Starting phenix.real_space_refine on Thu Sep 18 16:13:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yef_39193/09_2025/8yef_39193.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yef_39193/09_2025/8yef_39193.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yef_39193/09_2025/8yef_39193.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yef_39193/09_2025/8yef_39193.map" model { file = "/net/cci-nas-00/data/ceres_data/8yef_39193/09_2025/8yef_39193.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yef_39193/09_2025/8yef_39193.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.049 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 102 5.16 5 C 11476 2.51 5 N 3041 2.21 5 O 3455 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18074 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 951 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "B" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 833 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "C" Number of atoms: 3258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3258 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 25, 'TRANS': 390} Chain breaks: 1 Chain: "H" Number of atoms: 3258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3258 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 25, 'TRANS': 390} Chain breaks: 1 Chain: "I" Number of atoms: 3258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3258 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 25, 'TRANS': 390} Chain breaks: 1 Chain: "J" Number of atoms: 3258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3258 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 25, 'TRANS': 390} Chain breaks: 1 Chain: "K" Number of atoms: 3258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3258 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 25, 'TRANS': 390} Chain breaks: 1 Time building chain proxies: 4.66, per 1000 atoms: 0.26 Number of scatterers: 18074 At special positions: 0 Unit cell: (125.84, 125.84, 139.36, 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 102 16.00 O 3455 8.00 N 3041 7.00 C 11476 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 782.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4238 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 44 sheets defined 14.0% alpha, 34.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.878A pdb=" N THR A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.528A pdb=" N PHE B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 18 removed outlier: 3.641A pdb=" N ALA C 18 " --> pdb=" O ALA C 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 15 through 18' Processing helix chain 'C' and resid 198 through 203 Processing helix chain 'C' and resid 210 through 215 removed outlier: 4.242A pdb=" N GLY C 215 " --> pdb=" O ILE C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 227 Processing helix chain 'C' and resid 313 through 315 No H-bonds generated for 'chain 'C' and resid 313 through 315' Processing helix chain 'C' and resid 344 through 346 No H-bonds generated for 'chain 'C' and resid 344 through 346' Processing helix chain 'C' and resid 372 through 383 Processing helix chain 'C' and resid 383 through 391 removed outlier: 4.027A pdb=" N LEU C 387 " --> pdb=" O ASN C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 431 removed outlier: 3.636A pdb=" N LYS C 430 " --> pdb=" O ASP C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 459 removed outlier: 4.336A pdb=" N GLN C 459 " --> pdb=" O LYS C 455 " (cutoff:3.500A) Processing helix chain 'H' and resid 15 through 18 Processing helix chain 'H' and resid 198 through 203 Processing helix chain 'H' and resid 222 through 229 Processing helix chain 'H' and resid 344 through 347 Processing helix chain 'H' and resid 372 through 383 Processing helix chain 'H' and resid 384 through 391 removed outlier: 3.842A pdb=" N ASN H 391 " --> pdb=" O LEU H 387 " (cutoff:3.500A) Processing helix chain 'H' and resid 427 through 431 Processing helix chain 'H' and resid 446 through 449 removed outlier: 3.538A pdb=" N GLN H 449 " --> pdb=" O GLU H 446 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 446 through 449' Processing helix chain 'H' and resid 450 through 459 removed outlier: 3.561A pdb=" N ARG H 454 " --> pdb=" O TYR H 450 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS H 455 " --> pdb=" O PRO H 451 " (cutoff:3.500A) Processing helix chain 'I' and resid 15 through 18 Processing helix chain 'I' and resid 198 through 203 Processing helix chain 'I' and resid 222 through 228 Processing helix chain 'I' and resid 313 through 315 No H-bonds generated for 'chain 'I' and resid 313 through 315' Processing helix chain 'I' and resid 372 through 383 Processing helix chain 'I' and resid 383 through 391 removed outlier: 3.983A pdb=" N LEU I 387 " --> pdb=" O ASN I 383 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN I 391 " --> pdb=" O LEU I 387 " (cutoff:3.500A) Processing helix chain 'I' and resid 427 through 431 removed outlier: 3.745A pdb=" N ASN I 431 " --> pdb=" O PRO I 428 " (cutoff:3.500A) Processing helix chain 'I' and resid 446 through 449 removed outlier: 3.643A pdb=" N GLN I 449 " --> pdb=" O GLU I 446 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 446 through 449' Processing helix chain 'I' and resid 450 through 459 removed outlier: 3.690A pdb=" N GLN I 459 " --> pdb=" O LYS I 455 " (cutoff:3.500A) Processing helix chain 'J' and resid 15 through 18 Processing helix chain 'J' and resid 210 through 215 removed outlier: 4.531A pdb=" N GLY J 215 " --> pdb=" O ILE J 211 " (cutoff:3.500A) Processing helix chain 'J' and resid 222 through 228 Processing helix chain 'J' and resid 313 through 315 No H-bonds generated for 'chain 'J' and resid 313 through 315' Processing helix chain 'J' and resid 372 through 383 Processing helix chain 'J' and resid 383 through 391 removed outlier: 4.084A pdb=" N LEU J 387 " --> pdb=" O ASN J 383 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN J 391 " --> pdb=" O LEU J 387 " (cutoff:3.500A) Processing helix chain 'J' and resid 427 through 431 removed outlier: 3.501A pdb=" N LYS J 430 " --> pdb=" O ASP J 427 " (cutoff:3.500A) Processing helix chain 'J' and resid 446 through 449 Processing helix chain 'J' and resid 450 through 459 removed outlier: 3.835A pdb=" N GLN J 459 " --> pdb=" O LYS J 455 " (cutoff:3.500A) Processing helix chain 'K' and resid 15 through 19 Processing helix chain 'K' and resid 198 through 203 Processing helix chain 'K' and resid 210 through 214 Processing helix chain 'K' and resid 222 through 228 Processing helix chain 'K' and resid 313 through 315 No H-bonds generated for 'chain 'K' and resid 313 through 315' Processing helix chain 'K' and resid 344 through 346 No H-bonds generated for 'chain 'K' and resid 344 through 346' Processing helix chain 'K' and resid 372 through 383 Processing helix chain 'K' and resid 383 through 391 removed outlier: 4.055A pdb=" N LEU K 387 " --> pdb=" O ASN K 383 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN K 391 " --> pdb=" O LEU K 387 " (cutoff:3.500A) Processing helix chain 'K' and resid 427 through 431 removed outlier: 3.538A pdb=" N LYS K 430 " --> pdb=" O ASP K 427 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASN K 431 " --> pdb=" O PRO K 428 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 427 through 431' Processing helix chain 'K' and resid 446 through 449 Processing helix chain 'K' and resid 450 through 459 removed outlier: 4.018A pdb=" N GLN K 459 " --> pdb=" O LYS K 455 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.450A pdb=" N GLU A 10 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG A 99 " --> pdb=" O TYR A 33 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N TYR A 33 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.450A pdb=" N GLU A 10 " --> pdb=" O THR A 117 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 13 removed outlier: 4.055A pdb=" N ILE B 48 " --> pdb=" O TRP B 35 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLN B 37 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE B 46 " --> pdb=" O GLN B 37 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.949A pdb=" N GLN B 90 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR B 97 " --> pdb=" O GLN B 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 300 through 301 removed outlier: 6.816A pdb=" N ILE C 363 " --> pdb=" O THR C 93 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LEU C 95 " --> pdb=" O GLN C 361 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN C 361 " --> pdb=" O LEU C 95 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ILE C 25 " --> pdb=" O LEU C 366 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N SER C 368 " --> pdb=" O THR C 23 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N THR C 23 " --> pdb=" O SER C 368 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N THR