid 330 through 349 removed outlier: 3.941A pdb=" N TYR A 334 " --> pdb=" O ASP A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 Processing helix chain 'A' and resid 369 through 383 Processing helix chain 'A' and resid 396 through 408 removed outlier: 3.883A pdb=" N THR A 400 " --> pdb=" O ASN A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 411 No H-bonds generated for 'chain 'A' and resid 409 through 411' Processing helix chain 'A' and resid 445 through 452 Processing helix chain 'A' and resid 477 through 487 Processing helix chain 'A' and resid 495 through 500 removed outlier: 3.510A pdb=" N PHE A 498 " --> pdb=" O GLU A 495 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU A 499 " --> pdb=" O ALA A 496 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N MET A 500 " --> pdb=" O GLN A 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 495 through 500' Processing helix chain 'A' and resid 627 through 631 Processing helix chain 'B' and resid 63 through 67 Processing helix chain 'B' and resid 69 through 73 removed outlier: 3.908A pdb=" N CYS B 73 " --> pdb=" O GLU B 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 36 removed outlier: 3.507A pdb=" N GLN E 36 " --> pdb=" O ALA E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 62 removed outlier: 3.560A pdb=" N ARG E 62 " --> pdb=" O ALA E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 73 removed outlier: 3.780A pdb=" N LEU E 72 " --> pdb=" O SER E 69 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU E 73 " --> pdb=" O ASP E 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 69 through 73' Processing helix chain 'E' and resid 74 through 81 Processing helix chain 'E' and resid 96 through 118 Processing helix chain 'E' and resid 131 through 143 Processing helix chain 'E' and resid 159 through 163 Processing helix chain 'E' and resid 184 through 196 Processing helix chain 'E' and resid 214 through 223 Processing helix chain 'E' and resid 234 through 236 No H-bonds generated for 'chain 'E' and resid 234 through 236' Processing helix chain 'E' and resid 247 through 260 removed outlier: 3.582A pdb=" N LYS E 259 " --> pdb=" O PHE E 255 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU E 260 " --> pdb=" O ARG E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 289 removed outlier: 4.171A pdb=" N LEU E 281 " --> pdb=" O PHE E 277 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU E 284 " --> pdb=" O TYR E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 301 Processing helix chain 'E' and resid 320 through 329 removed outlier: 3.614A pdb=" N VAL E 326 " --> pdb=" O GLN E 322 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE E 327 " --> pdb=" O THR E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 349 removed outlier: 4.146A pdb=" N TYR E 334 " --> pdb=" O ASP E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 354 removed outlier: 3.517A pdb=" N LYS E 354 " --> pdb=" O GLU E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 383 Processing helix chain 'E' and resid 394 through 408 removed outlier: 3.654A pdb=" N VAL E 399 " --> pdb=" O PRO E 395 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR E 400 " --> pdb=" O ASN E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 411 No H-bonds generated for 'chain 'E' and resid 409 through 411' Processing helix chain 'E' and resid 445 through 452 Processing helix chain 'E' and resid 477 through 487 Processing helix chain 'E' and resid 495 through 500 removed outlier: 4.037A pdb=" N MET E 500 " --> pdb=" O GLN E 497 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 631 Processing helix chain 'F' and resid 63 through 67 removed outlier: 3.689A pdb=" N ALA F 67 " --> pdb=" O PRO F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 73 removed outlier: 3.866A pdb=" N CYS F 73 " --> pdb=" O GLU F 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 25 through 37 removed outlier: 3.533A pdb=" N GLN I 36 " --> pdb=" O ALA I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 62 removed outlier: 3.582A pdb=" N ARG I 62 " --> pdb=" O ALA I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 73 removed outlier: 3.987A pdb=" N LEU I 72 " --> pdb=" O SER I 69 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU I 73 " --> pdb=" O ASP I 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 69 through 73' Processing helix chain 'I' and resid 74 through 81 Processing helix chain 'I' and resid 96 through 118 Processing helix chain 'I' and resid 131 through 143 Processing helix chain 'I' and resid 184 through 196 Processing helix chain 'I' and resid 214 through 222 Processing helix chain 'I' and resid 234 through 236 No H-bonds generated for 'chain 'I' and resid 234 through 236' Processing helix chain 'I' and resid 247 through 260 removed outlier: 3.648A pdb=" N LEU I 260 " --> pdb=" O ARG I 256 " (cutoff:3.500A) Processing helix chain 'I' and resid 276 through 290 removed outlier: 3.800A pdb=" N TYR I 280 " --> pdb=" O GLU I 276 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU I 284 " --> pdb=" O TYR I 280 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN I 289 " --> pdb=" O GLU I 285 " (cutoff:3.500A) Processing helix chain 'I' and resid 320 through 329 Processing helix chain 'I' and resid 330 through 347 removed outlier: 4.047A pdb=" N TYR I 334 " --> pdb=" O ASP I 330 " (cutoff:3.500A) Processing helix chain 'I' and resid 350 through 354 Processing helix chain 'I' and resid 369 through 383 Processing helix chain 'I' and resid 394 through 408 removed outlier: 3.679A pdb=" N THR I 400 " --> pdb=" O ASN I 396 " (cutoff:3.500A) Processing helix chain 'I' and resid 409 through 411 No H-bonds generated for 'chain 'I' and resid 409 through 411' Processing helix chain 'I' and resid 445 through 453 removed outlier: 3.521A pdb=" N GLY I 452 " --> pdb=" O GLU I 448 " (cutoff:3.500A) Processing helix chain 'I' and resid 477 through 487 Processing helix chain 'I' and resid 495 through 500 removed outlier: 4.019A pdb=" N MET I 500 " --> pdb=" O GLN I 497 " (cutoff:3.500A) Processing helix chain 'I' and resid 627 through 631 Processing helix chain 'J' and resid 63 through 67 Processing helix chain 'J' and resid 69 through 73 removed outlier: 3.547A pdb=" N CYS J 73 " --> pdb=" O GLU J 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 36 removed outlier: 3.913A pdb=" N GLN M 36 " --> pdb=" O ALA M 32 " (cutoff:3.500A) Processing helix chain 'M' and resid 58 through 62 Processing helix chain 'M' and resid 69 through 73 removed outlier: 3.948A pdb=" N LEU M 72 " --> pdb=" O SER M 69 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU M 73 " --> pdb=" O ASP M 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 69 through 73' Processing helix chain 'M' and resid 74 through 81 Processing helix chain 'M' and resid 96 through 118 Processing helix chain 'M' and resid 131 through 143 Processing helix chain 'M' and resid 184 through 196 Processing helix chain 'M' and resid 214 through 224 removed outlier: 3.510A pdb=" N ILE M 218 " --> pdb=" O SER M 214 " (cutoff:3.500A) Processing helix chain 'M' and resid 247 through 260 removed outlier: 3.647A pdb=" N LEU M 260 " --> pdb=" O ARG M 256 " (cutoff:3.500A) Processing helix chain 'M' and resid 277 through 291 removed outlier: 4.308A pdb=" N LEU M 281 " --> pdb=" O PHE M 277 " (cutoff:3.500A) Processing helix chain 'M' and resid 297 through 302 Processing helix chain 'M' and resid 320 through 329 removed outlier: 3.747A pdb=" N VAL M 326 " --> pdb=" O GLN M 322 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE M 327 " --> pdb=" O THR M 323 " (cutoff:3.500A) Processing helix chain 'M' and resid 330 through 349 removed outlier: 4.050A pdb=" N TYR M 334 " --> pdb=" O ASP M 330 " (cutoff:3.500A) Processing helix chain 'M' and resid 350 through 354 removed outlier: 3.597A pdb=" N LYS M 354 " --> pdb=" O GLU M 351 " (cutoff:3.500A) Processing helix chain 'M' and resid 369 through 383 Processing helix chain 'M' and resid 394 through 408 removed outlier: 3.759A pdb=" N THR M 400 " --> pdb=" O ASN M 396 " (cutoff:3.500A) Processing helix chain 'M' and resid 409 through 411 No H-bonds generated for 'chain 'M' and resid 409 through 411' Processing helix chain 'M' and resid 445 through 454 Processing helix chain 'M' and resid 477 through 487 Processing helix chain 'M' and resid 496 through 500 removed outlier: 3.959A pdb=" N MET M 500 " --> pdb=" O GLN M 497 " (cutoff:3.500A) Processing helix chain 'M' and resid 627 through 631 Processing helix chain 'N' and resid 63 through 67 Processing helix chain 'N' and resid 69 through 73 removed outlier: 3.900A pdb=" N CYS N 73 " --> pdb=" O GLU N 70 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 19 removed outlier: 6.954A pdb=" N SER A 16 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N CYS A 42 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ARG A 18 " --> pdb=" O CYS A 42 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LEU A 41 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LYS A 85 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N MET A 43 " --> pdb=" O LYS A 85 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ILE A 82 " --> pdb=" O ALA A 121 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N LEU A 123 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLY A 84 " --> pdb=" O LEU A 123 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N PHE A 122 " --> pdb=" O TRP A 152 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ARG A 154 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU A 124 " --> pdb=" O ARG A 154 " (cutoff:3.500A) removed outlier: 11.061A pdb=" N ILE A 202 " --> pdb=" O ILE A 226 " (cutoff:3.500A) removed outlier: 9.994A pdb=" N ALA A 228 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL A 204 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ILE A 230 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU A 206 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LYS A 227 " --> pdb=" O GLN A 263 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ILE A 265 " --> pdb=" O LYS A 227 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ALA A 229 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N THR A 267 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU A 231 " --> pdb=" O THR A 267 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 237 through 238 Processing sheet with id=AA3, first strand: chain 'A' and resid 308 through 309 removed outlier: 3.683A pdb=" N ILE A 586 " --> pdb=" O HIS A 549 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N HIS A 549 " --> pdb=" O ILE A 586 " (cutoff:3.500A) removed outlier: 10.444A pdb=" N GLN A 588 " --> pdb=" O VAL A 547 " (cutoff:3.500A) removed outlier: 10.140A pdb=" N VAL A 547 " --> pdb=" O GLN A 588 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE A 475 " --> pdb=" O HIS A 549 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N PHE A 551 " --> pdb=" O ALA A 473 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ALA A 473 " --> pdb=" O PHE A 551 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLY A 553 " --> pdb=" O PHE A 471 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N PHE A 471 " --> pdb=" O GLY A 553 