Starting phenix.real_space_refine on Mon Jun 16 05:11:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yef_39193/06_2025/8yef_39193.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yef_39193/06_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_39193/06_2025/8yef_39193.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yef_39193/06_2025/8yef_39193.map" model { file = "/net/cci-nas-00/data/ceres_data/8yef_39193/06_2025/8yef_39193.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yef_39193/06_2025/8yef_39193.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.34, per 1000 atoms: 0.57 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: 4.21 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 2.38 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: 6.04 Time building geometry restraints manager: 5.13 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: 0.670 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: 0.750 Check model and map are aligned: 0.150 Set scattering table: 0.170 Process input model: 41.340 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.080 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.690 ------------------------------------------------------------------------------- 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 : 10.30 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.099 0.004 TRP J 390 HIS 0.013 0.002 HIS K 110 PHE 0.034 0.002 PHE C 434 TYR 0.049 0.002 TYR J 116 ARG 0.014 0.001 ARG I 133 Details of bonding type rmsd hydrogen bonds : bond 0.17808 ( 476) hydrogen bonds : angle 8.84483 ( 1284) SS BOND : bond 0.00549 ( 2) SS BOND : angle 1.76096 ( 4) covalent geometry : bond 0.00471 (18540) covalent geometry : angle 0.90346 (25209) *********************** 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 : 2.246 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: 0.2843 time to fit residues: 125.8373 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 : 2.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 191 optimal weight: 10.0000 chunk 172 optimal weight: 0.8980 chunk 95 optimal weight: 9.9990 chunk 58 optimal weight: 8.9990 chunk 116 optimal weight: 5.9990 chunk 91 optimal weight: 0.0470 chunk 177 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 108 optimal weight: 0.0570 chunk 132 optimal weight: 1.9990 chunk 206 optimal weight: 10.0000 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 132 ASN ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 316 ASN ** H 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 132 ASN ** J 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 309 ASN ** 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 = 0.3202 r_free = 0.3202 target = 0.059815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.047645 restraints weight = 87432.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.049729 restraints weight = 46350.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.051209 restraints weight = 29610.028| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 18542 Z= 0.117 Angle : 0.583 5.800 25213 Z= 0.305 Chirality : 0.044 0.166 2737 Planarity : 0.005 0.062 3281 Dihedral : 4.843 21.953 2491 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.15 % Allowed : 4.09 % Favored : 95.