C 370 " --> pdb=" O THR C 21 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N THR C 21 " --> pdb=" O THR C 370 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 34 through 38 Processing sheet with id=AA9, first strand: chain 'C' and resid 280 through 285 removed outlier: 7.194A pdb=" N VAL C 281 " --> pdb=" O PHE C 249 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N PHE C 249 " --> pdb=" O VAL C 281 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N THR C 283 " --> pdb=" O ARG C 247 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE C 237 " --> pdb=" O VAL C 148 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL C 62 " --> pdb=" O TRP C 435 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL C 437 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N LYS C 64 " --> pdb=" O VAL C 437 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 280 through 285 removed outlier: 7.194A pdb=" N VAL C 281 " --> pdb=" O PHE C 249 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N PHE C 249 " --> pdb=" O VAL C 281 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N THR C 283 " --> pdb=" O ARG C 247 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 108 through 113 removed outlier: 4.232A pdb=" N GLY C 109 " --> pdb=" O MET C 138 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N MET C 138 " --> pdb=" O GLY C 109 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N VAL C 136 " --> pdb=" O PRO C 111 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 178 through 183 removed outlier: 3.537A pdb=" N TYR C 220 " --> pdb=" O GLU C 156 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N TRP C 158 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N CYS C 218 " --> pdb=" O TRP C 158 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N MET C 189 " --> pdb=" O LYS C 219 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 255 through 256 removed outlier: 6.881A pdb=" N GLU C 255 " --> pdb=" O GLU I 350 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N MET I 352 " --> pdb=" O GLU C 255 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 255 through 256 removed outlier: 6.881A pdb=" N GLU C 255 " --> pdb=" O GLU I 350 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N MET I 352 " --> pdb=" O GLU C 255 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 289 through 290 removed outlier: 3.534A pdb=" N MET H 244 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N THR H 283 " --> pdb=" O ARG H 247 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N PHE H 249 " --> pdb=" O VAL H 281 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL H 281 " --> pdb=" O PHE H 249 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 117 through 118 removed outlier: 4.112A pdb=" N ASP H 117 " --> pdb=" O ASN H 251 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N PHE H 237 " --> pdb=" O VAL H 148 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL H 148 " --> pdb=" O PHE H 237 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N VAL H 62 " --> pdb=" O TRP H 435 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL H 437 " --> pdb=" O VAL H 62 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LYS H 64 " --> pdb=" O VAL H 437 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 20 through 30 removed outlier: 7.119A pdb=" N THR H 23 " --> pdb=" O SER H 368 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N SER H 368 " --> pdb=" O THR H 23 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ILE H 25 " --> pdb=" O LEU H 366 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE H 363 " --> pdb=" O THR H 93 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 34 through 38 Processing sheet with id=AC1, first strand: chain 'H' and resid 34 through 38 Processing sheet with id=AC2, first strand: chain 'H' and resid 44 through 46 removed outlier: 7.760A pdb=" N ILE H 44 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL H 51 " --> pdb=" O ILE H 44 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 108 through 113 removed outlier: 3.737A pdb=" N PHE H 112 " --> pdb=" O VAL H 134 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N VAL H 134 " --> pdb=" O PHE H 112 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 177 through 183 Processing sheet with id=AC5, first strand: chain 'H' and resid 289 through 290 removed outlier: 3.512A pdb=" N MET J 244 " --> pdb=" O VAL H 289 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR J 283 " --> pdb=" O ARG J 247 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N PHE J 249 " --> pdb=" O VAL J 281 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL J 281 " --> pdb=" O PHE J 249 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 117 through 118 removed outlier: 4.504A pdb=" N ASP J 117 " --> pdb=" O ASN J 251 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN J 251 " --> pdb=" O ASP J 117 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N PHE J 237 " --> pdb=" O VAL J 148 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL J 148 " --> pdb=" O PHE J 237 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL J 62 " --> pdb=" O TRP J 435 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N VAL J 437 " --> pdb=" O VAL J 62 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LYS J 64 " --> pdb=" O VAL J 437 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 20 through 30 removed outlier: 5.062A pdb=" N LEU I 366 " --> pdb=" O THR I 23 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE I 25 " --> pdb=" O PHE I 364 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N PHE I 364 " --> pdb=" O ILE I 25 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N TYR I 27 " --> pdb=" O PHE I 362 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N PHE I 362 " --> pdb=" O TYR I 27 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA I 29 " --> pdb=" O LEU I 360 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU I 360 " --> pdb=" O ALA I 29 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLN I 361 " --> pdb=" O LEU I 95 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU I 95 " --> pdb=" O GLN I 361 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE I 363 " --> pdb=" O THR I 93 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 44 through 45 removed outlier: 7.116A pdb=" N ILE I 44 " --> pdb=" O VAL I 51 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL I 51 " --> pdb=" O ILE I 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'I' and resid 237 through 243 removed outlier: 4.139A pdb=" N PHE I 237 " --> pdb=" O VAL I 148 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL I 148 " --> pdb=" O PHE I 237 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL I 62 " --> pdb=" O TRP I 435 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL I 437 " --> pdb=" O VAL I 62 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N LYS I 64 " --> pdb=" O VAL I 437 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 107 through 113 removed outlier: 4.720A pdb=" N GLY I 109 " --> pdb=" O MET I 138 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N MET I 138 " --> pdb=" O GLY I 109 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N VAL I 136 " --> pdb=" O PRO I 111 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 117 through 118 removed outlier: 4.092A pdb=" N ASP I 117 " --> pdb=" O ASN I 251 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ALA I 246 " --> pdb=" O SER I 285 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N SER I 285 " --> pdb=" O ALA I 246 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N HIS I 248 " --> pdb=" O THR I 283 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 177 through 183 Processing sheet with id=AD4, first strand: chain 'I' and resid 255 through 256 removed outlier: 6.764A pdb=" N GLU I 255 " --> pdb=" O GLU K 350 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N MET K 352 " --> pdb=" O GLU I 255 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 20 through 30 removed outlier: 8.422A pdb=" N THR J 21 " --> pdb=" O THR J 370 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N THR J 370 " --> pdb=" O THR J 21 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N THR J 23 " --> pdb=" O SER J 368 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N SER J 368 " --> pdb=" O THR J 23 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ILE J 25 " --> pdb=" O LEU J 366 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLN J 361 " --> pdb=" O LEU J 95 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LEU J 95 " --> pdb=" O GLN J 361 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE J 363 " --> pdb=" O THR J 93 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG J 87 " --> pdb=" O ILE J 369 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 34 through 38 Processing sheet with id=AD7, first strand: chain 'J' and resid 34 through 