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N PHE A 555 " --> pdb=" O THR A 469 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR A 469 " --> pdb=" O PHE A 555 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N THR A 557 " --> pdb=" O GLU A 467 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLU A 467 " --> pdb=" O THR A 557 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TYR A 468 " --> pdb=" O THR A 520 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N THR A 520 " --> pdb=" O TYR A 468 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N SER A 470 " --> pdb=" O CYS A 518 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 510 through 511 removed outlier: 6.696A pdb=" N GLU A 467 " --> pdb=" O THR A 557 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N THR A 557 " --> pdb=" O GLU A 467 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR A 469 " --> pdb=" O PHE A 555 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N PHE A 555 " --> pdb=" O THR A 469 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N PHE A 471 " --> pdb=" O GLY A 553 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLY A 553 " --> pdb=" O PHE A 471 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ALA A 473 " --> pdb=" O PHE A 551 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N PHE A 551 " --> pdb=" O ALA A 473 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE A 475 " --> pdb=" O HIS A 549 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 413 through 416 removed outlier: 11.579A pdb=" N VAL A 358 " --> pdb=" O ALA A 429 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ILE A 431 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL A 360 " --> pdb=" O ILE A 431 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VAL A 433 " --> pdb=" O VAL A 360 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N MET A 362 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASP A 430 " --> pdb=" O VAL A 462 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ILE A 464 " --> pdb=" O ASP A 430 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE A 432 " --> pdb=" O ILE A 464 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 534 through 541 removed outlier: 6.078A pdb=" N CYS A 599 " --> pdb=" O THR A 618 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 30 through 36 removed outlier: 3.557A pdb=" N GLN B 30 " --> pdb=" O SER B 47 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLY B 45 " --> pdb=" O GLU B 32 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA B 34 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU B 43 " --> pdb=" O ALA B 34 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY B 56 " --> pdb=" O THR B 79 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 83 through 88 removed outlier: 3.628A pdb=" N ASP B 85 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA B 102 " --> pdb=" O SER B 98 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL B 103 " --> pdb=" O CYS B 120 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N CYS B 120 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU B 105 " --> pdb=" O LYS B 118 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 133 removed outlier: 6.455A pdb=" N ILE B 149 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N SER B 162 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL B 151 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 170 through 175 removed outlier: 3.558A pdb=" N CYS B 172 " --> pdb=" O CYS B 186 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 215 through 220 removed outlier: 6.447A pdb=" N GLY B 231 " --> pdb=" O THR B 216 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LEU B 218 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL B 229 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N TRP B 220 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N VAL B 227 " --> pdb=" O TRP B 220 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N THR B 236 " --> pdb=" O ASP B 232 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 258 through 263 removed outlier: 3.682A pdb=" N GLY B 260 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU B 280 " --> pdb=" O ARG B 292 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ARG B 292 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL B 282 " --> pdb=" O LEU B 290 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 300 through 305 removed outlier: 3.939A pdb=" N ASP B 302 " --> pdb=" O VAL B 316 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 16 through 19 removed outlier: 7.033A pdb=" N SER E 16 " --> pdb=" O PHE E 40 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N CYS E 42 " --> pdb=" O SER E 16 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ARG E 18 " --> pdb=" O CYS E 42 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU E 41 " --> pdb=" O VAL E 83 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LYS E 85 " --> pdb=" O LEU E 41 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N MET E 43 " --> pdb=" O LYS E 85 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ILE E 82 " --> pdb=" O ALA E 121 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N LEU E 123 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLY E 84 " --> pdb=" O LEU E 123 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N PHE E 122 " --> pdb=" O TRP E 152 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ARG E 154 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU E 124 " --> pdb=" O ARG E 154 " (cutoff:3.500A) removed outlier: 11.080A pdb=" N ILE E 202 " --> pdb=" O ILE E 226 " (cutoff:3.500A) removed outlier: 10.027A pdb=" N ALA E 228 " --> pdb=" O ILE E 202 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL E 204 " --> pdb=" O ALA E 228 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ILE E 230 " --> pdb=" O VAL E 204 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU E 206 " --> pdb=" O ILE E 230 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LYS E 227 " --> pdb=" O GLN E 263 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ILE E 265 " --> pdb=" O LYS E 227 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ALA E 229 " --> pdb=" O ILE E 265 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N THR E 267 " --> pdb=" O ALA E 229 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU E 231 " --> pdb=" O THR E 267 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLY E 17 " --> pdb=" O ILE E 266 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 237 through 238 Processing sheet with id=AB7, first strand: chain 'E' and resid 310 through 311 Processing sheet with id=AB8, first strand: chain 'E' and resid 413 through 416 removed outlier: 6.976A pdb=" N ASP E 430 " --> pdb=" O VAL E 358 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N VAL E 360 " --> pdb=" O ASP E 430 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N ILE E 432 " --> pdb=" O VAL E 360 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N MET E 362 " --> pdb=" O ILE E 432 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N SER E 434 " --> pdb=" O MET E 362 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU E 364 " --> pdb=" O SER E 434 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ASP E 430 " --> pdb=" O VAL E 462 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ILE E 464 " --> pdb=" O ASP E 430 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE E 432 " --> pdb=" O ILE E 464 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 502 through 503 removed outlier: 13.185A pdb=" N ILE E 582 " --> pdb=" O GLU E 556 " (cutoff:3.500A) removed outlier: 12.295A pdb=" N GLU E 556 " --> pdb=" O ILE E 582 " (cutoff:3.500A) removed outlier: 10.700A pdb=" N PHE E 584 " --> pdb=" O TYR E 554 " (cutoff:3.500A) removed outlier: 10.862A pdb=" N TYR E 554 " --> pdb=" O PHE E 584 " (cutoff:3.500A) removed outlier: 11.763A pdb=" N ILE E 586 " --> pdb=" O ALA E 552 " (cutoff:3.500A) removed outlier: 11.583A pdb=" N ALA E 552 " --> pdb=" O ILE E 586 " (cutoff:3.500A) removed outlier: 10.801A pdb=" N GLN E 588 " --> pdb=" O GLY E 550 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N GLY E 550 " --> pdb=" O GLN E 588 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY E 550 " --> pdb=" O ILE E 475 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N TYR E 468 " --> pdb=" O THR E 520 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N THR E 520 " --> pdb=" O TYR E 468 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N SER E 470 " --> pdb=" O CYS E 518 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 510 through 511 removed outlier: 3.588A pdb=" N GLY E 550 " --> pdb=" O ILE E 475 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE E 563 " --> pdb=" O LEU E 559 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 534 through 540 removed outlier: 6.073A pdb=" N CYS E 599 " --> pdb=" O THR E 618 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 30 through 36 removed outlier: 6.475A pdb=" N GLY F 45 " --> pdb=" O GLU F 32 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA F 34 " --> pdb=" O LEU F 43 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LEU F 43 " --> pdb=" O ALA F 34 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY F 56 " --> pdb=" O THR F 79 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 83 through 89 removed outlier: 3.543A pdb=" N ASP F 85 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ALA F 102 " --> pdb=" O SER F 98 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL F 103 " --> pdb=" O CYS F 120 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N CYS F 120 " --> pdb=" O VAL F 103 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU F 105 " --> pdb=" O LYS F 118 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 130 through 133 removed outlier: 5.961A pdb=" N ASP F 153 " --> pdb=" O VAL F 159 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N VAL F 159 " --> pdb=" O ASP F 153 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 170 through 175 removed outlier: 3.606A pdb=" N CYS F 172 " --> pdb=" O CYS F 186 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG F 191 " --> pdb=" O SER F 187 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 215 through 220 removed outlier: 6.534A pdb=" N GLY F 231 " --> pdb=" O THR F 216 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LEU F 218 " --> pdb=" O VAL F 229 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL F 229 " --> pdb=" O LEU F 218 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N TRP F 220 " --> pdb=" O VAL F 227 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N VAL F 227 " --> pdb=" O TRP F 220 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N THR F 236 " --> pdb=" O ASP F 232 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 258 through 263 removed outlier: 3.697A pdb=" N GLY F 260 " --> pdb=" O LEU F 274 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU F 280 " --> pdb=" O ARG F 292 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ARG F 292 " --> pdb=" O LEU F 280 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL F 282 " --> pdb=" O LEU F 290 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 300 through 305 