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.17), residues: 2283 helix: -0.89 (0.38), residues: 190 sheet: -0.25 (0.20), residues: 641 loop : -1.28 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP J 390 HIS 0.004 0.001 HIS K 110 PHE 0.013 0.001 PHE I 456 TYR 0.016 0.001 TYR J 116 ARG 0.004 0.000 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.03768 ( 476) hydrogen bonds : angle 6.75653 ( 1284) SS BOND : bond 0.00551 ( 2) SS BOND : angle 1.65552 ( 4) covalent geometry : bond 0.00247 (18540) covalent geometry : angle 0.58258 (25209) *********************** 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 285 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 282 time to evaluate : 2.125 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: 0.8898 (mm110) cc_final: 0.8494 (mm110) REVERT: A 66 ASP cc_start: 0.9453 (p0) cc_final: 0.9182 (p0) REVERT: B 31 ASN cc_start: 0.9154 (p0) cc_final: 0.8728 (p0) REVERT: B 37 GLN cc_start: 0.9005 (pp30) cc_final: 0.8655 (pp30) REVERT: B 78 LEU cc_start: 0.9475 (mt) cc_final: 0.9247 (mt) REVERT: B 83 PHE cc_start: 0.9074 (m-10) cc_final: 0.8762 (m-10) REVERT: B 87 TYR cc_start: 0.8711 (m-80) cc_final: 0.8423 (m-80) REVERT: C 138 MET cc_start: 0.8278 (ppp) cc_final: 0.7930 (ppp) REVERT: C 183 VAL cc_start: 0.9193 (m) cc_final: 0.8957 (p) REVERT: C 212 ASP cc_start: 0.9169 (p0) cc_final: 0.8893 (p0) REVERT: C 213 ILE cc_start: 0.9416 (pt) cc_final: 0.9056 (tp) REVERT: C 222 ASP cc_start: 0.7567 (p0) cc_final: 0.6936 (p0) REVERT: C 244 MET cc_start: 0.8662 (tpt) cc_final: 0.8379 (tpt) REVERT: C 292 GLU cc_start: 0.9058 (pm20) cc_final: 0.8804 (pm20) REVERT: C 321 THR cc_start: 0.8976 (m) cc_final: 0.8509 (m) REVERT: C 390 TRP cc_start: 0.8981 (m-90) cc_final: 0.8404 (m-90) REVERT: H 96 GLU cc_start: 0.7848 (tp30) cc_final: 0.7483 (tp30) REVERT: H 119 VAL cc_start: 0.9394 (OUTLIER) cc_final: 0.9005 (p) REVERT: H 188 ASP cc_start: 0.9138 (m-30) cc_final: 0.8768 (m-30) REVERT: H 197 MET cc_start: 0.9126 (ppp) cc_final: 0.8083 (ppp) REVERT: H 251 ASN cc_start: 0.8760 (p0) cc_final: 0.8262 (p0) REVERT: H 316 ASN cc_start: 0.8025 (OUTLIER) cc_final: 0.7614 (t0) REVERT: H 359 ASP cc_start: 0.6547 (m-30) cc_final: 0.6345 (m-30) REVERT: I 197 MET cc_start: 0.7742 (mpp) cc_final: 0.7331 (mpp) REVERT: I 244 MET cc_start: 0.8914 (ppp) cc_final: 0.8266 (ppp) REVERT: I 446 GLU cc_start: 0.8767 (tp30) cc_final: 0.8314 (tp30) REVERT: I 448 ASP cc_start: 0.9623 (m-30) cc_final: 0.9397 (m-30) REVERT: J 27 TYR cc_start: 0.8692 (m-80) cc_final: 0.8390 (m-10) REVERT: J 110 HIS cc_start: 0.9372 (t-90) cc_final: 0.8900 (t-90) REVERT: J 118 ASP cc_start: 0.7222 (t70) cc_final: 0.6949 (t0) REVERT: J 138 MET cc_start: 0.9288 (pmm) cc_final: 0.8821 (pmm) REVERT: J 147 MET cc_start: 0.8748 (mmp) cc_final: 0.8429 (mmm) REVERT: J 197 MET cc_start: 0.7323 (mmp) cc_final: 0.6980 (mmp) REVERT: J 218 CYS cc_start: 0.8969 (m) cc_final: 0.8767 (m) REVERT: J 222 ASP cc_start: 0.7739 (t0) cc_final: 0.6023 (t0) REVERT: J 226 MET cc_start: 0.9345 (tpp) cc_final: 0.9113 (tpp) REVERT: J 248 HIS cc_start: 0.8554 (m90) cc_final: 0.8225 (m90) REVERT: J 313 CYS cc_start: 0.8753 (m) cc_final: 0.8527 (m) REVERT: K 115 LYS cc_start: 0.9495 (tptp) cc_final: 0.9100 (tptp) REVERT: K 145 LEU cc_start: 0.9351 (tp) cc_final: 0.8901 (tp) REVERT: K 147 MET cc_start: 0.9185 (mmm) cc_final: 0.8767 (mmm) REVERT: K 272 ARG cc_start: 0.4254 (mpt180) cc_final: 0.3828 (mmt-90) outliers start: 3 outliers final: 0 residues processed: 285 average time/residue: 0.2679 time to fit residues: 121.6097 Evaluate side-chains 224 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 222 time to evaluate : 2.