38 removed outlier: 3.881A pdb=" N GLU K 255 " --> pdb=" O TYR J 348 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 44 through 45 removed outlier: 3.769A pdb=" N VAL J 52 " --> pdb=" O ILE J 44 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 108 through 113 removed outlier: 4.421A pdb=" N GLY J 109 " --> pdb=" O MET J 138 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N MET J 138 " --> pdb=" O GLY J 109 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N VAL J 136 " --> pdb=" O PRO J 111 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 154 through 159 Processing sheet with id=AE2, first strand: chain 'J' and resid 289 through 290 removed outlier: 5.551A pdb=" N ALA K 246 " --> pdb=" O SER K 285 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N SER K 285 " --> pdb=" O ALA K 246 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N HIS K 248 " --> pdb=" O THR K 283 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 115 through 118 removed outlier: 6.616A pdb=" N ASN K 251 " --> pdb=" O TYR K 116 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ASP K 118 " --> pdb=" O PHE K 249 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N PHE K 249 " --> pdb=" O ASP K 118 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL K 62 " --> pdb=" O TRP K 435 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL K 437 " --> pdb=" O VAL K 62 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LYS K 64 " --> pdb=" O VAL K 437 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 21 through 30 removed outlier: 8.710A pdb=" N THR K 21 " --> pdb=" O THR K 370 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N THR K 370 " --> pdb=" O THR K 21 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR K 23 " --> pdb=" O SER K 368 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N SER K 368 " --> pdb=" O THR K 23 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ILE K 25 " --> pdb=" O LEU K 366 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU K 366 " --> pdb=" O ILE K 25 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLN K 361 " --> pdb=" O LEU K 95 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU K 95 " --> pdb=" O GLN K 361 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE K 363 " --> pdb=" O THR K 93 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL K 89 " --> pdb=" O CYS K 367 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE K 369 " --> pdb=" O ARG K 87 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG K 87 " --> pdb=" O ILE K 369 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 34 through 37 Processing sheet with id=AE6, first strand: chain 'K' and resid 44 through 46 removed outlier: 7.431A pdb=" N ILE K 44 " --> pdb=" O VAL K 51 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL K 51 " --> pdb=" O ILE K 44 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 108 through 113 removed outlier: 4.197A pdb=" N PHE K 112 " --> pdb=" O VAL K 134 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N VAL K 134 " --> pdb=" O PHE K 112 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 154 through 160 500 hydrogen bonds defined for protein. 1284 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: 3.97 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5793 1.34 - 1.46: 4316 1.46 - 1.58: 8281 1.58 - 1.70: 0 1.70 - 1.82: 150 Bond restraints: 18540 Sorted by residual: bond pdb=" CB ASN J 121 " pdb=" CG ASN J 121 " ideal model delta sigma weight residual 1.516 1.566 -0.050 2.50e-02 1.60e+03 3.93e+00 bond pdb=" CA ASN J 166 " pdb=" CB ASN J 166 " ideal model delta sigma weight residual 1.530 1.557 -0.027 1.69e-02 3.50e+03 2.51e+00 bond pdb=" CB GLU C 242 " pdb=" CG GLU C 242 " ideal model delta sigma weight residual 1.520 1.566 -0.046 3.00e-02 1.11e+03 2.30e+00 bond pdb=" CA ASN J 121 " pdb=" CB ASN J 121 " ideal model delta sigma weight residual 1.533 1.557 -0.023 1.66e-02 3.63e+03 1.99e+00 bond pdb=" CB GLN C 142 " pdb=" CG GLN C 142 " ideal model delta sigma weight residual 1.520 1.478 0.042 3.00e-02 1.11e+03 1.98e+00 ... (remaining 18535 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 24552 2.59 - 5.18: 570 5.18 - 7.77: 69 7.77 - 10.36: 14 10.36 - 12.95: 4 Bond angle restraints: 25209 Sorted by residual: angle pdb=" C THR J 165 " pdb=" N ASN J 166 " pdb=" CA ASN J 166 " ideal model delta sigma weight residual 121.54 130.19 -8.65 1.91e+00 2.74e-01 2.05e+01 angle pdb=" C TRP J 390 " pdb=" N ASN J 391 " pdb=" CA ASN J 391 " ideal model delta sigma weight residual 122.82 129.21 -6.39 1.42e+00 4.96e-01 2.03e+01 angle pdb=" CB MET H 352 " pdb=" CG MET H 352 " pdb=" SD MET H 352 " ideal model delta sigma weight residual 112.70 99.75 12.95 3.00e+00 1.11e-01 1.86e+01 angle pdb=" CB LYS H 304 " pdb=" CG LYS H 304 " pdb=" CD LYS H 304 " ideal model delta sigma weight residual 111.30 121.22 -9.92 2.30e+00 1.89e-01 1.86e+01 angle pdb=" C ALA J 47 " pdb=" N ASN J 48 " pdb=" CA ASN J 48 " ideal model delta sigma weight residual 121.54 129.67 -8.13 1.91e+00 2.74e-01 1.81e+01 ... (remaining 25204 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 9911 17.83 - 35.65: 847 35.65 - 53.48: 124 53.48 - 71.31: 35 71.31 - 89.14: 18 Dihedral angle restraints: 10935 sinusoidal: 4291 harmonic: 6644 Sorted by residual: dihedral pdb=" CB CYS B 23 " pdb=" SG CYS B 23 " pdb=" SG CYS B 88 " pdb=" CB CYS B 88 " ideal model delta sinusoidal sigma weight residual 93.00 149.62 -56.62 1 1.00e+01 1.00e-02 4.32e+01 dihedral pdb=" CB CYS A 22 " pdb=" SG CYS A 22 " pdb=" SG CYS A 96 " pdb=" CB CYS A 96 " ideal model delta sinusoidal sigma weight residual 93.00 144.05 -51.05 1 1.00e+01 1.00e-02 3.57e+01 dihedral pdb=" CA GLN C 243 " pdb=" C GLN C 243 " pdb=" N MET C 244 " pdb=" CA MET C 244 " ideal model delta harmonic sigma weight residual -180.00 -152.69 -27.31 0 5.00e+00 4.00e-02 2.98e+01 ... (remaining 10932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2087 0.061 - 0.121: 555 0.121 - 0.182: 82 0.182 - 0.243: 8 0.243 - 0.304: 5 Chirality restraints: 2737 Sorted by residual: chirality pdb=" CA TYR J 116 " pdb=" N TYR J 116 " pdb=" C TYR J 116 " pdb=" CB TYR J 116 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CB THR J 50 " pdb=" CA THR J 50 " pdb=" OG1 THR J 50 " pdb=" CG2 THR J 50 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CB THR K 50 " pdb=" CA THR K 50 " pdb=" OG1 THR K 50 " pdb=" CG2 THR K 50 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 2734 not shown) Planarity restraints: 3281 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP J 390 " 0.034 2.00e-02 2.50e+03 3.82e-02 3.64e+01 pdb=" CG TRP J 390 " -0.099 2.00e-02 2.50e+03 pdb=" CD1 TRP J 390 " 0.057 2.00e-02 2.50e+03 pdb=" CD2 TRP J 390 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP J 390 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP J 390 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP J 390 " 0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 390 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 390 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP J 390 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP I 390 " 0.026 2.00e-02 2.50e+03 2.78e-02 1.93e+01 pdb=" CG TRP I 390 " -0.075 2.00e-02 2.50e+03 pdb=" CD1 TRP I 390 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP I 390 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP I 390 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP I 390 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP I 390 " 0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 390 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 390 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP I 390 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 390 " 0.024 2.00e-02 2.50e+03 2.50e-02 1.56e+01 pdb=" CG TRP C 390 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 TRP C 390 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP C 390 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 390 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 390 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 390 " 0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 390 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 390 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 390 " 0.001 2.00e-02 2.50e+03 ... (remaining 3278 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 3236 2.77 - 3.30: 17777 3.30 - 3.83: 31794 3.83 - 4.37: 36002 4.37 - 4.90: 60404 Nonbonded interactions: 149213 Sorted by model distance: nonbonded pdb=" OE1 GLN K 142 " pdb=" OG1 THR K 325 " model vdw 2.234 3.040 nonbonded pdb=" O GLY C 172 " pdb=" OH TYR I 351 " model vdw 2.237 3.040 nonbonded pdb=" OG1 THR H 338 " pdb=" OD1 ASP H 347 " model vdw 2.262 3.040 nonbonded pdb=" ND1 HIS H 248 " pdb=" OE2 GLU J 120 " model vdw 2.270 3.120 nonbonded pdb=" O GLY C 193 " pdb=" OG1 THR I 329 " model vdw 2.278 3.040 ... (remaining 149208 