removed outlier: 3.598A pdb=" N ASP F 302 " --> pdb=" O VAL F 316 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 16 through 19 removed outlier: 7.093A pdb=" N SER I 16 " --> pdb=" O PHE I 40 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N CYS I 42 " --> pdb=" O SER I 16 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ARG I 18 " --> pdb=" O CYS I 42 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N LEU I 41 " --> pdb=" O VAL I 83 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N LYS I 85 " --> pdb=" O LEU I 41 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N MET I 43 " --> pdb=" O LYS I 85 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ILE I 82 " --> pdb=" O ALA I 121 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N LEU I 123 " --> pdb=" O ILE I 82 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLY I 84 " --> pdb=" O LEU I 123 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N PHE I 122 " --> pdb=" O TRP I 152 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ARG I 154 " --> pdb=" O PHE I 122 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU I 124 " --> pdb=" O ARG I 154 " (cutoff:3.500A) removed outlier: 11.118A pdb=" N ILE I 202 " --> pdb=" O ILE I 226 " (cutoff:3.500A) removed outlier: 10.155A pdb=" N ALA I 228 " --> pdb=" O ILE I 202 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL I 204 " --> pdb=" O ALA I 228 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ILE I 230 " --> pdb=" O VAL I 204 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU I 206 " --> pdb=" O ILE I 230 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLY I 17 " --> pdb=" O ILE I 266 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 237 through 238 Processing sheet with id=AD3, first strand: chain 'I' and resid 310 through 311 removed outlier: 3.740A pdb=" N SER I 310 " --> pdb=" O ARG L 76 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 413 through 417 removed outlier: 11.727A pdb=" N VAL I 358 " --> pdb=" O ALA I 429 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N ILE I 431 " --> pdb=" O VAL I 358 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL I 360 " --> pdb=" O ILE I 431 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL I 433 " --> pdb=" O VAL I 360 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N MET I 362 " --> pdb=" O VAL I 433 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ASP I 430 " --> pdb=" O ASP I 460 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 502 through 503 removed outlier: 12.942A pdb=" N ILE I 582 " --> pdb=" O GLU I 556 " (cutoff:3.500A) removed outlier: 12.331A pdb=" N GLU I 556 " --> pdb=" O ILE I 582 " (cutoff:3.500A) removed outlier: 10.743A pdb=" N PHE I 584 " --> pdb=" O TYR I 554 " (cutoff:3.500A) removed outlier: 10.915A pdb=" N TYR I 554 " --> pdb=" O PHE I 584 " (cutoff:3.500A) removed outlier: 11.737A pdb=" N ILE I 586 " --> pdb=" O ALA I 552 " (cutoff:3.500A) removed outlier: 11.563A pdb=" N ALA I 552 " --> pdb=" O ILE I 586 " (cutoff:3.500A) removed outlier: 10.606A pdb=" N GLN I 588 " --> pdb=" O GLY I 550 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N GLY I 550 " --> pdb=" O GLN I 588 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY I 550 " --> pdb=" O ILE I 475 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N TYR I 468 " --> pdb=" O THR I 520 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N THR I 520 " --> pdb=" O TYR I 468 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N SER I 470 " --> pdb=" O CYS I 518 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 510 through 511 removed outlier: 3.682A pdb=" N GLY I 550 " --> pdb=" O ILE I 475 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 534 through 541 removed outlier: 6.095A pdb=" N CYS I 599 " --> pdb=" O THR I 618 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 30 through 36 removed outlier: 6.477A pdb=" N GLY J 45 " --> pdb=" O GLU J 32 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA J 34 " --> pdb=" O LEU J 43 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU J 43 " --> pdb=" O ALA J 34 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 83 through 89 removed outlier: 3.628A pdb=" N ASP J 85 " --> pdb=" O ALA J 97 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ALA J 102 " --> pdb=" O SER J 98 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N VAL J 103 " --> pdb=" O CYS J 120 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N CYS J 120 " --> pdb=" O VAL J 103 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU J 105 " --> pdb=" O LYS J 118 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 130 through 133 removed outlier: 5.981A pdb=" N ASP J 153 " --> pdb=" O VAL J 159 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL J 159 " --> pdb=" O ASP J 153 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 170 through 175 removed outlier: 3.814A pdb=" N CYS J 172 " --> pdb=" O CYS J 186 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 215 through 220 removed outlier: 6.507A pdb=" N GLY J 231 " --> pdb=" O THR J 216 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LEU J 218 " --> pdb=" O VAL J 229 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL J 229 " --> pdb=" O LEU J 218 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N TRP J 220 " --> pdb=" O VAL J 227 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N VAL J 227 " --> pdb=" O TRP J 220 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR J 236 " --> pdb=" O ASP J 232 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 258 through 263 removed outlier: 3.728A pdb=" N GLY J 260 " --> pdb=" O LEU J 274 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU J 280 " --> pdb=" O ARG J 292 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ARG J 292 " --> pdb=" O LEU J 280 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL J 282 " --> pdb=" O LEU J 290 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 300 through 305 removed outlier: 3.689A pdb=" N ASP J 302 " --> pdb=" O VAL J 316 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 16 through 19 removed outlier: 7.139A pdb=" N SER M 16 " --> pdb=" O PHE M 40 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N CYS M 42 " --> pdb=" O SER M 16 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ARG M 18 " --> pdb=" O CYS M 42 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LEU M 41 " --> pdb=" O VAL M 83 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N LYS M 85 " --> pdb=" O LEU M 41 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N MET M 43 " --> pdb=" O LYS M 85 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ILE M 82 " --> pdb=" O ALA M 121 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N LEU M 123 " --> pdb=" O ILE M 82 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N GLY M 84 " --> pdb=" O LEU M 123 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N PHE M 122 " --> pdb=" O TRP M 152 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ARG M 154 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU M 124 " --> pdb=" O ARG M 154 " (cutoff:3.500A) removed outlier: 11.061A pdb=" N ILE M 202 " --> pdb=" O ILE M 226 " (cutoff:3.500A) removed outlier: 10.007A pdb=" N ALA M 228 " --> pdb=" O ILE M 202 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL M 204 " --> pdb=" O ALA M 228 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ILE M 230 " --> pdb=" O VAL M 204 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU M 206 " --> pdb=" O ILE M 230 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LYS M 227 " --> pdb=" O GLN M 263 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ILE M 265 " --> pdb=" O LYS M 227 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ALA M 229 " --> pdb=" O ILE M 265 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N THR M 267 " --> pdb=" O ALA M 229 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU M 231 " --> pdb=" O THR M 267 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 237 through 238 Processing sheet with id=AE8, first strand: chain 'M' and resid 310 through 311 removed outlier: 3.844A pdb=" N SER M 310 " --> pdb=" O ARG P 76 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 413 through 416 removed outlier: 7.216A pdb=" N ASP M 430 " --> pdb=" O VAL M 358 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL M 360 " --> pdb=" O ASP M 430 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ILE M 432 " --> pdb=" O VAL M 360 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N MET M 362 " --> pdb=" O ILE M 432 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N SER M 434 " --> pdb=" O MET M 362 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU M 364 " --> pdb=" O SER M 434 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA M 429 " --> pdb=" O LYS M 458 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ASP M 460 " --> pdb=" O ALA M 429 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE M 431 " --> pdb=" O ASP M 460 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL M 462 " --> pdb=" O ILE M 431 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N VAL M 433 " --> pdb=" O VAL M 462 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE M 464 " --> pdb=" O VAL M 433 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 502 through 503 removed outlier: 3.632A pdb=" N ILE M 586 " --> pdb=" O HIS M 549 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N HIS M 549 " --> pdb=" O ILE M 586 " (cutoff:3.500A) removed outlier: 10.417A pdb=" N GLN M 588 " --> pdb=" O VAL M 547 " (cutoff:3.500A) removed outlier: 10.143A pdb=" N VAL M 547 " --> pdb=" O GLN M 588 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TYR M 468 " --> pdb=" O THR M 520 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N THR M 520 " --> pdb=" O TYR M 468 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N SER M 470 " --> pdb=" O CYS M 518 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 510 through 511 removed outlier: 6.922A pdb=" N ILE M 563 " --> pdb=" O LEU M 559 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 534 through 541 removed outlier: 6.120A pdb=" N CYS M 599 " --> pdb=" O THR M 618 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'N' and resid 30 through 36 removed outlier: 3.505A pdb=" N GLN N 30 " --> pdb=" O SER N 47 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLY N 45 " --> pdb=" O GLU N 32 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA N 34 " --> pdb=" O LEU N 43 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU N 43 " --> pdb=" O ALA N 34 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY N 56 " --> pdb=" O THR N 79 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'N' and resid 83 through 89 removed outlier: 3.578A pdb=" N ASP N 85 " --> pdb=" O ALA N 97 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA N 102 " --> pdb=" O SER N 98 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL N 103 " --> pdb=" O CYS N 120 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N CYS N 120 " --> pdb=" O VAL N 103 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU N 105 " --> pdb=" O LYS N 118 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'N' and resid 130 through 133 removed outlier: 6.243A pdb=" N ASP N 153 " --> pdb=" O VAL N 159 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N VAL N 159 " --> pdb=" O ASP N 153 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'N' and resid 170 through 175 removed outlier: 4.106A pdb=" N ARG N 191 " --> pdb=" O SER N 187 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'N' and resid 215 through 220 removed outlier: 6.381A pdb=" N GLY N 231 " --> pdb=" O THR N 216 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU N 218 " --> pdb=" O VAL N 229 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL N 229 " --> pdb=" O LEU N 218 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N TRP N 220 " --> pdb=" O VAL N 227 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL N 227 " --> pdb=" O TRP N 220 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N THR N 236 " --> pdb=" O ASP N 232 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'N' and resid 258 through 263 removed outlier: 3.771A pdb=" N GLY N 260 " --> pdb=" O LEU N 274 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU N 280 " --> pdb=" O ARG N 292 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ARG N 292 " --> pdb=" O LEU N 280 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL N 282 " --> pdb=" O LEU N 290 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'N' and resid 300 through 305 removed outlier: 3.698A pdb=" N ASP N 302 " --> pdb=" O VAL N 316 " (cutoff:3.500A) 1078 hydrogen bonds defined for protein. 