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 112 optimal weight: 0.7980 chunk 111 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 166 optimal weight: 6.9990 chunk 148 optimal weight: 1.9990 chunk 106 optimal weight: 30.0000 chunk 133 optimal weight: 8.9990 chunk 119 optimal weight: 8.9990 chunk 161 optimal weight: 10.0000 chunk 168 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- 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 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 361 GLN ** I 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 132 ASN ** J 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.056423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.044583 restraints weight = 91700.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.046478 restraints weight = 49302.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.047827 restraints weight = 31997.536| |-----------------------------------------------------------------------------| r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 18542 Z= 0.245 Angle : 0.647 8.581 25213 Z= 0.341 Chirality : 0.044 0.160 2737 Planarity : 0.005 0.060 3281 Dihedral : 5.008 20.499 2491 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.96 % Favored : 94.00 % Rotamer: Outliers : 0.05 % Allowed : 5.28 % Favored : 94.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.17), residues: 2283 helix: -0.82 (0.37), residues: 190 sheet: -0.38 (0.19), residues: 699 loop : -1.23 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP J 158 HIS 0.009 0.002 HIS H 354 PHE 0.016 0.002 PHE K 296 TYR 0.025 0.002 TYR J 116 ARG 0.007 0.001 ARG H 272 Details of bonding type rmsd hydrogen bonds : bond 0.03855 ( 476) hydrogen bonds : angle 6.54127 ( 1284) SS BOND : bond 0.00252 ( 2) SS BOND : angle 1.35903 ( 4) covalent geometry : bond 0.00518 (18540) covalent geometry : angle 0.64651 (25209) *********************** 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 253 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 252 time to evaluate : 2.037 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: symmetry clash REVERT: A 3 GLN cc_start: 0.8862 (mm110) cc_final: 0.8482 (mm110) REVERT: A 66 ASP cc_start: 0.9501 (p0) cc_final: 0.9273 (p0) REVERT: A 108 GLU cc_start: 0.7384 (mm-30) cc_final: 0.7142 (mm-30) REVERT: B 31 ASN cc_start: 0.9163 (p0) cc_final: 0.8745 (p0) REVERT: B 37 GLN cc_start: 0.8979 (pp30) cc_final: 0.8620 (pp30) REVERT: B 78 LEU cc_start: 0.9402 (mt) cc_final: 0.9096 (mt) REVERT: B 83 PHE cc_start: 0.9119 (m-10) cc_final: 0.8775 (m-10) REVERT: B 87 TYR cc_start: 0.8706 (m-80) cc_final: 0.8433 (m-80) REVERT: C 120 GLU cc_start: 0.8380 (mm-30) cc_final: 0.7795 (mm-30) REVERT: C 138 MET cc_start: 0.8444 (ppp) cc_final: 0.7949 (ppp) REVERT: C 183 VAL cc_start: 0.9162 (m) cc_final: 0.8932 (p) REVERT: C 213 ILE cc_start: 0.9402 (pt) cc_final: 0.9031 (tp) REVERT: C 222 ASP cc_start: 0.7666 (p0) cc_final: 0.6423 (p0) REVERT: C 244 MET cc_start: 0.8610 (tpt) cc_final: 0.8405 (tpt) REVERT: H 34 LEU cc_start: 0.9402 (tp) cc_final: 0.9050 (tt) REVERT: H 96 GLU cc_start: 0.7695 (tp30) cc_final: 0.7284 (tp30) REVERT: H 188 ASP cc_start: 0.9218 (m-30) cc_final: 0.8717 (m-30) REVERT: H 197 MET cc_start: 0.9333 (ppp) cc_final: 0.8526 (ppp) REVERT: H 244 MET cc_start: 0.8051 (tmm) cc_final: 0.7763 (tmm) REVERT: H 251 ASN cc_start: 0.8800 (p0) cc_final: 0.8487 (p0) REVERT: H 331 MET cc_start: 0.8632 (mmm) cc_final: 0.8327 (mmm) REVERT: H 359 ASP cc_start: 0.7031 (m-30) cc_final: 0.6667 (m-30) REVERT: I 197 MET cc_start: 0.7772 (mpp) cc_final: 0.7409 (mpp) REVERT: I 244 MET cc_start: 0.8987 (ppp) cc_final: 0.8318 (ppp) REVERT: I 296 PHE cc_start: 0.8887 (m-10) cc_final: 0.8639 (m-10) REVERT: J 27 TYR cc_start: 