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 'C' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 18.830 Find NCS groups from input model: 0.310 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:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 18542 Z= 0.216 Angle : 0.904 12.953 25213 Z= 0.464 Chirality : 0.056 0.304 2737 Planarity : 0.007 0.106 3281 Dihedral : 13.945 89.137 6691 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.10 % Allowed : 0.55 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % 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: -1.67 (0.16), residues: 2283 helix: -1.52 (0.34), residues: 190 sheet: -0.38 (0.19), residues: 662 loop : -1.45 (0.15), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG I 133 TYR 0.049 0.002 TYR J 116 PHE 0.034 0.002 PHE C 434 TRP 0.099 0.004 TRP J 390 HIS 0.013 0.002 HIS K 110 Details of bonding type rmsd covalent geometry : bond 0.00471 (18540) covalent geometry : angle 0.90346 (25209) SS BOND : bond 0.00549 ( 2) SS BOND : angle 1.76096 ( 4) hydrogen bonds : bond 0.17808 ( 476) hydrogen bonds : angle 8.84483 ( 1284) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 283 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8913 (mm110) cc_final: 0.8509 (mm110) REVERT: A 45 LEU cc_start: 0.8885 (mt) cc_final: 0.8681 (mp) REVERT: A 54 ASN cc_start: 0.8922 (t0) cc_final: 0.8720 (t0) REVERT: A 65 GLU cc_start: 0.9354 (pp20) cc_final: 0.9143 (pm20) REVERT: A 66 ASP cc_start: 0.9490 (p0) cc_final: 0.9215 (p0) REVERT: B 4 MET cc_start: 0.8605 (pmm) cc_final: 0.8260 (pmm) REVERT: B 31 ASN cc_start: 0.9104 (p0) cc_final: 0.8761 (p0) REVERT: B 37 GLN cc_start: 0.8776 (pp30) cc_final: 0.8344 (pp30) REVERT: B 83 PHE cc_start: 0.9043 (m-10) cc_final: 0.8716 (m-10) REVERT: B 87 TYR cc_start: 0.8730 (m-80) cc_final: 0.8468 (m-80) REVERT: C 138 MET cc_start: 0.8220 (ppp) cc_final: 0.7963 (ppp) REVERT: C 183 VAL cc_start: 0.9133 (m) cc_final: 0.8927 (p) REVERT: C 222 ASP cc_start: 0.7652 (p0) cc_final: 0.6817 (p0) REVERT: C 244 MET cc_start: 0.8754 (tpt) cc_final: 0.8261 (tpt) REVERT: C 310 ASN cc_start: 0.8014 (t0) cc_final: 0.7644 (t0) REVERT: H 34 LEU cc_start: 0.9048 (tt) cc_final: 0.8436 (mm) REVERT: H 188 ASP cc_start: 0.8963 (m-30) cc_final: 0.8583 (m-30) REVERT: H 251 ASN cc_start: 0.9079 (p0) cc_final: 0.8478 (p0) REVERT: H 359 ASP cc_start: 0.6619 (m-30) cc_final: 0.6082 (m-30) REVERT: I 197 MET cc_start: 0.7687 (mpp) cc_final: 0.7376 (mpp) REVERT: I 244 MET cc_start: 0.8885 (ppp) cc_final: 0.8283 (ppp) REVERT: I 446 GLU cc_start: 0.8698 (tp30) cc_final: 0.8463 (tp30) REVERT: J 110 HIS cc_start: 0.9215 (t-90) cc_final: 0.8767 (t-90) REVERT: J 118 ASP cc_start: 0.7668 (t70) cc_final: 0.7333 (t0) REVERT: J 138 MET cc_start: 0.9335 (pmm) cc_final: 0.8911 (pmm) REVERT: J 144 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8301 (tt0) REVERT: J 146 CYS cc_start: 0.8834 (p) cc_final: 0.8426 (p) REVERT: J 218 CYS cc_start: 0.9070 (m) cc_final: 0.8621 (t) REVERT: J 222 ASP cc_start: 0.7625 (t0) cc_final: 0.6035 (t0) REVERT: J 326 THR cc_start: 0.9384 (p) cc_final: 0.8187 (p) REVERT: J 327 ARG cc_start: 0.9136 (mpt180) cc_final: 0.8415 (mmt180) REVERT: J 367 CYS cc_start: 0.9295 (t) cc_final: 0.8894 (t) REVERT: K 147 MET cc_start: 0.9082 (mmm) cc_final: 0.8822 (mmm) outliers start: 2 outliers final: 0 residues processed: 284 average time/residue: 0.1317 time to fit residues: 58.9461 Evaluate side-chains 218 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 217 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 3.9990 chunk 212 optimal weight: 9.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 ASN ** H 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 361 GLN ** I 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 157 HIS J 132 ASN J 142 GLN ** J 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 316 ASN ** K 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.057059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.045213 restraints weight = 89662.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.047167 restraints weight = 47944.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.048558 restraints weight = 30900.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.049549 restraints weight = 22339.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.050258 restraints weight = 17485.191| |-----------------------------------------------------------------------------| r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 18542 Z= 0.217 Angle : 0.632 8.270 25213 Z= 0.334 Chirality : 0.044 0.171 2737 Planarity : 0.005 0.062 3281 Dihedral : 5.093 21.023 2491 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.10 % Allowed : 5.08 % Favored : 94.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % 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: -1.41 (0.17), residues: 2283 helix: -0.92 (0.37), residues: 190 sheet: -0.33 (0.19), residues: 707 loop : -1.29 (0.16), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 99 TYR 0.025 0.002 TYR J 116 PHE 0.015 0.002 PHE I 456 TRP 0.036 0.002 TRP J 390 HIS 0.007 0.001 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00460 (18540) covalent geometry : angle 0.63160 (25209) SS BOND : bond 0.00407 ( 2) SS BOND : angle 1.62435 ( 4) hydrogen bonds : bond 0.03838 ( 476) hydrogen bonds : angle 6.76036 ( 1284) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 256 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8795 (mm110) cc_final: 0.8410 (mm110) REVERT: A 66 ASP cc_start: 0.9491 (p0) cc_final: 0.9274 (p0) REVERT: B 31 ASN cc_start: 0.9139 (p0) cc_final: 0.8687 (p0) REVERT: B 37 GLN cc_start: 0.9044 (pp30) cc_final: 0.8695 (pp30) REVERT: B 78 LEU cc_start: 0.9435 (mt) cc_final: 0.9168 (mt) REVERT: B 83 PHE cc_start: 0.9101 (m-10) cc_final: 0.8770 (m-10) REVERT: B 87 TYR cc_start: 0.8777 (m-80) cc_final: 0.8477 (m-80) REVERT: C 120 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7656 (mm-30) REVERT: C 138 MET cc_start: 0.8373 (ppp) cc_final: 0.7663 (ppp) REVERT: C 183 VAL cc_start: 0.9165 (m) cc_final: 0.8940 (p) REVERT: C 212 ASP cc_start: 0.9046 (p0) cc_final: 0.8752 (p0) REVERT: C 213 ILE cc_start: 0.9396 (pt) cc_final: 0.9064 (tp) REVERT: C 222 ASP cc_start: 0.7559 (p0) cc_final: 0.6869 (p0) REVERT: C 249 PHE cc_start: 0.9231 (m-80) cc_final: 0.9023 (m-10) REVERT: C 292 GLU cc_start: 0.9063 (pm20) cc_final: 0.8798 (pm20) REVERT: H 34 LEU cc_start: 0.9201 (tt) cc_final: 0.8921 (tt) REVERT: H 119 VAL cc_start: 0.9360 (OUTLIER) cc_final: 0.9123 (p) REVERT: H 188 ASP cc_start: 0.9120 (m-30) cc_final: 0.8547 (m-30) REVERT: H 197 MET cc_start: 0.9241 (ppp) cc_final: 0.8226 (ppp) REVERT: H 244 MET cc_start: 0.8112 (tmm) cc_final: 0.7823 (tmm) REVERT: H 251 ASN cc_start: 0.8800 (p0) cc_final: 0.8350 (p0) REVERT: H 359 ASP cc_start: 0.6897 (m-30) cc_final: 0.6646 (m-30) REVERT: I 197 MET cc_start: 0.7747 (mpp) cc_final: 0.7410 (mpp) REVERT: I 296 PHE cc_start: 0.8677 (m-10) cc_final: 0.8473 (m-10) REVERT: I 446 GLU cc_start: 0.8650 (tp30) cc_final: 0.8289 (tp30) REVERT: I 448 ASP cc_start: 0.9620 (m-30) cc_final: 0.9349 (m-30) REVERT: J 27 TYR cc_start: 0.8870 (m-80) cc_final: 0.8351 (m-10) REVERT: J 110 HIS cc_start: 0.9340 (t-90) cc_final: 0.8905 (t-90) REVERT: J 138 MET cc_start: 0.9317 (pmm) cc_final: 0.8829 (pmm) REVERT: J 147 MET cc_start: 0.8657 (mmp) cc_final: 0.8320 (mmm) REVERT: J 218 CYS cc_start: 0.9118 (m) cc_final: 0.8846 (m) REVERT: J 222 ASP cc_start: 0.7678 (t0) cc_final: 0.5958 (t0) REVERT: J 327 ARG cc_start: 0.9292 (mpt180) cc_final: 0.8314 (mmt180) REVERT: J 366 LEU cc_start: 0.9567 (mt) cc_final: 0.9346 (mm) REVERT: J 388 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.8792 (tm-30) REVERT: K 115 LYS cc_start: 0.9556 (tptp) cc_final: 0.9218 (tptp) REVERT: K 147 MET cc_start: 0.9194 (mmm) cc_final: 0.8799 (mmm) REVERT: K 272 ARG cc_start: 0.4456 (mpt180) cc_final: 0.4107 (mmt-90) outliers start: 2 outliers final: 0 residues processed: 258 average time/residue: 0.1287 time to fit residues: 52.7838 Evaluate side-chains 206 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 204 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 189 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 188 optimal weight: 5.9990 chunk 199 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 29 optimal weight: 10.0000 chunk 181 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 130 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 175 optimal weight: 7.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 132 ASN ** J 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.056151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.044389 restraints weight = 92485.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.046280 restraints weight = 49567.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.047630 restraints weight = 32189.