2940 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: 5.84 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 4831 1.29 - 1.42: 7986 1.42 - 1.55: 16778 1.55 - 1.68: 5 1.68 - 1.81: 188 Bond restraints: 29788 Sorted by residual: bond pdb=" C ARG M 220 " pdb=" O ARG M 220 " ideal model delta sigma weight residual 1.237 1.323 -0.086 1.17e-02 7.31e+03 5.42e+01 bond pdb=" C ARG A 220 " pdb=" O ARG A 220 " ideal model delta sigma weight residual 1.237 1.311 -0.074 1.17e-02 7.31e+03 4.00e+01 bond pdb=" C TRP A 221 " pdb=" O TRP A 221 " ideal model delta sigma weight residual 1.237 1.164 0.073 1.17e-02 7.31e+03 3.88e+01 bond pdb=" C TRP M 221 " pdb=" O TRP M 221 " ideal model delta sigma weight residual 1.237 1.177 0.059 1.17e-02 7.31e+03 2.58e+01 bond pdb=" C ASP E 219 " pdb=" O ASP E 219 " ideal model delta sigma weight residual 1.237 1.296 -0.060 1.19e-02 7.06e+03 2.51e+01 ... (remaining 29783 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 39471 2.64 - 5.27: 930 5.27 - 7.91: 93 7.91 - 10.54: 9 10.54 - 13.18: 5 Bond angle restraints: 40508 Sorted by residual: angle pdb=" N GLU M 224 " pdb=" CA GLU M 224 " pdb=" C GLU M 224 " ideal model delta sigma weight residual 110.07 121.90 -11.83 1.46e+00 4.69e-01 6.56e+01 angle pdb=" N GLU A 224 " pdb=" CA GLU A 224 " pdb=" C GLU A 224 " ideal model delta sigma weight residual 110.20 121.81 -11.61 1.44e+00 4.82e-01 6.50e+01 angle pdb=" C PHE M 440 " pdb=" N ALA M 441 " pdb=" CA ALA M 441 " ideal model delta sigma weight residual 121.54 132.95 -11.41 1.91e+00 2.74e-01 3.57e+01 angle pdb=" C PHE E 440 " pdb=" N ALA E 441 " pdb=" CA ALA E 441 " ideal model delta sigma weight residual 121.54 132.42 -10.88 1.91e+00 2.74e-01 3.25e+01 angle pdb=" N ASP I 162 " pdb=" CA ASP I 162 " pdb=" C ASP I 162 " ideal model delta sigma weight residual 114.12 106.45 7.67 1.39e+00 5.18e-01 3.04e+01 ... (remaining 40503 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 16056 17.89 - 35.78: 1339 35.78 - 53.67: 251 53.67 - 71.56: 90 71.56 - 89.45: 28 Dihedral angle restraints: 17764 sinusoidal: 7139 harmonic: 10625 Sorted by residual: dihedral pdb=" CA TYR A 560 " pdb=" C TYR A 560 " pdb=" N GLN A 561 " pdb=" CA GLN A 561 " ideal model delta harmonic sigma weight residual -180.00 -152.15 -27.85 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA TYR M 560 " pdb=" C TYR M 560 " pdb=" N GLN M 561 " pdb=" CA GLN M 561 " ideal model delta harmonic sigma weight residual 180.00 -154.64 -25.36 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" C ILE F 147 " pdb=" N ILE F 147 " pdb=" CA ILE F 147 " pdb=" CB ILE F 147 " ideal model delta harmonic sigma weight residual -122.00 -134.59 12.59 0 2.50e+00 1.60e-01 2.54e+01 ... (remaining 17761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 3705 0.080 - 0.161: 694 0.161 - 0.241: 37 0.241 - 0.321: 13 0.321 - 0.401: 4 Chirality restraints: 4453 Sorted by residual: chirality pdb=" CA HIS A 507 " pdb=" N HIS A 507 " pdb=" C HIS A 507 " pdb=" CB HIS A 507 " both_signs ideal model delta sigma weight residual False 2.51 2.91 -0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" CA ASP E 419 " pdb=" N ASP E 419 " pdb=" C ASP E 419 " pdb=" CB ASP E 419 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" CA ASP M 419 " pdb=" N ASP M 419 " pdb=" C ASP M 419 " pdb=" CB ASP M 419 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.35e+00 ... (remaining 4450 not shown) Planarity restraints: 5231 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS J 145 " -0.026 2.00e-02 2.50e+03 5.15e-02 2.65e+01 pdb=" C LYS J 145 " 0.089 2.00e-02 2.50e+03 pdb=" O LYS J 145 " -0.034 2.00e-02 2.50e+03 pdb=" N ASP J 146 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR I 560 " 0.021 2.00e-02 2.50e+03 4.31e-02 1.86e+01 pdb=" C TYR I 560 " -0.075 2.00e-02 2.50e+03 pdb=" O TYR I 560 " 0.027 2.00e-02 2.50e+03 pdb=" N GLN I 561 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS N 145 " -0.019 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" C LYS N 145 " 0.066 2.00e-02 2.50e+03 pdb=" O LYS N 145 " -0.025 2.00e-02 2.50e+03 pdb=" N ASP N 146 " -0.022 2.00e-02 2.50e+03 ... (remaining 5228 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 4047 2.75 - 3.29: 26149 3.29 - 3.83: 50572 3.83 - 4.36: 66143 4.36 - 4.90: 111831 Nonbonded interactions: 258742 Sorted by model distance: nonbonded pdb=" OE1 GLU J 226 " pdb=" OG1 THR J 242 " model vdw 2.214 3.040 nonbonded pdb=" OG SER B 135 " pdb=" O SER B 176 " model vdw 2.217 3.040 nonbonded pdb=" OH TYR A 334 " pdb=" OE1 GLU A 435 " model vdw 2.223 3.040 nonbonded pdb=" OD2 ASP A 70 " pdb=" OG1 THR I 400 " model vdw 2.246 3.040 nonbonded pdb=" O ARG I 76 " pdb=" OG1 THR I 80 " model vdw 2.247 3.040 ... (remaining 258737 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 291 or resid 297 through 525 or resid 532 throu \ gh 701)) selection = (chain 'E' and (resid 14 through 171 or resid 180 through 291 or resid 297 throu \ gh 525 or resid 532 through 701)) selection = (chain 'I' and (resid 14 through 171 or resid 180 through 525 or resid 532 throu \ gh 701)) selection = (chain 'M' and (resid 14 through 291 or resid 297 through 525 or resid 532 throu \ gh 701)) } ncs_group { reference = (chain 'B' and resid 26 through 327) selection = (chain 'F' and resid 26 through 327) selection = (chain 'J' and resid 26 through 327) selection = (chain 'N' and resid 26 through 327) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' selection = chain 'P' } ncs_group { reference = chain 'K' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.180 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: 0.030 Extract box with map and model: 0.460 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 24.870 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 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:7.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 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 : 0.009 0.086 29788 Z= 0.403 Angle : 0.930 13.179 40508 Z= 0.533 Chirality : 0.061 0.401 4453 Planarity : 0.006 0.051 5231 Dihedral : 14.791 89.447 10854 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.85 % Favored : 97.04 % Rotamer: Outliers : 0.59 % Allowed : 1.22 % Favored : 98.18 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 9.80 % 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 aren not related in a simple way. whole: -1.25 (0.13), residues: 3579 helix: -0.53 (0.17), residues: 795 sheet: -0.74 (0.15), residues: 1152 loop : -0.89 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 164 TYR 0.028 0.002 TYR I 342 PHE 0.045 0.003 PHE M 440 TRP 0.030 0.003 TRP A 603 HIS 0.007 0.001 HIS J 296 Details of bonding type rmsd covalent geometry : bond 0.00901 (29788) covalent geometry : angle 0.92959 (40508) hydrogen bonds : bond 0.15381 ( 1049) hydrogen bonds : angle 6.81665 ( 2940) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 453 time to evaluate : 1.199 Fit side-chains revert: symmetry clash REVERT: A 610 LYS cc_start: 0.7977 (mmtt) cc_final: 0.7454 (mtpt) REVERT: E 317 ASP cc_start: 0.7374 (m-30) cc_final: 0.6954 (m-30) REVERT: E 476 SER cc_start: 0.8485 (t) cc_final: 0.8219 (t) REVERT: F 234 ASN cc_start: 0.8639 (t0) cc_final: 0.8414 (t0) REVERT: F 297 ARG cc_start: 0.8052 (mtm110) cc_final: 0.7728 (mtm-85) REVERT: I 35 LYS cc_start: 0.7793 (mmtm) cc_final: 0.7548 (tmtt) REVERT: M 383 ASP cc_start: 0.7361 (t0) cc_final: 0.7029 (t0) REVERT: N 99 ASP cc_start: 0.8227 (m-30) cc_final: 0.7986 (m-30) REVERT: H 76 ARG cc_start: 0.6036 (OUTLIER) cc_final: 0.5578 (ttm170) outliers start: 19 outliers final: 6 residues processed: 466 average time/residue: 0.6721 time to fit residues: 361.2947 Evaluate side-chains 356 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 349 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain I residue 562 ASP Chi-restraints excluded: chain M residue 506 LEU Chi-restraints excluded: chain N residue 148 CYS Chi-restraints excluded: chain H residue 76 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.0870 chunk 298 optimal weight: 0.8980 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 128 GLN A 309 GLN A 482 ASN A 525 ASN B 190 ASN B 325 HIS E 79 ASN E 141 HIS E 239 ASN E 322 GLN E 482 ASN E 525 ASN F 256 GLN F 325 HIS I 79 ASN I 290 ASN I 454 GLN J 205 GLN J 321 GLN M 79 ASN M 141 HIS M 525 ASN N 156 GLN N 256 GLN N 325 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.162616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.135676 restraints weight = 30635.402| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.50 r_work: 0.3445 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 29788 Z= 0.116 Angle : 0.530 7.023 40508 Z= 0.279 Chirality : 0.045 0.141 4453 Planarity : 0.004 0.041 5231 Dihedral : 7.067 89.374 4021 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.93 % Favored : 97.96 % Rotamer: Outliers : 1.57 % Allowed : 8.89 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % 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 aren not related in a simple way. whole: -0.55 (0.14), residues: 3579 helix: 0.58 (0.18), residues: 801 sheet: -0.62 (0.15), residues: 1152 loop : -0.50 (0.16), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 488 TYR 0.019 0.001 TYR M 481 PHE 0.019 0.001 PHE B 119 TRP 0.024 0.001 TRP N 152 HIS 0.003 0.001 HIS E 216 Details of bonding type rmsd covalent geometry : bond 0.00267 (29788) covalent geometry : angle 0.52958 (40508) hydrogen bonds : bond 0.03522 ( 1049) hydrogen bonds : angle 5.15908 ( 2940) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 403 time to evaluate : 1.038 Fit side-chains revert: symmetry clash REVERT: A 101 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7793 (mtt180) REVERT: A 197 ASP cc_start: 0.8648 (t0) cc_final: 0.8312 (t0) REVERT: A 325 GLU cc_start: 0.7532 (tt0) cc_final: 0.7271 (tt0) REVERT: A 385 ARG cc_start: 0.7933 (mtm110) cc_final: 0.7643 (mtp180) REVERT: A 420 MET cc_start: 0.8961 (ptp) cc_final: 0.8682 (ptp) REVERT: A 593 ARG cc_start: 0.7318 (ptt-90) cc_final: 0.7118 (mtm-85) REVERT: A 610 LYS cc_start: 0.8134 (mmtt) cc_final: 0.7451 (mtpt) REVERT: B 69 ASN cc_start: 0.7710 (OUTLIER) cc_final: 0.7485 (t0) REVERT: E 248 LYS cc_start: 0.8197 (mmpt) cc_final: 0.7929 (tptt) REVERT: E 302 LYS cc_start: 0.7531 (OUTLIER) cc_final: 0.7254 (mttm) REVERT: E 317 ASP cc_start: 0.7432 (m-30) cc_final: 0.7170 (m-30) REVERT: E 489 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7512 (tt0) REVERT: E 539 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7939 (mt-10) REVERT: F 234 ASN cc_start: 0.8683 (t0) cc_final: 0.8366 (t0) REVERT: F 297 ARG cc_start: 0.8174 (mtm110) cc_final: 0.7964 (mtm-85) REVERT: I 35 LYS cc_start: 0.7783 (mmtm) cc_final: 0.7187 (tmtt) REVERT: I 248 LYS cc_start: 0.7789 (mmpt) cc_final: 0.7559 (mmmt) REVERT: I 320 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7194 (tt0) REVERT: I 407 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7947 (mt-10) REVERT: I 547 VAL cc_start: 0.7989 (OUTLIER) cc_final: 0.7593 (t) REVERT: M 101 ARG cc_start: 0.8325 (mtt-85) cc_final: 0.8032 (mmm160) REVERT: M 355 ASP cc_start: 0.7076 (t70) cc_final: 0.6874 (t70) REVERT: M 383 ASP cc_start: 0.7772 (t0) cc_final: 0.7305 (t0) REVERT: M 407 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7764 (mt-10) REVERT: M 609 LYS cc_start: 0.8347 (mtpt) cc_final: 0.7874 (mttt) REVERT: N 99 ASP cc_start: 0.8367 (m-30) cc_final: 0.7998 (m-30) outliers start: 50 outliers final: 16 residues processed: 432 average time/residue: 0.6040 time to fit residues: 306.2503 Evaluate side-chains 363 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 339 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 297 ARG Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 302 LYS Chi-restraints excluded: chain E residue 489 GLU Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain E residue 539 GLU Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 320 GLU Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain J residue 161 SER Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain M residue 237 LEU Chi-restraints excluded: chain M residue 388 LEU Chi-restraints excluded: chain M residue 407 GLU Chi-restraints excluded: chain M residue 506 LEU Chi-restraints excluded: chain N residue 116 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 112 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 124 optimal weight: 0.9990 chunk 159 optimal weight: 6.9990 chunk 252 optimal weight: 7.9990 chunk 348 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 186 optimal weight: 0.9980 chunk 337 optimal weight: 6.9990 chunk 276 optimal weight: 0.5980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 128 GLN A 309 GLN A 525 ASN E 79 ASN E 381 GLN E 525 ASN I 79 ASN I 270 ASN J 205 GLN J 320 HIS J 321 GLN N 256 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.161220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.133912 restraints weight = 30789.470| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.51 r_work: 0.3425 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29788 Z= 0.137 Angle : 0.522 7.262 40508 Z= 0.274 Chirality : 0.045 0.141 4453 Planarity : 0.004 0.051 5231 Dihedral : 6.018 88.946 4006 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.40 % Favored : 97.49 % Rotamer: Outliers : 2.29 % Allowed : 10.77 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % 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 aren not related in a simple way. whole: -0.30 (0.14), residues: 3579 helix: 1.02 (0.19), residues: 800 sheet: -0.63 (0.15), residues: 1148 loop : -0.34 (0.16), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 593 TYR 0.014 0.001 TYR A 342 PHE 0.020 0.001 PHE M 440 TRP 0.017 0.001 TRP N 152 HIS 0.006 0.001 HIS M 455 Details of bonding type rmsd covalent geometry : bond 0.00324 (29788) covalent geometry : angle 0.52234 (40508) hydrogen bonds : bond 0.03462 ( 1049) hydrogen bonds : angle 4.94483 ( 2940) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 361 time to evaluate : 0.804 Fit side-chains revert: symmetry clash REVERT: A 101 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7788 (mtt180) REVERT: A 197 ASP cc_start: 0.8696 (t0) cc_final: 0.8409 (t0) REVERT: A 325 GLU cc_start: 0.7547 (tt0) cc_final: 0.7309 (tt0) REVERT: A 385 ARG cc_start: 0.7912 (mtm110) cc_final: 0.7619 (mtp180) REVERT: A 420 MET cc_start: 0.8959 (ptp) cc_final: 0.8689 (ptp) REVERT: A 609 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.7923 (mptt) REVERT: A 610 LYS cc_start: 0.8162 (mmtt) cc_final: 0.7508 (mtpt) REVERT: B 69 ASN cc_start: 0.7693 (OUTLIER) cc_final: 0.7446 (t0) REVERT: B 126 ASP cc_start: 0.8429 (t0) cc_final: 0.8190 (t70) REVERT: B 148 CYS cc_start: 0.8284 (m) cc_final: 0.7645 (m) REVERT: E 302 LYS cc_start: 0.7562 (OUTLIER) cc_final: 0.7305 (mttm) REVERT: E 317 ASP cc_start: 0.7569 (m-30) cc_final: 0.7275 (m-30) REVERT: E 388 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7913 (tt) REVERT: E 489 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7439 (tt0) REVERT: E 594 GLU cc_start: 0.7846 (mp0) cc_final: 0.7534 (mp0) REVERT: F 110 GLU cc_start: 0.6559 (tp30) cc_final: 0.6258 (tm-30) REVERT: F 114 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.7876 (mp) REVERT: F 234 ASN cc_start: 0.8730 (t0) cc_final: 0.8417 (t0) REVERT: F 297 ARG cc_start: 0.8123 (mtm110) cc_final: 0.7909 (mtm-85) REVERT: I 25 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7886 (mm-30) REVERT: I 35 LYS cc_start: 0.7783 (mmtm) cc_final: 0.7205 (tmtt) REVERT: I 248 LYS cc_start: 0.7766 (mmpt) cc_final: 0.7556 (mmmt) REVERT: I 285 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7123 (mt-10) REVERT: I 320 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7202 (tt0) REVERT: I 326 VAL cc_start: 0.8113 (t) cc_final: 0.7843 (p) REVERT: I 407 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7936 (mt-10) REVERT: I 547 VAL cc_start: 0.7916 (OUTLIER) cc_final: 0.7512 (t) REVERT: M 383 ASP cc_start: 0.7781 (t0) cc_final: 0.7323 (t0) REVERT: M 609 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.7950 (mttt) REVERT: N 99 ASP cc_start: 0.8329 (m-30) cc_final: 0.7947 (m-30) REVERT: N 121 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7913 (mtpp) outliers start: 73 outliers final: 28 residues processed: 408 average time/residue: 0.6467 time to fit residues: 307.3449 Evaluate side-chains 376 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 337 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 482 ASN Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 609 LYS Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain E residue 302 LYS Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 467 GLU Chi-restraints excluded: chain E residue 489 GLU Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain I residue 320 GLU Chi-restraints excluded: chain I residue 422 GLU Chi-restraints excluded: chain I residue 500 MET Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain J residue 161 SER Chi-restraints excluded: chain J residue 227 VAL Chi-restraints excluded: chain M residue 237 LEU Chi-restraints excluded: chain M residue 288 SER Chi-restraints excluded: chain M residue 388 LEU Chi-restraints excluded: chain M residue 506 LEU Chi-restraints excluded: chain M residue 571 THR Chi-restraints excluded: chain M residue 609 LYS Chi-restraints excluded: chain M residue 629 THR Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain N residue 121 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 309 optimal weight: 3.9990 chunk 256 optimal weight: 2.9990 chunk 299 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 354 optimal weight: 10.0000 chunk 296 optimal weight: 3.9990 chunk 60 optimal weight: 0.0770 chunk 113 optimal weight: 6.9990 chunk 352 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 166 optimal weight: 0.0980 overall best weight: 2.2344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 128 GLN A 309 GLN A 394 ASN A 525 ASN E 56 GLN E 79 ASN E 239 ASN E 322 GLN E 381 GLN E 455 HIS E 482 ASN E 525 ASN I 79 ASN J 205 GLN M 56 GLN M 79 ASN M 455 HIS N 256 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.158907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.131696 restraints weight = 30565.959| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.49 r_work: 0.3401 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 29788 Z= 0.191 Angle : 0.564 7.482 40508 Z= 0.293 Chirality : 0.047 0.146 4453 Planarity : 0.004 0.041 5231 Dihedral : 6.053 89.271 4006 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.51 % Favored : 97.37 % Rotamer: Outliers : 2.57 % Allowed : 12.59 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % 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 aren not related in a simple way. whole: -0.31 (0.14), residues: 3579 helix: 1.01 (0.19), residues: 802 sheet: -0.64 (0.15), residues: 1144 loop : -0.35 (0.16), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 593 TYR 0.015 0.001 TYR A 116 PHE 0.019 0.002 PHE E 440 TRP 0.013 0.002 TRP I 186 HIS 0.005 0.001 HIS F 325 Details of bonding type rmsd covalent geometry : bond 0.00460 (29788) covalent geometry : angle 0.56401 (40508) hydrogen bonds : bond 0.03753 ( 1049) hydrogen bonds : angle 5.03642 ( 2940) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 354 time to evaluate : 1.116 Fit side-chains revert: symmetry clash REVERT: A 101 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7809 (mtt180) REVERT: A 325 GLU cc_start: 0.7657 (tt0) cc_final: 0.7404 (tt0) REVERT: A 385 ARG cc_start: 0.7980 (mtm180) cc_final: 0.7757 (mtp180) REVERT: A 420 MET cc_start: 0.9033 (ptp) cc_final: 0.8810 (ptp) REVERT: A 610 LYS cc_start: 0.8209 (mmtt) cc_final: 0.7547 (mtpt) REVERT: B 69 ASN cc_start: 0.7658 (OUTLIER) cc_final: 0.7401 (t0) REVERT: E 302 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.7282 (mttm) REVERT: E 317 ASP cc_start: 0.7646 (m-30) cc_final: 0.7411 (m-30) REVERT: E 388 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.7991 (tt) REVERT: E 539 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7996 (mt-10) REVERT: E 594 GLU cc_start: 0.7887 (mp0) cc_final: 0.7643 (mp0) REVERT: F 110 GLU cc_start: 0.6562 (tp30) cc_final: 0.6144 (tm-30) REVERT: F 114 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.7916 (mp) REVERT: F 234 ASN cc_start: 0.8779 (t0) cc_final: 0.8486 (t0) REVERT: F 294 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8494 (mt0) REVERT: F 297 ARG cc_start: 0.8134 (mtm110) cc_final: 0.7885 (mtm-85) REVERT: I 25 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7896 (mm-30) REVERT: I 35 LYS cc_start: 0.7851 (mmtm) cc_final: 0.7307 (tmtt) REVERT: I 248 LYS cc_start: 0.7790 (mmtt) cc_final: 0.7520 (mmmt) REVERT: I 316 MET cc_start: 0.8494 (ttm) cc_final: 0.8263 (ttp) REVERT: I 320 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7190 (tt0) REVERT: I 325 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7241 (tt0) REVERT: I 326 VAL cc_start: 0.8231 (t) cc_final: 0.7912 (p) REVERT: I 407 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7934 (mt-10) REVERT: I 588 GLN cc_start: 0.7661 (mm-40) cc_final: 0.7443 (mm110) REVERT: J 294 GLN cc_start: 0.8914 (OUTLIER) cc_final: 0.8556 (mt0) REVERT: M 383 ASP cc_start: 0.7802 (t0) cc_final: 0.7325 (t0) REVERT: M 609 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.7938 (mttt) REVERT: N 99 ASP cc_start: 0.8386 (m-30) cc_final: 0.8029 (m-30) outliers start: 82 outliers final: 38 residues processed: 406 average time/residue: 0.6432 time to fit residues: 305.0920 Evaluate side-chains 382 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 333 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 482 ASN Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 297 ARG Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain E residue 302 LYS Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain E residue 539 GLU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain F residue 294 GLN Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain I residue 320 GLU Chi-restraints excluded: chain I residue 325 GLU Chi-restraints excluded: chain I residue 422 GLU Chi-restraints excluded: chain I residue 500 MET Chi-restraints excluded: chain I residue 522 SER Chi-restraints excluded: chain I residue 597 THR Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 161 SER Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 227 VAL Chi-restraints excluded: chain J residue 294 GLN Chi-restraints excluded: chain M residue 237 LEU Chi-restraints excluded: chain M residue 288 SER Chi-restraints excluded: chain M residue 388 LEU Chi-restraints excluded: chain M residue 506 LEU Chi-restraints excluded: chain M residue 571 THR Chi-restraints excluded: chain M residue 609 LYS Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain N residue 161 SER Chi-restraints excluded: chain N residue 268 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 214 optimal weight: 0.3980 chunk 147 optimal weight: 2.9990 chunk 150 optimal weight: 9.9990 chunk 168 optimal weight: 10.0000 chunk 294 optimal weight: 2.9990 chunk 311 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 247 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 176 optimal weight: 6.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 128 GLN A 309 GLN A 525 ASN B 69 ASN E 79 ASN E 147 HIS E 239 ASN E 322 GLN E 381 GLN E 525 ASN I 79 ASN M 79 ASN N 256 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.161499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.134354 restraints weight = 30559.961| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.50 r_work: 0.3429 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 29788 Z= 0.126 Angle : 0.505 7.303 40508 Z= 0.265 Chirality : 0.045 0.145 4453 Planarity : 0.004 0.045 5231 Dihedral : 5.687 89.172 4006 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.29 % Favored : 97.60 % Rotamer: Outliers : 2.54 % Allowed : 13.96 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % 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 aren not related in a simple way. whole: -0.15 (0.14), residues: 3579 helix: 1.25 (0.19), residues: 805 sheet: -0.60 (0.15), residues: 1143 loop : -0.26 (0.16), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 593 TYR 0.014 0.001 TYR M 116 PHE 0.015 0.001 PHE J 119 TRP 0.016 0.001 TRP N 152 HIS 0.004 0.001 HIS E 549 Details of bonding type rmsd covalent geometry : bond 0.00297 (29788) covalent geometry : angle 0.50475 (40508) hydrogen bonds : bond 0.03202 ( 1049) hydrogen bonds : angle 4.81148 ( 2940) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 355 time to evaluate : 1.043 Fit side-chains revert: symmetry clash REVERT: A 101 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7778 (mtt180) REVERT: A 325 GLU cc_start: 0.7577 (tt0) cc_final: 0.7342 (tt0) REVERT: A 385 ARG cc_start: 0.7947 (mtm180) cc_final: 0.7724 (mtp180) REVERT: A 420 MET cc_start: 0.9008 (ptp) cc_final: 0.8710 (ptp) REVERT: A 609 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.7972 (mptt) REVERT: A 610 LYS cc_start: 0.8205 (mmtt) cc_final: 0.7550 (mtmt) REVERT: B 148 CYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7788 (m) REVERT: B 232 ASP cc_start: 0.8896 (p0) cc_final: 0.8657 (p0) REVERT: B 239 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8458 (tt) REVERT: E 68 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.7199 (ptp-170) REVERT: E 302 LYS cc_start: 0.7558 (OUTLIER) cc_final: 0.7297 (mttm) REVERT: E 317 ASP cc_start: 0.7629 (m-30) cc_final: 0.7311 (m-30) REVERT: E 388 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.7937 (tt) REVERT: E 594 GLU cc_start: 0.7827 (mp0) cc_final: 0.7521 (mp0) REVERT: F 110 GLU cc_start: 0.6699 (tp30) cc_final: 0.6203 (tm-30) REVERT: F 114 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.7893 (mp) REVERT: F 234 ASN cc_start: 0.8738 (t0) cc_final: 0.8475 (t0) REVERT: F 297 ARG cc_start: 0.8115 (mtm110) cc_final: 0.7888 (mtm-85) REVERT: I 25 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7826 (mm-30) REVERT: I 35 LYS cc_start: 0.7799 (mmtm) cc_final: 0.7258 (tmtt) REVERT: I 285 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7168 (mt-10) REVERT: I 316 MET cc_start: 0.8459 (ttm) cc_final: 0.8249 (ttp) REVERT: I 320 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7215 (tt0) REVERT: I 326 VAL cc_start: 0.8120 (t) cc_final: 0.7846 (p) REVERT: I 407 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7903 (mt-10) REVERT: I 547 VAL cc_start: 0.7865 (OUTLIER) cc_final: 0.7468 (t) REVERT: M 290 ASN cc_start: 0.7001 (t0) cc_final: 0.6300 (t0) REVERT: M 383 ASP cc_start: 0.7825 (t0) cc_final: 0.7332 (t0) REVERT: M 609 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.8025 (mttt) REVERT: N 99 ASP cc_start: 0.8248 (m-30) cc_final: 0.7884 (m-30) REVERT: N 121 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7892 (mtpp) outliers start: 81 outliers final: 33 residues processed: 403 average time/residue: 0.6244 time to fit residues: 294.6910 Evaluate side-chains 386 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 341 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 482 ASN Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 609 LYS Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 297 ARG Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain E residue 302 LYS Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain E residue 609 LYS Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 320 GLU Chi-restraints excluded: chain I residue 500 MET Chi-restraints excluded: chain I residue 522 SER Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 597 THR Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 161 SER Chi-restraints excluded: chain J residue 227 VAL Chi-restraints excluded: chain M residue 237 LEU Chi-restraints excluded: chain M residue 288 SER Chi-restraints excluded: chain M residue 388 LEU Chi-restraints excluded: chain M residue 506 LEU Chi-restraints excluded: chain M residue 571 THR Chi-restraints excluded: chain M residue 609 LYS Chi-restraints excluded: chain M residue 629 THR Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain N residue 121 LYS Chi-restraints excluded: chain N residue 268 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 100 optimal weight: 0.0770 chunk 84 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 333 optimal weight: 7.9990 chunk 293 optimal weight: 0.8980 chunk 15 optimal weight: 8.9990 chunk 260 optimal weight: 0.8980 chunk 298 optimal weight: 0.9990 chunk 300 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 128 GLN A 309 GLN A 525 ASN E 79 ASN E 147 HIS E 322 GLN E 525 ASN I 79 ASN M 79 ASN ** M 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 455 HIS N 256 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.161956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.134735 restraints weight = 30413.272| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.51 r_work: 0.3435 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 29788 Z= 0.123 Angle : 0.499 7.249 40508 Z= 0.261 Chirality : 0.045 0.145 4453 Planarity : 0.004 0.048 5231 Dihedral : 5.571 88.635 4006 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.18 % Favored : 97.71 % Rotamer: Outliers : 2.22 % Allowed : 14.93 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % 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 aren not related in a simple way. whole: -0.07 (0.14), residues: 3579 helix: 1.38 (0.19), residues: 804 sheet: -0.58 (0.15), residues: 1143 loop : -0.23 (0.16), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 593 TYR 0.014 0.001 TYR A 342 PHE 0.014 0.001 PHE F 119 TRP 0.014 0.001 TRP N 152 HIS 0.005 0.001 HIS F 325 Details of bonding type rmsd covalent geometry : bond 0.00293 (29788) covalent geometry : angle 0.49854 (40508) hydrogen bonds : bond 0.03144 ( 1049) hydrogen bonds : angle 4.73552 ( 2940) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 351 time to evaluate : 0.996 Fit side-chains revert: symmetry clash REVERT: A 101 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7795 (mtt180) REVERT: A 187 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7916 (mmt) REVERT: A 325 GLU cc_start: 0.7612 (tt0) cc_final: 0.7393 (tt0) REVERT: A 407 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7374 (mt-10) REVERT: A 609 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.7929 (mptt) REVERT: A 610 LYS cc_start: 0.8186 (mmtt) cc_final: 0.7461 (mtmt) REVERT: A 634 THR cc_start: 0.8444 (p) cc_final: 0.8041 (p) REVERT: B 232 ASP cc_start: 0.8923 (p0) cc_final: 0.8681 (p0) REVERT: B 239 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8436 (tt) REVERT: E 68 ARG cc_start: 0.9029 (OUTLIER) cc_final: 0.7202 (ptp-170) REVERT: E 302 LYS cc_start: 0.7539 (OUTLIER) cc_final: 0.7284 (mttm) REVERT: E 388 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.7945 (tt) REVERT: F 110 GLU cc_start: 0.6699 (tp30) cc_final: 0.6174 (tm-30) REVERT: F 114 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.7843 (mp) REVERT: F 234 ASN cc_start: 0.8732 (t0) cc_final: 0.8477 (t0) REVERT: I 25 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7850 (mm-30) REVERT: I 35 LYS cc_start: 0.7790 (mmtm) cc_final: 0.7261 (tmtt) REVERT: I 285 GLU cc_start: 0.7438 (mt-10) cc_final: 0.7123 (mt-10) REVERT: I 316 MET cc_start: 0.8456 (ttm) cc_final: 0.8242 (ttp) REVERT: I 326 VAL cc_start: 0.8131 (t) cc_final: 0.7854 (p) REVERT: I 407 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7878 (mt-10) REVERT: I 485 ARG cc_start: 0.7991 (mtm180) cc_final: 0.7770 (mtm180) REVERT: I 547 VAL cc_start: 0.7867 (OUTLIER) cc_final: 0.7493 (t) REVERT: M 290 ASN cc_start: 0.6985 (t0) cc_final: 0.6330 (t0) REVERT: M 383 ASP cc_start: 0.7858 (t0) cc_final: 0.7626 (t0) REVERT: M 609 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.7980 (mttt) REVERT: N 99 ASP cc_start: 0.8250 (m-30) cc_final: 0.7885 (m-30) outliers start: 71 outliers final: 32 residues processed: 397 average time/residue: 0.6317 time to fit residues: 293.0947 Evaluate side-chains 381 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 339 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 