0.8844 (m-80) cc_final: 0.8318 (m-10) REVERT: J 110 HIS cc_start: 0.9332 (t-90) cc_final: 0.8913 (t-90) REVERT: J 138 MET cc_start: 0.9259 (pmm) cc_final: 0.8799 (pmm) REVERT: J 140 TYR cc_start: 0.7887 (m-80) cc_final: 0.7660 (m-80) REVERT: J 147 MET cc_start: 0.8513 (mmp) cc_final: 0.8218 (mmm) REVERT: J 218 CYS cc_start: 0.9339 (m) cc_final: 0.8830 (t) REVERT: J 222 ASP cc_start: 0.7980 (t0) cc_final: 0.6555 (t0) REVERT: J 226 MET cc_start: 0.9432 (tpp) cc_final: 0.9222 (tpp) REVERT: K 138 MET cc_start: 0.9043 (mmm) cc_final: 0.8763 (mmm) REVERT: K 147 MET cc_start: 0.9203 (mmm) cc_final: 0.8786 (mmm) REVERT: K 212 ASP cc_start: 0.9185 (p0) cc_final: 0.8918 (p0) REVERT: K 272 ARG cc_start: 0.4853 (mpt180) cc_final: 0.4482 (mmt-90) outliers start: 1 outliers final: 0 residues processed: 253 average time/residue: 0.2860 time to fit residues: 112.8574 Evaluate side-chains 207 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 211 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 172 optimal weight: 7.9990 chunk 38 optimal weight: 0.0970 chunk 134 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 26 optimal weight: 0.0050 chunk 209 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 4 optimal weight: 0.0670 overall best weight: 2.2334 ------------------------------------------------------------------------------- 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 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 HIS ** 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 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 157 HIS ** J 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.057615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.045689 restraints weight = 89934.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.047627 restraints weight = 47906.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.049039 restraints weight = 31071.550| |-----------------------------------------------------------------------------| r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18542 Z= 0.146 Angle : 0.573 6.602 25213 Z= 0.299 Chirality : 0.044 0.163 2737 Planarity : 0.005 0.078 3281 Dihedral : 4.759 19.851 2491 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.99 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.17), residues: 2283 helix: -0.75 (0.37), residues: 190 sheet: -0.35 (0.19), residues: 695 loop : -1.17 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP J 390 HIS 0.009 0.001 HIS I 28 PHE 0.010 0.001 PHE A 29 TYR 0.014 0.001 TYR H 58 ARG 0.014 0.001 ARG J 133 Details of bonding type rmsd hydrogen bonds : bond 0.03459 ( 476) hydrogen bonds : angle 6.28073 ( 1284) SS BOND : bond 0.00626 ( 2) SS BOND : angle 1.61472 ( 4) covalent geometry : bond 0.00318 (18540) covalent geometry : angle 0.57288 (25209) *********************** 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 268 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 2.075 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: symmetry clash REVERT: A 3 GLN cc_start: 0.8923 (mm110) cc_final: 0.8505 (mm110) REVERT: A 66 ASP cc_start: 0.9473 (p0) cc_final: 0.9210 (p0) REVERT: B 31 ASN cc_start: 0.9044 (p0) cc_final: 0.8578 (p0) REVERT: B 78 LEU cc_start: 0.9421 (mt) cc_final: 0.9179 (mt) REVERT: B 83 PHE cc_start: 0.9103 (m-10) cc_final: 0.8776 (m-10) REVERT: C 120 GLU cc_start: 0.8340 (mm-30) cc_final: 0.7717 (mm-30) REVERT: C 138 MET cc_start: 0.8523 (ppp) cc_final: 0.8111 (ppp) REVERT: C 183 VAL cc_start: 0.9185 (m) cc_final: 0.8936 (p) REVERT: C 213 ILE cc_start: 0.9412 (pt) cc_final: 0.9123 (tp) REVERT: C 222 ASP cc_start: 0.7631 (p0) cc_final: 0.6847 (p0) REVERT: C 244 MET cc_start: 0.8692 (tpt) cc_final: 0.8442 (tpt) REVERT: C 321 THR cc_start: 0.8782 (m) cc_final: 0.8570 (m) REVERT: H 34 LEU cc_start: 0.9310 (tp) cc_final: 0.9030 (tt) REVERT: H 96 GLU cc_start: 0.7759 (tp30) cc_final: 0.7435 (tp30) REVERT: H 188 ASP cc_start: 0.9188 (m-30) cc_final: 0.8707 (m-30) REVERT: H 197 MET cc_start: 0.9332 (ppp) cc_final: 0.8444 (ppp) REVERT: H 243 GLN cc_start: 0.7881 (pm20) cc_final: 0.7539 (pm20) REVERT: H 244 MET cc_start: 0.8016 (tmm) cc_final: 0.7725 (tmm) REVERT: H 251 ASN cc_start: 0.8876 (p0) cc_final: 0.8563 (p0) REVERT: H 317 GLN cc_start: 0.9304 (pm20) cc_final: 0.9102 (pm20) REVERT: H 352 MET cc_start: 0.8615 (mmm) cc_final: 0.8318 (mmm) REVERT: H 359 ASP cc_start: 0.7053 (m-30) cc_final: 0.6737 (m-30) REVERT: H 390 TRP cc_start: 0.8461 (m-90) cc_final: 0.7776 (m-90) REVERT: I 197 MET cc_start: 0.7609 (mpp) cc_final: 0.7380 (mpp) REVERT: I 244 MET cc_start: 0.8996 (ppp) cc_final: 0.8341 (ppp) REVERT: J 27 TYR cc_start: 0.8862 (m-80) cc_final: 0.8473 (m-80) REVERT: J 58 TYR cc_start: 0.8874 (m-80) cc_final: 0.8480 (m-10) REVERT: J 110 HIS cc_start: 0.9370 (t-90) cc_final: 0.8889 (t-90) REVERT: J 116 TYR cc_start: 0.4055 (m-10) cc_final: 0.3421 (m-80) REVERT: J 138 MET cc_start: 0.9255 (pmm) cc_final: 0.8782 (pmm) REVERT: J 140 TYR cc_start: 0.7718 (m-80) cc_final: 0.7478 (m-80) REVERT: J 222 ASP cc_start: 0.7975 (t0) cc_final: 0.6418 (t0) REVERT: J 226 MET cc_start: 0.9377 (tpp) cc_final: 0.9132 (tpp) REVERT: K 147 MET cc_start: 0.9069 (mmm) cc_final: 0.8445 (mmm) REVERT: K 212 ASP cc_start: 0.9254 (p0) cc_final: 0.9041 (p0) REVERT: K 244 MET cc_start: 0.8523 (tmm) cc_final: 0.8131 (tmm) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.2980 time to fit residues: 123.9049 Evaluate side-chains 217 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 2.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 101 optimal weight: 0.0870 chunk 115 optimal weight: 7.9990 chunk 222 optimal weight: 10.0000 chunk 188 optimal weight: 20.0000 chunk 104 optimal weight: 9.9990 chunk 125 optimal weight: 0.0970 chunk 75 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 overall best weight: 4.4362 ------------------------------------------------------------------------------- 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 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 157 HIS I 330 ASN ** J 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 354 HIS K 308 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.055542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.043780 restraints weight = 93523.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.045654 restraints weight = 50142.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.046993 restraints weight = 32598.160| |-----------------------------------------------------------------------------| r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2265 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= 0.244 Angle : 0.640 9.106 25213 Z= 0.334 Chirality : 0.044 0.182 2737 Planarity : 0.005 0.084 3281 Dihedral : 5.022 19.604 2491 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.17), residues: 2283 helix: -0.94 (0.37), residues: 190 sheet: -0.43 (0.19), residues: 701 loop : -1.25 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP J 390 HIS 0.011 0.002 HIS I 28 PHE 0.029 0.002 PHE K 245 TYR 0.022 0.002 TYR H 58 ARG 0.012 0.001 ARG H 272 Details of bonding type rmsd hydrogen bonds : bond 