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.048470 restraints weight = 23451.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.049208 restraints weight = 18962.860| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 18542 Z= 0.224 Angle : 0.626 8.846 25213 Z= 0.330 Chirality : 0.044 0.197 2737 Planarity : 0.005 0.087 3281 Dihedral : 5.032 20.295 2491 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.18 % Favored : 93.78 % Rotamer: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % 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: -1.46 (0.17), residues: 2283 helix: -0.93 (0.37), residues: 190 sheet: -0.43 (0.19), residues: 689 loop : -1.27 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 33 TYR 0.023 0.002 TYR H 58 PHE 0.021 0.002 PHE I 456 TRP 0.039 0.002 TRP J 158 HIS 0.011 0.001 HIS H 354 Details of bonding type rmsd covalent geometry : bond 0.00477 (18540) covalent geometry : angle 0.62588 (25209) SS BOND : bond 0.00217 ( 2) SS BOND : angle 1.59892 ( 4) hydrogen bonds : bond 0.03854 ( 476) hydrogen bonds : angle 6.60122 ( 1284) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8865 (mm110) cc_final: 0.8481 (mm110) REVERT: A 66 ASP cc_start: 0.9513 (p0) cc_final: 0.9264 (p0) REVERT: B 31 ASN cc_start: 0.8979 (p0) cc_final: 0.8516 (p0) REVERT: B 37 GLN cc_start: 0.9002 (pp30) cc_final: 0.8681 (pp30) REVERT: B 78 LEU cc_start: 0.9392 (mt) cc_final: 0.9090 (mt) REVERT: B 83 PHE cc_start: 0.9103 (m-10) cc_final: 0.8771 (m-10) REVERT: C 183 VAL cc_start: 0.9165 (m) cc_final: 0.8927 (p) REVERT: C 212 ASP cc_start: 0.9103 (p0) cc_final: 0.8783 (p0) REVERT: C 222 ASP cc_start: 0.7619 (p0) cc_final: 0.6476 (p0) REVERT: H 96 GLU cc_start: 0.7556 (tp30) cc_final: 0.7271 (tp30) REVERT: H 188 ASP cc_start: 0.9144 (m-30) cc_final: 0.8576 (m-30) REVERT: H 197 MET cc_start: 0.9375 (ppp) cc_final: 0.8536 (ppp) REVERT: H 244 MET cc_start: 0.8001 (tmm) cc_final: 0.7624 (tmm) REVERT: H 251 ASN cc_start: 0.8808 (p0) cc_final: 0.8462 (p0) REVERT: H 331 MET cc_start: 0.8757 (mmm) cc_final: 0.8363 (mmm) REVERT: I 115 LYS cc_start: 0.9448 (tptt) cc_final: 0.9228 (tptp) REVERT: I 197 MET cc_start: 0.7632 (mpp) cc_final: 0.7377 (mpp) REVERT: I 244 MET cc_start: 0.8913 (ppp) cc_final: 0.8186 (ppp) REVERT: I 296 PHE cc_start: 0.8803 (m-10) cc_final: 0.8591 (m-10) REVERT: J 27 TYR cc_start: 0.8891 (m-80) cc_final: 0.8539 (m-80) REVERT: J 58 TYR cc_start: 0.8829 (m-80) cc_final: 0.8353 (m-80) REVERT: J 110 HIS cc_start: 0.9313 (t-90) cc_final: 0.8867 (t-90) REVERT: J 138 MET cc_start: 0.9257 (pmm) cc_final: 0.8816 (pmm) REVERT: J 140 TYR cc_start: 0.7961 (m-80) cc_final: 0.7578 (m-80) REVERT: J 147 MET cc_start: 0.8446 (mmp) cc_final: 0.8162 (mmm) REVERT: J 218 CYS cc_start: 0.9365 (m) cc_final: 0.9126 (m) REVERT: J 222 ASP cc_start: 0.7871 (t0) cc_final: 0.6347 (t0) REVERT: J 226 MET cc_start: 0.9410 (tpp) cc_final: 0.9204 (tpp) REVERT: J 327 ARG cc_start: 0.9318 (mpt180) cc_final: 0.8328 (mmt180) REVERT: J 366 LEU cc_start: 0.9568 (mt) cc_final: 0.9141 (mt) REVERT: K 138 MET cc_start: 0.9105 (mmm) cc_final: 0.8672 (mmm) REVERT: K 147 MET cc_start: 0.9057 (mmm) cc_final: 0.8408 (mmm) REVERT: K 244 MET cc_start: 0.8484 (tmm) cc_final: 0.8266 (tmm) REVERT: K 272 ARG cc_start: 0.4907 (mpt180) cc_final: 0.4490 (mmt-90) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.1341 time to fit residues: 53.5884 Evaluate side-chains 197 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 210 optimal weight: 5.9990 chunk 114 optimal weight: 10.0000 chunk 4 optimal weight: 0.0570 chunk 116 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 184 optimal weight: 9.9990 chunk 60 optimal weight: 8.9990 chunk 133 optimal weight: 7.9990 chunk 192 optimal weight: 9.9990 overall best weight: 4.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 380 HIS ** H 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 459 GLN ** I 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 354 HIS ** K 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.055264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.043603 restraints weight = 93501.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.045445 restraints weight = 50226.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.046793 restraints weight = 32803.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.047741 restraints weight = 23795.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.048397 restraints weight = 18775.204| |-----------------------------------------------------------------------------| r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 18542 Z= 0.252 Angle : 0.647 10.340 25213 Z= 0.339 Chirality : 0.044 0.174 2737 Planarity : 0.005 0.090 3281 Dihedral : 5.117 19.926 2491 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 19.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 0.05 % Allowed : 3.89 % Favored : 96.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % 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: -1.56 (0.17), residues: 2283 helix: -1.01 (0.37), residues: 190 sheet: -0.53 (0.19), residues: 699 loop : -1.33 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 133 TYR 0.020 0.002 TYR H 58 PHE 0.025 0.002 PHE K 245 TRP 0.028 0.002 TRP J 158 HIS 0.011 0.002 HIS I 28 Details of bonding type rmsd covalent geometry : bond 0.00535 (18540) covalent geometry : angle 0.64642 (25209) SS BOND : bond 0.00449 ( 2) SS BOND : angle 1.58158 ( 4) hydrogen bonds : bond 0.03766 ( 476) hydrogen bonds : angle 6.50337 ( 1284) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 254 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8795 (mm110) cc_final: 0.8415 (mm110) REVERT: A 66 ASP cc_start: 0.9524 (p0) cc_final: 0.9306 (p0) REVERT: B 31 ASN cc_start: 0.8924 (p0) cc_final: 0.8478 (p0) REVERT: B 37 GLN cc_start: 0.9041 (pp30) cc_final: 0.8701 (pp30) REVERT: B 78 LEU cc_start: 0.9365 (mt) cc_final: 0.9139 (mt) REVERT: B 83 PHE cc_start: 0.9120 (m-10) cc_final: 0.8794 (m-10) REVERT: C 120 GLU cc_start: 0.8541 (mm-30) cc_final: 0.7734 (mm-30) REVERT: C 138 MET cc_start: 0.8450 (ppp) cc_final: 0.7993 (ppp) REVERT: C 183 VAL cc_start: 0.9198 (m) cc_final: 0.8928 (p) REVERT: C 189 MET cc_start: 0.9293 (mmp) cc_final: 0.9057 (mmp) REVERT: C 222 ASP cc_start: 0.7683 (p0) cc_final: 0.7262 (p0) REVERT: C 243 GLN cc_start: 0.8621 (tp-100) cc_final: 0.8311 (tp-100) REVERT: C 300 TYR cc_start: 0.8122 (m-80) cc_final: 0.7480 (m-80) REVERT: H 96 GLU cc_start: 0.7586 (tp30) cc_final: 0.7277 (tp30) REVERT: H 188 ASP cc_start: 0.9103 (m-30) cc_final: 0.8603 (m-30) REVERT: H 197 MET cc_start: 0.9438 (ppp) cc_final: 0.8476 (ppp) REVERT: H 244 MET cc_start: 0.8075 (tmm) cc_final: 0.7666 (tmm) REVERT: H 251 ASN cc_start: 0.8794 (p0) cc_final: 0.8423 (p0) REVERT: I 244 MET cc_start: 0.9004 (ppp) cc_final: 0.8239 (ppp) REVERT: J 27 TYR cc_start: 0.9033 (m-80) cc_final: 0.8545 (m-80) REVERT: J 58 TYR cc_start: 0.8802 (m-80) cc_final: 0.8379 (m-80) REVERT: J 110 HIS cc_start: 0.9323 (t-90) cc_final: 0.8912 (t-90) REVERT: J 138 MET cc_start: 0.9175 (pmm) cc_final: 0.8815 (pmm) REVERT: J 140 TYR cc_start: 0.8120 (m-80) cc_final: 0.7817 (m-10) REVERT: J 222 ASP cc_start: 0.7964 (t0) cc_final: 0.6520 (t0) REVERT: J 226 MET cc_start: 0.9426 (tpp) cc_final: 0.9199 (tpp) REVERT: J 366 LEU cc_start: 0.9592 (mt) cc_final: 0.9110 (mt) REVERT: K 147 MET cc_start: 0.9046 (mmm) cc_final: 0.8492 (mmm) REVERT: K 272 ARG cc_start: 0.5124 (mpt180) cc_final: 0.4916 (mmt180) outliers start: 1 outliers final: 1 residues processed: 255 average time/residue: 0.1311 time to fit residues: 52.4619 Evaluate side-chains 193 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 192 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 49 optimal weight: 9.9990 chunk 129 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 0.0970 chunk 191 optimal weight: 6.9990 chunk 166 optimal weight: 0.4980 chunk 95 optimal weight: 4.9990 chunk 182 optimal weight: 0.0270 chunk 84 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 chunk 60 optimal weight: 0.0270 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 380 HIS ** H 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 HIS ** H 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 316 ASN ** I 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 142 GLN ** J 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 380 HIS ** K 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 308 HIS ** K 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.057989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.045832 restraints weight = 89555.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.047797 restraints weight = 47748.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.049216 restraints weight = 31034.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.050236 restraints weight = 22524.