482 ASN Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 609 LYS Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 297 ARG Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain E residue 302 LYS Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain E residue 609 LYS Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain I residue 200 LYS Chi-restraints excluded: chain I residue 500 MET Chi-restraints excluded: chain I residue 522 SER Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 597 THR Chi-restraints excluded: chain J residue 161 SER Chi-restraints excluded: chain M residue 237 LEU Chi-restraints excluded: chain M residue 288 SER Chi-restraints excluded: chain M residue 388 LEU Chi-restraints excluded: chain M residue 506 LEU Chi-restraints excluded: chain M residue 571 THR Chi-restraints excluded: chain M residue 609 LYS Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain N residue 161 SER Chi-restraints excluded: chain N residue 268 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 291 optimal weight: 5.9990 chunk 163 optimal weight: 0.7980 chunk 308 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 350 optimal weight: 0.4980 chunk 293 optimal weight: 0.0030 chunk 342 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 138 optimal weight: 0.7980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 309 GLN A 394 ASN A 525 ASN E 79 ASN E 147 HIS E 239 ASN E 322 GLN E 507 HIS E 525 ASN I 79 ASN I 147 HIS M 507 HIS N 256 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.165022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.138197 restraints weight = 30513.724| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.50 r_work: 0.3479 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 29788 Z= 0.094 Angle : 0.468 7.041 40508 Z= 0.246 Chirality : 0.044 0.142 4453 Planarity : 0.003 0.046 5231 Dihedral : 5.259 87.684 4006 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.87 % Favored : 98.02 % Rotamer: Outliers : 1.91 % Allowed : 15.94 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % 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 aren not related in a simple way. whole: 0.10 (0.14), residues: 3579 helix: 1.58 (0.19), residues: 808 sheet: -0.51 (0.15), residues: 1145 loop : -0.13 (0.16), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 593 TYR 0.014 0.001 TYR A 342 PHE 0.012 0.001 PHE N 119 TRP 0.017 0.001 TRP N 152 HIS 0.004 0.001 HIS E 549 Details of bonding type rmsd covalent geometry : bond 0.00218 (29788) covalent geometry : angle 0.46840 (40508) hydrogen bonds : bond 0.02804 ( 1049) hydrogen bonds : angle 4.51876 ( 2940) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 361 time to evaluate : 0.763 Fit side-chains REVERT: A 101 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7837 (mtt180) REVERT: A 407 GLU cc_start: 0.7357 (mt-10) cc_final: 0.7095 (mm-30) REVERT: A 609 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.7908 (mptt) REVERT: A 610 LYS cc_start: 0.8131 (mmtt) cc_final: 0.7471 (mtmt) REVERT: B 190 ASN cc_start: 0.8284 (t0) cc_final: 0.8029 (t0) REVERT: B 232 ASP cc_start: 0.8897 (p0) cc_final: 0.8687 (p0) REVERT: E 68 ARG cc_start: 0.9009 (OUTLIER) cc_final: 0.7168 (ptp-170) REVERT: E 302 LYS cc_start: 0.7467 (OUTLIER) cc_final: 0.7217 (mttm) REVERT: F 114 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7977 (mp) REVERT: I 35 LYS cc_start: 0.7693 (mmtm) cc_final: 0.7165 (tmtt) REVERT: I 285 GLU cc_start: 0.7317 (mt-10) cc_final: 0.7016 (mt-10) REVERT: I 320 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7154 (tt0) REVERT: I 326 VAL cc_start: 0.8094 (t) cc_final: 0.7826 (p) REVERT: I 407 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7745 (mt-10) REVERT: I 547 VAL cc_start: 0.7793 (OUTLIER) cc_final: 0.7503 (t) REVERT: J 153 ASP cc_start: 0.7896 (t0) cc_final: 0.7678 (t0) REVERT: M 101 ARG cc_start: 0.8325 (mtt-85) cc_final: 0.7969 (mmm160) REVERT: M 290 ASN cc_start: 0.7045 (t0) cc_final: 0.6491 (t0) REVERT: M 355 ASP cc_start: 0.7196 (t70) cc_final: 0.6686 (p0) REVERT: M 383 ASP cc_start: 0.7766 (t0) cc_final: 0.7245 (t0) REVERT: M 385 ARG cc_start: 0.8380 (mtm180) cc_final: 0.8150 (mtm180) REVERT: M 609 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7986 (mttt) REVERT: N 35 ARG cc_start: 0.8098 (mmt90) cc_final: 0.7703 (mmt90) REVERT: N 99 ASP cc_start: 0.8243 (m-30) cc_final: 0.7832 (m-30) outliers start: 61 outliers final: 23 residues processed: 400 average time/residue: 0.6700 time to fit residues: 314.7464 Evaluate side-chains 369 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 338 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 609 LYS Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 297 ARG Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 302 LYS Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 320 GLU Chi-restraints excluded: chain I residue 522 SER Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 161 SER Chi-restraints excluded: chain M residue 237 LEU Chi-restraints excluded: chain M residue 288 SER Chi-restraints excluded: chain M residue 388 LEU Chi-restraints excluded: chain M residue 506 LEU Chi-restraints excluded: chain M residue 571 THR Chi-restraints excluded: chain M residue 609 LYS Chi-restraints excluded: chain M residue 635 ILE Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain N residue 268 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 334 optimal weight: 9.9990 chunk 256 optimal weight: 3.9990 chunk 184 optimal weight: 3.9990 chunk 276 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 181 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 344 optimal weight: 4.9990 chunk 303 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 250 optimal weight: 10.0000 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 309 GLN A 381 GLN A 525 ASN E 79 ASN E 147 HIS E 394 ASN E 525 ASN I 79 ASN ** M 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 394 ASN M 455 HIS M 482 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.161054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.133808 restraints weight = 30564.598| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.50 r_work: 0.3423 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 29788 Z= 0.157 Angle : 0.527 7.416 40508 Z= 0.275 Chirality : 0.046 0.171 4453 Planarity : 0.004 0.047 5231 Dihedral : 5.572 86.435 4006 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.43 % Favored : 97.46 % Rotamer: Outliers : 1.91 % Allowed : 16.41 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % 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 aren not related in a simple way. whole: 0.02 (0.14), residues: 3579 helix: 1.45 (0.19), residues: 805 sheet: -0.53 (0.15), residues: 1130 loop : -0.18 (0.16), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 593 TYR 0.023 0.001 TYR M 481 PHE 0.016 0.002 PHE F 119 TRP 0.011 0.001 TRP I 186 HIS 0.005 0.001 HIS F 325 Details of bonding type rmsd covalent geometry : bond 0.00379 (29788) covalent geometry : angle 0.52743 (40508) hydrogen bonds : bond 0.03360 ( 1049) hydrogen bonds : angle 4.73877 ( 2940) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 339 time to evaluate : 1.200 Fit side-chains REVERT: A 25 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7797 (tp30) REVERT: A 101 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7838 (mtt180) REVERT: A 187 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7895 (mmt) REVERT: A 407 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7067 (mm-30) REVERT: A 609 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.7897 (mptt) REVERT: A 610 LYS cc_start: 0.8187 (mmtt) cc_final: 0.7473 (mtmt) REVERT: A 634 THR cc_start: 0.8465 (OUTLIER) cc_final: 0.8075 (p) REVERT: E 68 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.7276 (ptp-170) REVERT: E 317 ASP cc_start: 0.7579 (OUTLIER) cc_final: 0.7049 (m-30) REVERT: E 388 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.7981 (tt) REVERT: F 110 GLU cc_start: 0.6767 (tp30) cc_final: 0.6168 (tm-30) REVERT: F 114 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.7847 (mp) REVERT: F 294 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8491 (mt0) REVERT: F 297 ARG cc_start: 0.8112 (mtm110) cc_final: 0.7886 (mtm-85) REVERT: I 35 LYS cc_start: 0.7805 (mmtm) cc_final: 0.7295 (tmtt) REVERT: I 285 GLU cc_start: 0.7472 (mt-10) cc_final: 0.7185 (mt-10) REVERT: I 326 VAL cc_start: 0.8173 (t) cc_final: 0.7895 (p) REVERT: I 407 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7882 (mt-10) REVERT: I 547 VAL cc_start: 0.7899 (OUTLIER) cc_final: 0.7526 (t) REVERT: J 153 ASP cc_start: 0.7952 (t0) cc_final: 0.7714 (t0) REVERT: M 290 ASN cc_start: 0.7099 (t0) cc_final: 0.6528 (t0) REVERT: M 383 ASP cc_start: 0.7843 (t0) cc_final: 0.7579 (t0) REVERT: M 520 THR cc_start: 0.9100 (OUTLIER) cc_final: 0.8802 (m) REVERT: M 609 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8036 (mttt) REVERT: N 99 ASP cc_start: 0.8321 (m-30) cc_final: 0.7929 (m-30) outliers start: 61 outliers final: 32 residues processed: 377 average time/residue: 0.7405 time to fit residues: 325.1865 Evaluate side-chains 376 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 331 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 147 HIS Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 482 ASN Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 609 LYS Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 297 ARG Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain E residue 609 LYS Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 294 GLN Chi-restraints excluded: chain F residue 312 LEU Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 500 MET Chi-restraints excluded: chain I residue 522 SER Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 597 THR Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 161 SER Chi-restraints excluded: chain M residue 237 LEU Chi-restraints excluded: chain M residue 288 SER Chi-restraints excluded: chain M residue 388 LEU Chi-restraints excluded: chain M residue 506 LEU Chi-restraints excluded: chain M residue 520 THR Chi-restraints excluded: chain M residue 571 THR Chi-restraints excluded: chain M residue 609 LYS Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain N residue 268 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 47 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 323 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 233 optimal weight: 0.9990 chunk 158 optimal weight: 2.9990 chunk 194 optimal weight: 0.9990 chunk 350 optimal weight: 6.9990 chunk 101 optimal weight: 0.8980 chunk 237 optimal weight: 3.