0.03700 ( 476) hydrogen bonds : angle 6.29605 ( 1284) SS BOND : bond 0.00427 ( 2) SS BOND : angle 1.43544 ( 4) covalent geometry : bond 0.00521 (18540) covalent geometry : angle 0.63942 (25209) *********************** 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 253 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 2.195 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: 0.8881 (mm110) cc_final: 0.8475 (mm110) REVERT: A 66 ASP cc_start: 0.9502 (p0) cc_final: 0.9274 (p0) REVERT: A 70 MET cc_start: 0.8569 (ppp) cc_final: 0.8322 (ppp) REVERT: B 31 ASN cc_start: 0.8971 (p0) cc_final: 0.8518 (p0) REVERT: B 37 GLN cc_start: 0.8991 (pp30) cc_final: 0.8597 (pp30) REVERT: B 78 LEU cc_start: 0.9392 (mt) cc_final: 0.9096 (mt) REVERT: B 83 PHE cc_start: 0.9136 (m-10) cc_final: 0.8808 (m-10) REVERT: C 120 GLU cc_start: 0.8550 (mm-30) cc_final: 0.7734 (mm-30) REVERT: C 138 MET cc_start: 0.8575 (ppp) cc_final: 0.8117 (ppp) REVERT: C 183 VAL cc_start: 0.9199 (m) cc_final: 0.8939 (p) REVERT: C 222 ASP cc_start: 0.7540 (p0) cc_final: 0.6361 (p0) REVERT: C 244 MET cc_start: 0.8800 (tpt) cc_final: 0.8506 (tpt) REVERT: C 249 PHE cc_start: 0.9165 (m-80) cc_final: 0.8937 (m-10) REVERT: H 96 GLU cc_start: 0.7743 (tp30) cc_final: 0.7333 (tp30) REVERT: H 188 ASP cc_start: 0.9220 (m-30) cc_final: 0.8760 (m-30) REVERT: H 197 MET cc_start: 0.9389 (ppp) cc_final: 0.8455 (ppp) REVERT: H 244 MET cc_start: 0.8113 (tmm) cc_final: 0.7752 (tmm) REVERT: H 251 ASN cc_start: 0.8794 (p0) cc_final: 0.8501 (p0) REVERT: H 317 GLN cc_start: 0.9331 (pm20) cc_final: 0.9042 (pm20) REVERT: H 352 MET cc_start: 0.8681 (mmm) cc_final: 0.8400 (mmm) REVERT: I 244 MET cc_start: 0.9057 (ppp) cc_final: 0.8306 (ppp) REVERT: I 362 PHE cc_start: 0.9359 (m-80) cc_final: 0.9153 (m-80) REVERT: J 27 TYR cc_start: 0.8938 (m-80) cc_final: 0.8539 (m-80) REVERT: J 58 TYR cc_start: 0.8940 (m-80) cc_final: 0.8600 (m-10) REVERT: J 110 HIS cc_start: 0.9366 (t-90) cc_final: 0.8987 (t-90) REVERT: J 138 MET cc_start: 0.9277 (pmm) cc_final: 0.8840 (pmm) REVERT: J 140 TYR cc_start: 0.7847 (m-80) cc_final: 0.7494 (m-80) REVERT: J 147 MET cc_start: 0.8456 (mmp) cc_final: 0.8173 (mmm) REVERT: K 147 MET cc_start: 0.9063 (mmm) cc_final: 0.8504 (mmm) REVERT: K 212 ASP cc_start: 0.9196 (p0) cc_final: 0.8938 (p0) REVERT: K 244 MET cc_start: 0.8345 (tmm) cc_final: 0.8001 (tmm) outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.2986 time to fit residues: 116.3295 Evaluate side-chains 200 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 2.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 114 optimal weight: 0.8980 chunk 85 optimal weight: 8.9990 chunk 189 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 146 optimal weight: 10.0000 chunk 127 optimal weight: 6.9990 chunk 70 optimal weight: 8.9990 chunk 123 optimal weight: 6.9990 chunk 214 optimal weight: 0.6980 chunk 167 optimal weight: 7.9990 chunk 174 optimal weight: 7.9990 overall best weight: 3.2984 ------------------------------------------------------------------------------- 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 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 459 GLN ** J 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 316 ASN ** 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 = 0.3105 r_free = 0.3105 target = 0.055974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.044038 restraints weight = 92404.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.045932 restraints weight = 49524.