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.050933 restraints weight = 17670.415| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 18542 Z= 0.107 Angle : 0.595 7.791 25213 Z= 0.304 Chirality : 0.045 0.167 2737 Planarity : 0.004 0.058 3281 Dihedral : 4.705 19.557 2491 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.05 % Allowed : 1.89 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % 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: -1.34 (0.17), residues: 2283 helix: -0.87 (0.37), residues: 190 sheet: -0.34 (0.20), residues: 612 loop : -1.16 (0.16), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 133 TYR 0.016 0.001 TYR J 116 PHE 0.019 0.001 PHE I 456 TRP 0.039 0.002 TRP J 390 HIS 0.005 0.001 HIS I 28 Details of bonding type rmsd covalent geometry : bond 0.00232 (18540) covalent geometry : angle 0.59517 (25209) SS BOND : bond 0.00634 ( 2) SS BOND : angle 1.55728 ( 4) hydrogen bonds : bond 0.03470 ( 476) hydrogen bonds : angle 6.22757 ( 1284) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 279 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8899 (mm110) cc_final: 0.8482 (mm110) REVERT: A 66 ASP cc_start: 0.9458 (p0) cc_final: 0.9220 (p0) REVERT: A 106 LEU cc_start: 0.9092 (mp) cc_final: 0.8789 (mp) REVERT: B 31 ASN cc_start: 0.8987 (p0) cc_final: 0.8533 (p0) REVERT: B 78 LEU cc_start: 0.9372 (mt) cc_final: 0.9087 (mt) REVERT: B 83 PHE cc_start: 0.9127 (m-10) cc_final: 0.8811 (m-10) REVERT: C 120 GLU cc_start: 0.8373 (mm-30) cc_final: 0.7462 (mm-30) REVERT: C 138 MET cc_start: 0.8227 (ppp) cc_final: 0.7894 (ppp) REVERT: C 183 VAL cc_start: 0.9144 (m) cc_final: 0.8874 (p) REVERT: C 222 ASP cc_start: 0.7429 (p0) cc_final: 0.7033 (p0) REVERT: C 243 GLN cc_start: 0.8445 (tp-100) cc_final: 0.8163 (tp-100) REVERT: C 244 MET cc_start: 0.8685 (tpt) cc_final: 0.8437 (tpt) REVERT: C 300 TYR cc_start: 0.7943 (m-80) cc_final: 0.7252 (m-10) REVERT: C 390 TRP cc_start: 0.9061 (m-10) cc_final: 0.8623 (m-90) REVERT: H 96 GLU cc_start: 0.7752 (tp30) cc_final: 0.7398 (tp30) REVERT: H 188 ASP cc_start: 0.9089 (m-30) cc_final: 0.8592 (m-30) REVERT: H 197 MET cc_start: 0.9309 (ppp) cc_final: 0.8313 (ppp) REVERT: H 244 MET cc_start: 0.8093 (tmm) cc_final: 0.7713 (tmm) REVERT: H 251 ASN cc_start: 0.8864 (p0) cc_final: 0.8513 (p0) REVERT: H 352 MET cc_start: 0.8522 (mmm) cc_final: 0.8281 (mmm) REVERT: H 379 ILE cc_start: 0.9679 (tp) cc_final: 0.9468 (tp) REVERT: I 244 MET cc_start: 0.9051 (ppp) cc_final: 0.8329 (ppp) REVERT: I 296 PHE cc_start: 0.8864 (m-80) cc_final: 0.8651 (m-10) REVERT: J 27 TYR cc_start: 0.8926 (m-80) cc_final: 0.8333 (m-80) REVERT: J 58 TYR cc_start: 0.8699 (m-80) cc_final: 0.8270 (m-80) REVERT: J 110 HIS cc_start: 0.9389 (t-90) cc_final: 0.8815 (t-90) REVERT: J 138 MET cc_start: 0.9216 (pmm) cc_final: 0.8808 (pmm) REVERT: J 140 TYR cc_start: 0.7990 (m-80) cc_final: 0.7692 (m-10) REVERT: J 222 ASP cc_start: 0.7938 (t0) cc_final: 0.6370 (t0) REVERT: J 226 MET cc_start: 0.9381 (tpp) cc_final: 0.9125 (tpp) REVERT: J 313 CYS cc_start: 0.8872 (m) cc_final: 0.8611 (m) REVERT: J 366 LEU cc_start: 0.9610 (mt) cc_final: 0.9086 (mt) REVERT: K 147 MET cc_start: 0.8997 (mmm) cc_final: 0.8431 (mmm) REVERT: K 212 ASP cc_start: 0.9261 (p0) cc_final: 0.8939 (p0) outliers start: 1 outliers final: 0 residues processed: 280 average time/residue: 0.1232 time to fit residues: 54.9353 Evaluate side-chains 219 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 156 optimal weight: 9.9990 chunk 185 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 187 optimal weight: 0.8980 chunk 179 optimal weight: 9.9990 chunk 206 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 197 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 chunk 151 optimal weight: 7.9990 overall best weight: 6.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 310 ASN ** C 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 380 HIS ** H 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 308 HIS ** J 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 132 ASN ** K 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.053662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.042226 restraints weight = 95703.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.043983 restraints weight = 51992.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.045276 restraints weight = 34221.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.046065 restraints weight = 24998.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.046750 restraints weight = 20374.969| |-----------------------------------------------------------------------------| r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.097 18542 Z= 0.362 Angle : 0.767 11.227 25213 Z= 0.400 Chirality : 0.046 0.227 2737 Planarity : 0.006 0.061 3281 Dihedral : 5.377 26.980 2491 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 24.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % 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: -1.71 (0.17), residues: 2283 helix: -1.20 (0.35), residues: 190 sheet: -0.62 (0.19), residues: 695 loop : -1.42 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 133 TYR 0.031 0.003 TYR H 58 PHE 0.025 0.003 PHE K 296 TRP 0.033 0.003 TRP A 36 HIS 0.015 0.002 HIS I 28 Details of bonding type rmsd covalent geometry : bond 0.00767 (18540) covalent geometry : angle 0.76682 (25209) SS BOND : bond 0.00313 ( 2) SS BOND : angle 1.33701 ( 4) hydrogen bonds : bond 0.04119 ( 476) hydrogen bonds : angle 6.56127 ( 1284) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8782 (mm110) cc_final: 0.8401 (mm110) REVERT: A 70 MET cc_start: 0.8525 (ppp) cc_final: 0.8221 (ppp) REVERT: B 4 MET cc_start: 0.8431 (pmm) cc_final: 0.8018 (pmm) REVERT: B 31 ASN cc_start: 0.8846 (p0) cc_final: 0.8471 (p0) REVERT: B 37 GLN cc_start: 0.9006 (pp30) cc_final: 0.8612 (pp30) REVERT: B 78 LEU cc_start: 0.9348 (mt) cc_final: 0.9100 (mt) REVERT: B 83 PHE cc_start: 0.9154 (m-10) cc_final: 0.8728 (m-10) REVERT: C 120 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8021 (mm-30) REVERT: C 138 MET cc_start: 0.8536 (ppp) cc_final: 0.8058 (ppp) REVERT: C 147 MET cc_start: 0.8369 (ppp) cc_final: 0.8020 (ppp) REVERT: C 183 VAL cc_start: 0.9274 (m) cc_final: 0.9028 (p) REVERT: C 222 ASP cc_start: 0.7608 (p0) cc_final: 0.6248 (p0) REVERT: C 244 MET cc_start: 0.8861 (tpt) cc_final: 0.8609 (tpt) REVERT: C 249 PHE cc_start: 0.9418 (m-10) cc_final: 0.9113 (m-10) REVERT: C 310 ASN cc_start: 0.7984 (t160) cc_final: 0.7638 (t0) REVERT: H 96 GLU cc_start: 0.7679 (tp30) cc_final: 0.7239 (tp30) REVERT: H 188 ASP cc_start: 0.9184 (m-30) cc_final: 0.8692 (m-30) REVERT: H 244 MET cc_start: 0.8119 (tmm) cc_final: 0.7853 (tmm) REVERT: H 248 HIS cc_start: 0.8896 (m90) cc_final: 0.8542 (m90) REVERT: H 251 ASN cc_start: 0.8797 (p0) cc_final: 0.8429 (p0) REVERT: H 352 MET cc_start: 0.8642 (mmm) cc_final: 0.8269 (mmm) REVERT: H 361 GLN cc_start: 0.9111 (mt0) cc_final: 0.8877 (tt0) REVERT: H 379 ILE cc_start: 0.9643 (tp) cc_final: 0.9422 (tp) REVERT: I 147 MET cc_start: 0.8507 (tpp) cc_final: 0.8302 (tpt) REVERT: I 197 MET cc_start: 0.7537 (mpp) cc_final: 0.7213 (mpp) REVERT: I 296 PHE cc_start: 0.9091 (m-80) cc_final: 0.8857 (m-10) REVERT: I 300 TYR cc_start: 0.8267 (m-10) cc_final: 0.7810 (m-10) REVERT: J 27 TYR cc_start: 0.9113 (m-80) cc_final: 0.8462 (m-80) REVERT: J 54 LYS cc_start: 0.8666 (mmtm) cc_final: 0.8425 (tppt) REVERT: J 110 HIS cc_start: 0.9325 (t-90) cc_final: 0.8895 (t-90) REVERT: J 116 TYR cc_start: 0.3106 (m-80) cc_final: 0.2231 (m-80) REVERT: J 138 MET cc_start: 0.9161 (pmm) cc_final: 0.8807 (pmm) REVERT: J 140 TYR cc_start: 0.8399 (m-10) cc_final: 0.7859 (m-10) REVERT: J 191 ASP cc_start: 0.9037 (p0) cc_final: 0.8807 (p0) REVERT: J 218 CYS cc_start: 0.9227 (m) cc_final: 0.8941 (m) REVERT: J 226 MET cc_start: 0.9446 (tpp) cc_final: 0.9139 (tpp) REVERT: J 366 LEU cc_start: 0.9614 (mt) cc_final: 0.9064 (mt) REVERT: K 147 MET cc_start: 0.9066 (mmm) cc_final: 0.8631 (mmm) REVERT: K 352 MET cc_start: 0.7874 (ttp) cc_final: 0.7065 (ppp) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.1283 time to fit residues: 47.9481 Evaluate side-chains 185 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 175 optimal weight: 4.9990 chunk 171 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 184 optimal weight: 6.9990 chunk 161 optimal weight: 1.9990 chunk 112 optimal weight: 8.9990 chunk 155 optimal weight: 3.9990 chunk 218 optimal weight: 8.9990 chunk 160 optimal weight: 0.8980 chunk 140 optimal weight: 9.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 380 HIS ** H 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 365 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.055083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.043362 restraints weight = 92981.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.045225 restraints weight = 49833.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.046574 restraints weight = 32406.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.047516 restraints weight = 23566.