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 309 GLN A 525 ASN E 79 ASN E 147 HIS E 239 ASN E 525 ASN I 79 ASN ** M 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 455 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.163235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.136279 restraints weight = 30387.767| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.49 r_work: 0.3456 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 29788 Z= 0.110 Angle : 0.490 8.007 40508 Z= 0.257 Chirality : 0.044 0.162 4453 Planarity : 0.004 0.048 5231 Dihedral : 5.364 86.075 4006 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.10 % Favored : 97.79 % Rotamer: Outliers : 1.85 % Allowed : 16.84 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % 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 aren not related in a simple way. whole: 0.06 (0.14), residues: 3579 helix: 1.46 (0.19), residues: 820 sheet: -0.50 (0.15), residues: 1139 loop : -0.16 (0.16), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 593 TYR 0.017 0.001 TYR A 342 PHE 0.013 0.001 PHE F 119 TRP 0.015 0.001 TRP F 152 HIS 0.004 0.001 HIS E 549 Details of bonding type rmsd covalent geometry : bond 0.00265 (29788) covalent geometry : angle 0.49011 (40508) hydrogen bonds : bond 0.02967 ( 1049) hydrogen bonds : angle 4.59826 ( 2940) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 338 time to evaluate : 1.175 Fit side-chains REVERT: A 25 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7745 (tp30) REVERT: A 56 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8209 (tt0) REVERT: A 101 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7816 (mtt180) REVERT: A 146 HIS cc_start: 0.7042 (t-90) cc_final: 0.6729 (m90) REVERT: A 187 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.7119 (mmt) REVERT: A 384 ARG cc_start: 0.7724 (mmt-90) cc_final: 0.7470 (mmt-90) REVERT: A 407 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7049 (mm-30) REVERT: A 495 GLU cc_start: 0.8480 (mt-10) cc_final: 0.7899 (mt-10) REVERT: A 609 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.7900 (mptt) REVERT: A 610 LYS cc_start: 0.8139 (mmtt) cc_final: 0.7446 (mtmt) REVERT: A 634 THR cc_start: 0.8380 (OUTLIER) cc_final: 0.7945 (p) REVERT: B 190 ASN cc_start: 0.8350 (t0) cc_final: 0.8121 (t0) REVERT: B 232 ASP cc_start: 0.8974 (p0) cc_final: 0.8769 (p0) REVERT: E 68 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.7188 (ptp-170) REVERT: E 302 LYS cc_start: 0.7463 (OUTLIER) cc_final: 0.7213 (mttm) REVERT: E 317 ASP cc_start: 0.7610 (OUTLIER) cc_final: 0.7048 (m-30) REVERT: E 388 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.7986 (tt) REVERT: F 114 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.7993 (mp) REVERT: I 35 LYS cc_start: 0.7771 (mmtm) cc_final: 0.7269 (tmtt) REVERT: I 285 GLU cc_start: 0.7415 (mt-10) cc_final: 0.7160 (mt-10) REVERT: I 320 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.7157 (tt0) REVERT: I 326 VAL cc_start: 0.8136 (t) cc_final: 0.7872 (p) REVERT: I 547 VAL cc_start: 0.7839 (OUTLIER) cc_final: 0.7496 (t) REVERT: J 153 ASP cc_start: 0.7892 (t0) cc_final: 0.7662 (t0) REVERT: M 290 ASN cc_start: 0.6994 (t0) cc_final: 0.6489 (t0) REVERT: M 355 ASP cc_start: 0.7186 (t70) cc_final: 0.6682 (p0) REVERT: M 383 ASP cc_start: 0.7884 (t0) cc_final: 0.7607 (t0) REVERT: M 385 ARG cc_start: 0.8390 (mtm180) cc_final: 0.8165 (mtm180) REVERT: M 520 THR cc_start: 0.9004 (OUTLIER) cc_final: 0.8670 (m) REVERT: M 609 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7965 (mttt) REVERT: N 99 ASP cc_start: 0.8263 (m-30) cc_final: 0.7860 (m-30) outliers start: 59 outliers final: 29 residues processed: 374 average time/residue: 0.7213 time to fit residues: 318.5606 Evaluate side-chains 379 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 335 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 147 HIS Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 482 ASN Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 609 LYS Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 297 ARG Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain E residue 302 LYS Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain E residue 609 LYS Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 320 GLU Chi-restraints excluded: chain I residue 522 SER Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 161 SER Chi-restraints excluded: chain M residue 237 LEU Chi-restraints excluded: chain M residue 288 SER Chi-restraints excluded: chain M residue 388 LEU Chi-restraints excluded: chain M residue 506 LEU Chi-restraints excluded: chain M residue 520 THR Chi-restraints excluded: chain M residue 571 THR Chi-restraints excluded: chain M residue 609 LYS Chi-restraints excluded: chain M residue 635 ILE Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain N residue 268 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 12 optimal weight: 1.9990 chunk 167 optimal weight: 10.0000 chunk 336 optimal weight: 4.9990 chunk 306 optimal weight: 3.9990 chunk 198 optimal weight: 0.0670 chunk 276 optimal weight: 0.9980 chunk 83 optimal weight: 8.9990 chunk 297 optimal weight: 8.9990 chunk 113 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 309 GLN A 507 HIS A 525 ASN E 79 ASN E 147 HIS E 525 ASN I 79 ASN ** M 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 394 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.161734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.134666 restraints weight = 30336.493| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.49 r_work: 0.3436 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 29788 Z= 0.138 Angle : 0.515 7.364 40508 Z= 0.269 Chirality : 0.045 0.167 4453 Planarity : 0.004 0.048 5231 Dihedral : 5.482 85.619 4006 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.29 % Favored : 97.60 % Rotamer: Outliers : 1.72 % Allowed : 16.97 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % 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 aren not related in a simple way. whole: -0.01 (0.14), residues: 3579 helix: 1.37 (0.19), residues: 821 sheet: -0.53 (0.15), residues: 1141 loop : -0.17 (0.16), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 593 TYR 0.018 0.001 TYR A 342 PHE 0.015 0.001 PHE F 119 TRP 0.012 0.001 TRP F 152 HIS 0.006 0.001 HIS M 455 Details of bonding type rmsd covalent geometry : bond 0.00333 (29788) covalent geometry : angle 0.51502 (40508) hydrogen bonds : bond 0.03196 ( 1049) hydrogen bonds : angle 4.69522 ( 2940) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 338 time to evaluate : 1.189 Fit side-chains REVERT: A 25 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7760 (tp30) REVERT: A 101 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7821 (mtt180) REVERT: A 146 HIS cc_start: 0.7054 (t-90) cc_final: 0.6731 (m90) REVERT: A 187 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7888 (mmt) REVERT: A 384 ARG cc_start: 0.7771 (mmt-90) cc_final: 0.7542 (mmt-90) REVERT: A 407 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7069 (mm-30) REVERT: A 495 GLU cc_start: 0.8509 (mt-10) cc_final: 0.7921 (mt-10) REVERT: A 609 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.7891 (mptt) REVERT: A 610 LYS cc_start: 0.8170 (mmtt) cc_final: 0.7464 (mtmt) REVERT: A 634 THR cc_start: 0.8442 (OUTLIER) cc_final: 0.8023 (p) REVERT: E 68 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.7236 (ptp-170) REVERT: E 302 LYS cc_start: 0.7523 (OUTLIER) cc_final: 0.7260 (mttm) REVERT: E 316 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7881 (ptm) REVERT: E 388 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.7992 (tt) REVERT: F 110 GLU cc_start: 0.6733 (tp30) cc_final: 0.6183 (tm-30) REVERT: F 114 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.7882 (mp) REVERT: I 35 LYS cc_start: 0.7800 (mmtm) cc_final: 0.7300 (tmtt) REVERT: I 285 GLU cc_start: 0.7456 (mt-10) cc_final: 0.7228 (mt-10) REVERT: I 320 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7223 (tt0) REVERT: I 326 VAL cc_start: 0.8173 (t) cc_final: 0.7898 (p) REVERT: I 547 VAL cc_start: 0.7889 (OUTLIER) cc_final: 0.7516 (t) REVERT: J 92 ARG cc_start: 0.7736 (mtt-85) cc_final: 0.7496 (mtt-85) REVERT: J 153 ASP cc_start: 0.7891 (t0) cc_final: 0.7638 (t0) REVERT: M 290 ASN cc_start: 0.7011 (t0) cc_final: 0.6504 (t0) REVERT: M 383 ASP cc_start: 0.7894 (t0) cc_final: 0.7618 (t0) REVERT: M 520 THR cc_start: 0.9075 (OUTLIER) cc_final: 0.8769 (m) REVERT: M 576 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7374 (ttt) REVERT: M 609 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.8002 (mttt) REVERT: N 35 ARG cc_start: 0.8124 (mmt90) cc_final: 0.7796 (mmm-85) REVERT: N 99 ASP cc_start: 0.8311 (m-30) cc_final: 0.7921 (m-30) outliers start: 55 outliers final: 31 residues processed: 368 average time/residue: 0.6415 time to fit residues: 275.6647 Evaluate side-chains 377 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 331 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 147 HIS Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 482 ASN Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 609 LYS Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 297 ARG Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain E residue 302 LYS Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain E residue 609 LYS Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 320 GLU Chi-restraints excluded: chain I residue 522 SER Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 161 SER Chi-restraints excluded: chain M residue 237 LEU Chi-restraints excluded: chain M residue 288 SER Chi-restraints excluded: chain M residue 388 LEU Chi-restraints excluded: chain M residue 506 LEU Chi-restraints excluded: chain M residue 520 THR Chi-restraints excluded: chain M residue 571 THR Chi-restraints excluded: chain M residue 576 MET Chi-restraints excluded: chain M residue 609 LYS Chi-restraints excluded: chain M residue 635 ILE Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain N residue 268 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 315 optimal weight: 0.9980 chunk 223 optimal weight: 0.4980 chunk 119 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 253 optimal weight: 7.9990 chunk 242 optimal weight: 10.0000 chunk 330 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 147 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 272 HIS A 309 GLN A 525 ASN E 79 ASN E 147 HIS E 525 ASN I 79 ASN ** M 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 455 HIS M 507 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.164063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.137054 restraints weight = 30541.839| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.50 r_work: 0.3465 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.095 29788 Z= 0.103 Angle : 0.483 7.150 40508 Z= 0.254 Chirality : 0.044 0.158 4453 Planarity : 0.004 0.051 5231 Dihedral : 5.265 84.855 4006 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.84 % Favored : 98.04 % Rotamer: Outliers : 1.78 % Allowed : 17.06 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % 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 aren not related in a simple way. whole: 0.11 (0.14), residues: 3579 helix: 1.55 (0.19), residues: 820 sheet: -0.50 (0.15), residues: 1132 loop : -0.12 (0.16), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 593 TYR 0.021 0.001 TYR A 481 PHE 0.012 0.001 PHE F 183 TRP 0.016 0.001 TRP F 152 HIS 0.004 0.001 HIS E 549 Details of bonding type rmsd covalent geometry : bond 0.00246 (29788) covalent geometry : angle 0.48272 (40508) hydrogen bonds : bond 0.02881 ( 1049) hydrogen bonds : angle 4.53917 ( 2940) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9740.36 seconds wall clock time: 166 minutes 58.17 seconds (10018.17 seconds total)