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.047308 restraints weight = 32245.399| |-----------------------------------------------------------------------------| r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18542 Z= 0.191 Angle : 0.600 7.667 25213 Z= 0.313 Chirality : 0.044 0.164 2737 Planarity : 0.005 0.056 3281 Dihedral : 4.912 21.586 2491 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.05 % Allowed : 1.49 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.17), residues: 2283 helix: -0.89 (0.37), residues: 190 sheet: -0.31 (0.19), residues: 711 loop : -1.26 (0.17), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP I 390 HIS 0.010 0.001 HIS I 28 PHE 0.019 0.002 PHE I 456 TYR 0.020 0.001 TYR H 58 ARG 0.012 0.001 ARG H 272 Details of bonding type rmsd hydrogen bonds : bond 0.03477 ( 476) hydrogen bonds : angle 6.26403 ( 1284) SS BOND : bond 0.00458 ( 2) SS BOND : angle 1.35570 ( 4) covalent geometry : bond 0.00412 (18540) covalent geometry : angle 0.60014 (25209) *********************** 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 248 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 247 time to evaluate : 2.040 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: A 3 GLN cc_start: 0.8913 (mm110) cc_final: 0.8480 (mm110) REVERT: A 66 ASP cc_start: 0.9492 (p0) cc_final: 0.9287 (p0) REVERT: B 31 ASN cc_start: 0.8954 (p0) cc_final: 0.8471 (p0) REVERT: B 37 GLN cc_start: 0.8950 (pp30) cc_final: 0.8589 (pp30) REVERT: B 78 LEU cc_start: 0.9408 (mt) cc_final: 0.9186 (mt) REVERT: B 83 PHE cc_start: 0.9126 (m-10) cc_final: 0.8792 (m-10) REVERT: C 120 GLU cc_start: 0.8513 (mm-30) cc_final: 0.7758 (mm-30) REVERT: C 147 MET cc_start: 0.8173 (ppp) cc_final: 0.7907 (ppp) REVERT: C 183 VAL cc_start: 0.9184 (m) cc_final: 0.8907 (p) REVERT: C 212 ASP cc_start: 0.9212 (p0) cc_final: 0.8689 (p0) REVERT: C 213 ILE cc_start: 0.9379 (pt) cc_final: 0.9064 (tp) REVERT: C 242 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8270 (mm-30) REVERT: C 244 MET cc_start: 0.8830 (tpt) cc_final: 0.8506 (tpt) REVERT: C 249 PHE cc_start: 0.9175 (m-80) cc_final: 0.8929 (m-10) REVERT: C 300 TYR cc_start: 0.8064 (m-80) cc_final: 0.7448 (m-10) REVERT: H 96 GLU cc_start: 0.7865 (tp30) cc_final: 0.7505 (tp30) REVERT: H 188 ASP cc_start: 0.9233 (m-30) cc_final: 0.8773 (m-30) REVERT: H 197 MET cc_start: 0.9389 (ppp) cc_final: 0.8468 (ppp) REVERT: H 244 MET cc_start: 0.8030 (tmm) cc_final: 0.7668 (tmm) REVERT: H 251 ASN cc_start: 0.8802 (p0) cc_final: 0.8437 (p0) REVERT: H 317 GLN cc_start: 0.9326 (pm20) cc_final: 0.9096 (pm20) REVERT: H 352 MET cc_start: 0.8787 (mmm) cc_final: 0.8431 (mmm) REVERT: I 197 MET cc_start: 0.7565 (mpp) cc_final: 0.7278 (mpp) REVERT: I 244 MET cc_start: 0.9050 (ppp) cc_final: 0.8274 (ppp) REVERT: I 362 PHE cc_start: 0.9329 (m-80) cc_final: 0.9115 (m-80) REVERT: J 27 TYR cc_start: 0.8981 (m-80) cc_final: 0.8621 (m-80) REVERT: J 58 TYR cc_start: 0.8904 (m-80) cc_final: 0.8580 (m-10) REVERT: J 110 HIS cc_start: 0.9393 (t-90) cc_final: 0.8873 (t-90) REVERT: J 116 TYR cc_start: 0.3943 (m-10) cc_final: 0.2215 (m-10) REVERT: J 138 MET cc_start: 0.9270 (pmm) cc_final: 0.8826 (pmm) REVERT: J 140 TYR cc_start: 0.7770 (m-80) cc_final: 0.7406 (m-80) REVERT: J 147 MET cc_start: 0.8472 (mmp) cc_final: 0.8250 (mmm) REVERT: J 218 CYS cc_start: 0.9103 (m) cc_final: 0.8878 (m) REVERT: K 147 MET cc_start: 0.9049 (mmm) cc_final: 0.8499 (mmm) REVERT: K 212 ASP cc_start: 0.9259 (p0) cc_final: 0.8974 (p0) outliers start: 1 outliers final: 0 residues processed: 248 average time/residue: 0.2722 time to fit residues: 105.6775 Evaluate side-chains 199 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 2.