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.048164 restraints weight = 18679.060| |-----------------------------------------------------------------------------| r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18542 Z= 0.203 Angle : 0.630 8.862 25213 Z= 0.328 Chirality : 0.044 0.201 2737 Planarity : 0.005 0.088 3281 Dihedral : 5.134 23.879 2491 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 18.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % 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: -1.67 (0.17), residues: 2283 helix: -1.03 (0.36), residues: 190 sheet: -0.73 (0.19), residues: 740 loop : -1.33 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG J 133 TYR 0.023 0.002 TYR H 58 PHE 0.024 0.002 PHE I 456 TRP 0.029 0.002 TRP J 158 HIS 0.010 0.001 HIS I 28 Details of bonding type rmsd covalent geometry : bond 0.00435 (18540) covalent geometry : angle 0.62946 (25209) SS BOND : bond 0.00382 ( 2) SS BOND : angle 1.37987 ( 4) hydrogen bonds : bond 0.03633 ( 476) hydrogen bonds : angle 6.40772 ( 1284) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8851 (mm110) cc_final: 0.8414 (mm110) REVERT: B 4 MET cc_start: 0.8504 (pmm) cc_final: 0.7969 (pmm) REVERT: B 31 ASN cc_start: 0.8910 (p0) cc_final: 0.8412 (p0) REVERT: B 37 GLN cc_start: 0.8979 (pp30) cc_final: 0.8617 (pp30) REVERT: B 78 LEU cc_start: 0.9356 (mt) cc_final: 0.9119 (mt) REVERT: B 83 PHE cc_start: 0.9147 (m-10) cc_final: 0.8768 (m-10) REVERT: C 120 GLU cc_start: 0.8778 (mm-30) cc_final: 0.7897 (mm-30) REVERT: C 138 MET cc_start: 0.8547 (ppp) cc_final: 0.8173 (ppp) REVERT: C 183 VAL cc_start: 0.9262 (m) cc_final: 0.9002 (p) REVERT: C 244 MET cc_start: 0.8977 (tpt) cc_final: 0.8574 (tpt) REVERT: C 300 TYR cc_start: 0.8157 (m-80) cc_final: 0.7453 (m-10) REVERT: C 321 THR cc_start: 0.8966 (m) cc_final: 0.8583 (m) REVERT: H 96 GLU cc_start: 0.7805 (tp30) cc_final: 0.7403 (tp30) REVERT: H 188 ASP cc_start: 0.9140 (m-30) cc_final: 0.8640 (m-30) REVERT: H 197 MET cc_start: 0.9220 (ppp) cc_final: 0.8517 (ppp) REVERT: H 248 HIS cc_start: 0.8877 (m90) cc_final: 0.8665 (m90) REVERT: H 251 ASN cc_start: 0.8890 (p0) cc_final: 0.8483 (p0) REVERT: H 361 GLN cc_start: 0.9093 (mt0) cc_final: 0.8861 (tt0) REVERT: I 147 MET cc_start: 0.8423 (tpp) cc_final: 0.8183 (tpt) REVERT: I 197 MET cc_start: 0.7532 (mpp) cc_final: 0.7188 (mpp) REVERT: I 244 MET cc_start: 0.8952 (ppp) cc_final: 0.8220 (ppp) REVERT: I 300 TYR cc_start: 0.8016 (m-10) cc_final: 0.7688 (m-10) REVERT: J 27 TYR cc_start: 0.9065 (m-80) cc_final: 0.8373 (m-80) REVERT: J 54 LYS cc_start: 0.8616 (mmtm) cc_final: 0.8404 (tppt) REVERT: J 110 HIS cc_start: 0.9349 (t-90) cc_final: 0.8889 (t-90) REVERT: J 116 TYR cc_start: 0.2617 (m-80) cc_final: 0.2263 (m-80) REVERT: J 138 MET cc_start: 0.9161 (pmm) cc_final: 0.8816 (pmm) REVERT: J 140 TYR cc_start: 0.8300 (m-10) cc_final: 0.7802 (m-10) REVERT: J 218 CYS cc_start: 0.9222 (m) cc_final: 0.8945 (m) REVERT: J 226 MET cc_start: 0.9423 (tpp) cc_final: 0.9198 (tpp) REVERT: J 327 ARG cc_start: 0.9335 (mpt180) cc_final: 0.8196 (mmt180) REVERT: J 366 LEU cc_start: 0.9624 (mt) cc_final: 0.9038 (mt) REVERT: K 147 MET cc_start: 0.9045 (mmm) cc_final: 0.8534 (mmm) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.1241 time to fit residues: 47.6677 Evaluate side-chains 192 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 27 optimal weight: 0.9980 chunk 184 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 209 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 170 optimal weight: 2.9990 chunk 203 optimal weight: 20.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.055623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.043875 restraints weight = 92716.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.045723 restraints weight = 49671.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.047082 restraints weight = 32595.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.048073 restraints weight = 23651.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.048755 restraints weight = 18552.639| |-----------------------------------------------------------------------------| r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18542 Z= 0.189 Angle : 0.627 8.564 25213 Z= 0.325 Chirality : 0.044 0.190 2737 Planarity : 0.005 0.073 3281 Dihedral : 5.019 24.015 2491 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % 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: -1.56 (0.17), residues: 2283 helix: -1.00 (0.37), residues: 190 sheet: -0.62 (0.19), residues: 746 loop : -1.28 (0.17), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 133 TYR 0.024 0.002 TYR I 358 PHE 0.019 0.002 PHE I 456 TRP 0.057 0.002 TRP I 390 HIS 0.010 0.001 HIS I 28 Details of bonding type rmsd covalent geometry : bond 0.00409 (18540) covalent geometry : angle 0.62729 (25209) SS BOND : bond 0.00433 ( 2) SS BOND : angle 1.30752 ( 4) hydrogen bonds : bond 0.03599 ( 476) hydrogen bonds : angle 6.38607 ( 1284) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8840 (mm110) cc_final: 0.8391 (mm110) REVERT: B 4 MET cc_start: 0.8531 (pmm) cc_final: 0.7931 (pmm) REVERT: B 31 ASN cc_start: 0.8940 (p0) cc_final: 0.8430 (p0) REVERT: B 37 GLN cc_start: 0.8963 (pp30) cc_final: 0.8461 (tm-30) REVERT: B 78 LEU cc_start: 0.9318 (mt) cc_final: 0.9041 (mt) REVERT: B 87 TYR cc_start: 0.8780 (m-80) cc_final: 0.8566 (m-80) REVERT: C 120 GLU cc_start: 0.8499 (mm-30) cc_final: 0.7700 (mm-30) REVERT: C 138 MET cc_start: 0.8427 (ppp) cc_final: 0.7991 (ppp) REVERT: C 140 TYR cc_start: 0.8207 (m-80) cc_final: 0.7873 (m-10) REVERT: C 183 VAL cc_start: 0.9231 (m) cc_final: 0.8973 (p) REVERT: C 222 ASP cc_start: 0.7400 (p0) cc_final: 0.6275 (p0) REVERT: C 242 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8172 (mm-30) REVERT: C 244 MET cc_start: 0.8994 (tpt) cc_final: 0.8762 (tpt) REVERT: C 300 TYR cc_start: 0.8122 (m-80) cc_final: 0.7350 (m-10) REVERT: H 96 GLU cc_start: 0.7859 (tp30) cc_final: 0.7473 (tp30) REVERT: H 188 ASP cc_start: 0.9067 (m-30) cc_final: 0.8595 (m-30) REVERT: H 197 MET cc_start: 0.9255 (ppp) cc_final: 0.8499 (ppp) REVERT: H 248 HIS cc_start: 0.8921 (m90) cc_final: 0.8681 (m90) REVERT: H 251 ASN cc_start: 0.8905 (p0) cc_final: 0.8490 (p0) REVERT: H 352 MET cc_start: 0.8546 (mmm) cc_final: 0.8280 (mmm) REVERT: H 361 GLN cc_start: 0.9085 (mt0) cc_final: 0.8855 (tt0) REVERT: H 390 TRP cc_start: 0.8715 (m-10) cc_final: 0.7656 (m-90) REVERT: I 197 MET cc_start: 0.7447 (mpp) cc_final: 0.7193 (mpp) REVERT: J 27 TYR cc_start: 0.9039 (m-80) cc_final: 0.8325 (m-80) REVERT: J 54 LYS cc_start: 0.8574 (mmtm) cc_final: 0.8373 (tppt) REVERT: J 110 HIS cc_start: 0.9388 (t-90) cc_final: 0.9045 (t-90) REVERT: J 116 TYR cc_start: 0.2872 (m-80) cc_final: 0.2435 (m-80) REVERT: J 138 MET cc_start: 0.9145 (pmm) cc_final: 0.8828 (pmm) REVERT: J 140 TYR cc_start: 0.8239 (m-10) cc_final: 0.7804 (m-10) REVERT: J 191 ASP cc_start: 0.8938 (p0) cc_final: 0.8690 (p0) REVERT: J 218 CYS cc_start: 0.9211 (m) cc_final: 0.8998 (m) REVERT: J 226 MET cc_start: 0.9399 (tpp) cc_final: 0.9141 (tpp) REVERT: J 366 LEU cc_start: 0.9633 (mt) cc_final: 0.9011 (mt) REVERT: K 147 MET cc_start: 0.9044 (mmm) cc_final: 0.8484 (mmm) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.1297 time to fit residues: 48.1632 Evaluate side-chains 193 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 46 optimal weight: 9.9990 chunk 94 optimal weight: 7.9990 chunk 185 optimal weight: 8.9990 chunk 30 optimal weight: 0.6980 chunk 48 optimal weight: 9.9990 chunk 134 optimal weight: 0.7980 chunk 88 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 77 optimal weight: 0.9980 chunk 200 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.056662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.044824 restraints weight = 89958.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.046753 restraints weight = 48311.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.048142 restraints weight = 31282.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.049087 restraints weight = 22649.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.049813 restraints weight = 17886.739| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18542 Z= 0.129 Angle : 0.618 9.722 25213 Z= 0.313 Chirality : 0.045 0.180 2737 Planarity : 0.005 0.063 3281 Dihedral : 4.811 21.893 2491 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % 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: -1.38 (0.17), residues: 2283 helix: -0.87 (0.37), residues: 189 sheet: -0.46 (0.20), residues: 695 loop : -1.16 (0.17), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 133 TYR 0.019 0.001 TYR H 58 PHE 0.020 0.001 PHE I 456 TRP 0.070 0.002 TRP J 158 HIS 0.007 0.001 HIS I 28 Details of bonding type rmsd covalent geometry : bond 0.00284 (18540) covalent geometry : angle 0.61740 (25209) SS BOND : bond 0.00519 ( 2) SS BOND : angle 1.26501 ( 4) hydrogen bonds : bond 0.03385 ( 476) hydrogen bonds : angle 6.31138 ( 1284) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8840 (mm110) cc_final: 0.8354 (mm110) REVERT: B 4 MET cc_start: 0.8594 (pmm) cc_final: 0.7942 (pmm) REVERT: B 31 ASN cc_start: 0.8940 (p0) cc_final: 0.8393 (p0) REVERT: B 37 GLN cc_start: 0.8916 (pp30) cc_final: 0.8461 (tm-30) REVERT: B 78 LEU cc_start: 0.9335 (mt) cc_final: 0.9128 (mt) REVERT: B 83 PHE cc_start: 0.9092 (m-10) cc_final: 0.8777 (m-10) REVERT: B 87 TYR cc_start: 0.8746 (m-80) cc_final: 0.8536 (m-80) REVERT: C 120 GLU cc_start: 0.8523 (mm-30) cc_final: 0.7510 (mm-30) REVERT: C 138 MET cc_start: 0.8339 (ppp) cc_final: 0.7979 (ppp) REVERT: C 183 VAL cc_start: 0.9146 (m) cc_final: 0.8879 (p) REVERT: C 222 ASP cc_start: 0.7367 (p0) cc_final: 0.6631 (p0) REVERT: C 242 GLU cc_start: 0.8447 (mm-30) cc_final: 0.8156 (mm-30) REVERT: C 321 THR cc_start: 0.8950 (m) cc_final: 0.8727 (m) REVERT: H 96 GLU cc_start: 0.7865 (tp30) cc_final: 0.7435 (tp30) REVERT: H 188 ASP cc_start: 0.9056 (m-30) cc_final: 0.8627 (m-30) REVERT: H 197 MET cc_start: 0.9213 (ppp) cc_final: 0.8470 (ppp) REVERT: H 251 ASN cc_start: 0.8886 (p0) cc_final: 0.8455 (p0) REVERT: H 300 TYR cc_start: 0.9269 (m-80) cc_final: 0.8841 (m-80) REVERT: H 331 MET cc_start: 0.8271 (mmm) cc_final: 0.7272 (mmt) REVERT: H 352 MET cc_start: 0.8521 (mmm) cc_final: 0.8218 (mmm) REVERT: H 361 GLN cc_start: 0.8974 (mt0) cc_final: 0.8769 (tt0) REVERT: H 390 TRP cc_start: 0.8695 (m-10) cc_final: 0.7598 (m-90) REVERT: I 197 MET cc_start: 0.7444 (mpp) cc_final: 0.7120 (mpp) REVERT: I 244 MET cc_start: 0.9051 (ppp) cc_final: 0.8427 (ppp) REVERT: J 27 TYR cc_start: 0.8999 (m-80) cc_final: 0.8208 (m-80) REVERT: J 54 LYS cc_start: 0.8501 (mmtm) cc_final: 0.8268 (tppt) REVERT: J 58 TYR cc_start: 0.8715 (m-80) cc_final: 0.8422 (m-10) REVERT: J 110 HIS cc_start: 0.9424 (t-90) cc_final: 0.8897 (t-90) REVERT: J 138 MET cc_start: 0.9140 (pmm) cc_final: 0.8826 (pmm) REVERT: J 140 TYR cc_start: 0.8124 (m-10) cc_final: 0.7579 (m-10) REVERT: J 147 MET cc_start: 0.8510 (mmm) cc_final: 0.8114 (mmm) REVERT: J 191 ASP cc_start: 0.8851 (p0) cc_final: 0.8642 (p0) REVERT: J 197 MET cc_start: 0.7651 (mmp) cc_final: 0.7370 (mmp) REVERT: J 218 CYS cc_start: 0.9081 (m) cc_final: 0.8824 (m) REVERT: J 226 MET cc_start: 0.9357 (tpp) cc_final: 0.9109 (tpp) REVERT: J 366 LEU cc_start: 0.9634 (mt) cc_final: 0.8990 (mt) REVERT: J 382 MET cc_start: 0.9322 (tmm) cc_final: 0.9028 (ppp) REVERT: K 147 MET cc_start: 0.9020 (mmm) cc_final: 0.8509 (mmm) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.1244 time to fit residues: 50.1196 Evaluate side-chains 202 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 34 optimal weight: 10.0000 chunk 102 optimal weight: 8.9990 chunk 194 optimal weight: 20.0000 chunk 103 optimal weight: 8.9990 chunk 110 optimal weight: 0.0980 chunk 63 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 219 optimal weight: 10.0000 chunk 69 optimal weight: 9.9990 overall best weight: 5.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 345 ASN ** K 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.054481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.042934 restraints weight = 94317.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.044733 restraints weight = 50882.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.046057 restraints weight = 33207.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.047012 restraints weight = 24289.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.047657 restraints weight = 19177.821| |-----------------------------------------------------------------------------| r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 18542 Z= 0.278 Angle : 0.698 10.180 25213 Z= 0.361 Chirality : 0.045 0.203 2737 Planarity : 0.005 0.070 3281 Dihedral : 5.166 25.368 2491 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 21.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % 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: -1.65 (0.17), residues: 2283 helix: -1.10 (0.36), residues: 190 sheet: -0.67 (0.19), residues: 730 loop : -1.34 (0.17), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 133 TYR 0.034 0.002 TYR J 116 PHE 0.024 0.002 PHE I 456 TRP 0.056 0.002 TRP J 158 HIS 0.010 0.002 HIS I 28 Details of bonding type rmsd covalent geometry : bond 0.00592 (18540) covalent geometry : angle 0.69779 (25209) SS BOND : bond 0.00366 ( 2) SS BOND : angle 1.20428 ( 4) hydrogen bonds : bond 0.03826 ( 476) hydrogen bonds : angle 6.48590 ( 1284) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8802 (mm110) cc_final: 0.8391 (mm110) REVERT: A 54 ASN cc_start: 0.9104 (t0) cc_final: 0.8893 (t0) REVERT: A 70 MET cc_start: 0.8513 (ppp) cc_final: 0.8094 (ppp) REVERT: A 81 MET cc_start: 0.6366 (pmm) cc_final: 0.6002 (pmm) REVERT: B 4 MET cc_start: 0.8555 (pmm) cc_final: 0.8016 (pmm) REVERT: B 31 ASN cc_start: 0.8965 (p0) cc_final: 0.8478 (p0) REVERT: B 37 GLN cc_start: 0.9005 (pp30) cc_final: 0.8452 (tm-30) REVERT: B 78 LEU cc_start: 0.9328 (mt) cc_final: 0.9046 (mt) REVERT: B 87 TYR cc_start: 0.8715 (m-80) cc_final: 0.8487 (m-80) REVERT: C 120 GLU cc_start: 0.8578 (mm-30) cc_final: 0.7638 (mm-30) REVERT: C 183 VAL cc_start: 0.9268 (m) cc_final: 0.9017 (p) REVERT: C 222 ASP cc_start: 0.7452 (p0) cc_final: 0.6438 (p0) REVERT: C 242 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8135 (mm-30) REVERT: C 321 THR cc_start: 0.8993 (m) cc_final: 0.8791 (m) REVERT: H 96 GLU cc_start: 0.7845 (tp30) cc_final: 0.7470 (tp30) REVERT: H 188 ASP cc_start: 0.9133 (m-30) cc_final: 0.8691 (m-30) REVERT: H 197 MET cc_start: 0.9315 (ppp) cc_final: 0.8532 (ppp) REVERT: H 251 ASN cc_start: 0.8835 (p0) cc_final: 0.8447 (p0) REVERT: H 352 MET cc_start: 0.8561 (mmm) cc_final: 0.8232 (mmm) REVERT: H 361 GLN cc_start: 0.9064 (mt0) cc_final: 0.8838 (tt0) REVERT: H 390 TRP cc_start: 0.8770 (m-10) cc_final: 0.7685 (m-90) REVERT: I 115 LYS cc_start: 0.9436 (tptt) cc_final: 0.9177 (tppt) REVERT: I 244 MET cc_start: 0.9069 (ppp) cc_final: 0.8410 (ppp) REVERT: J 27 TYR cc_start: 0.9057 (m-80) cc_final: 0.8288 (m-80) REVERT: J 110 HIS cc_start: 0.9386 (t-90) cc_final: 0.8929 (t-90) REVERT: J 138 MET cc_start: 0.9138 (pmm) cc_final: 0.8822 (pmm) REVERT: J 140 TYR cc_start: 0.8375 (m-10) cc_final: 0.7835 (m-10) REVERT: J 191 ASP cc_start: 0.8899 (p0) cc_final: 0.8646 (p0) REVERT: J 218 CYS cc_start: 0.9187 (m) cc_final: 0.8839 (m) REVERT: J 226 MET cc_start: 0.9430 (tpp) cc_final: 0.9167 (tpp) REVERT: J 327 ARG cc_start: 0.9322 (mpt180) cc_final: 0.9000 (mpt180) REVERT: J 366 LEU cc_start: 0.9634 (mt) cc_final: 0.8981 (mt) REVERT: J 382 MET cc_start: 0.9300 (tmm) cc_final: 0.9019 (ppp) REVERT: J 390 TRP cc_start: 0.7674 (m-90) cc_final: 0.7308 (m-90) REVERT: K 147 MET cc_start: 0.9041 (mmm) cc_final: 0.8535 (mmm) REVERT: K 331 MET cc_start: 0.8950 (mmm) cc_final: 0.8695 (mmm) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.1195 time to fit residues: 43.8797 Evaluate side-chains 186 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 154 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 5 optimal weight: 0.3980 chunk 11 optimal weight: 10.0000 chunk 221 optimal weight: 0.9980 chunk 98 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 54 optimal weight: 20.0000 chunk 209 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 380 HIS ** H 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.056165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.044383 restraints weight = 91422.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.046269 restraints weight = 49041.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.047646 restraints weight = 31836.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.048596 restraints weight = 23079.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.049328 restraints weight = 18244.639| |-----------------------------------------------------------------------------| r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18542 Z= 0.144 Angle : 0.626 9.982 25213 Z= 0.319 Chirality : 0.045 0.173 2737 Planarity : 0.005 0.061 3281 Dihedral : 4.926 24.995 2491 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % 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: -1.49 (0.17), residues: 2283 helix: -0.87 (0.37), residues: 190 sheet: -0.71 (0.19), residues: 727 loop : -1.15 (0.17), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 133 TYR 0.021 0.001 TYR H 58 PHE 0.014 0.001 PHE C 296 TRP 0.049 0.002 TRP J 158 HIS 0.008 0.001 HIS I 28 Details of bonding type rmsd covalent geometry : bond 0.00319 (18540) covalent geometry : angle 0.62542 (25209) SS BOND : bond 0.00498 ( 2) SS BOND : angle 1.27387 ( 4) hydrogen bonds : bond 0.03443 ( 476) hydrogen bonds : angle 6.36428 ( 1284) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2448.05 seconds wall clock time: 43 minutes 47.35 seconds (2627.35 seconds total)