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 131 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 143 optimal weight: 0.7980 chunk 209 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 102 optimal weight: 8.9990 chunk 99 optimal weight: 1.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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** ** J 144 GLN ** 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 317 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 = 0.3098 r_free = 0.3098 target = 0.055609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.043831 restraints weight = 92263.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.045710 restraints weight = 49605.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.047050 restraints weight = 32265.862| |-----------------------------------------------------------------------------| r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 18542 Z= 0.202 Angle : 0.613 9.240 25213 Z= 0.318 Chirality : 0.044 0.172 2737 Planarity : 0.005 0.075 3281 Dihedral : 4.934 20.212 2491 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.17), residues: 2283 helix: -0.87 (0.37), residues: 190 sheet: -0.55 (0.18), residues: 768 loop : -1.19 (0.17), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP I 390 HIS 0.010 0.001 HIS I 28 PHE 0.017 0.002 PHE C 296 TYR 0.021 0.002 TYR H 58 ARG 0.013 0.001 ARG J 133 Details of bonding type rmsd hydrogen bonds : bond 0.03504 ( 476) hydrogen bonds : angle 6.28571 ( 1284) SS BOND : bond 0.00471 ( 2) SS BOND : angle 1.39878 ( 4) covalent geometry : bond 0.00434 (18540) covalent geometry : angle 0.61247 (25209) *********************** 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 244 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 2.020 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: A 3 GLN cc_start: 0.8902 (mm110) cc_final: 0.8466 (mm110) REVERT: B 4 MET cc_start: 0.8353 (pmm) cc_final: 0.7846 (pmm) REVERT: B 31 ASN cc_start: 0.8947 (p0) cc_final: 0.8499 (p0) REVERT: B 37 GLN cc_start: 0.8926 (pp30) cc_final: 0.8444 (tm-30) REVERT: B 78 LEU cc_start: 0.9366 (mt) cc_final: 0.9142 (mt) REVERT: B 83 PHE cc_start: 0.9063 (m-10) cc_final: 0.8702 (m-10) REVERT: C 120 GLU cc_start: 0.8555 (mm-30) cc_final: 0.7743 (mm-30) REVERT: C 147 MET cc_start: 0.8203 (ppp) cc_final: 0.7954 (ppp) REVERT: C 183 VAL cc_start: 0.9196 (m) cc_final: 0.8920 (p) REVERT: C 222 ASP cc_start: 0.7594 (p0) cc_final: 0.6643 (p0) REVERT: C 243 GLN cc_start: 0.8646 (tp-100) cc_final: 0.8337 (tp-100) REVERT: C 249 PHE cc_start: 0.9225 (m-80) cc_final: 0.8975 (m-10) REVERT: C 300 TYR cc_start: 0.8218 (m-80) cc_final: 0.7516 (m-10) REVERT: H 96 GLU cc_start: 0.7909 (tp30) cc_final: 0.7531 (tp30) REVERT: H 188 ASP cc_start: 0.9178 (m-30) cc_final: 0.8747 (m-30) REVERT: H 244 MET cc_start: 0.8033 (tmm) cc_final: 0.7650 (tmm) REVERT: H 251 ASN cc_start: 0.8824 (p0) cc_final: 0.8457 (p0) REVERT: H 317 GLN cc_start: 0.9313 (pm20) cc_final: 0.9072 (pm20) REVERT: I 197 MET cc_start: 0.7635 (mpp) cc_final: 0.7343 (mpp) REVERT: I 244 MET cc_start: 0.9091 (ppp) cc_final: 0.8313 (ppp) REVERT: J 27 TYR cc_start: 0.8954 (m-80) cc_final: 0.8593 (m-80) REVERT: J 58 TYR cc_start: 0.8884 (m-80) cc_final: 0.8596 (m-10) REVERT: J 110 HIS cc_start: 0.9401 (t-90) cc_final: 0.8921 (t-90) REVERT: J 138 MET cc_start: 0.9226 (pmm) cc_final: 0.8803 (pmm) REVERT: J 140 TYR cc_start: 0.7883 (m-80) cc_final: 0.7489 (m-80) REVERT: J 218 CYS cc_start: 0.9169 (m) cc_final: 0.8929 (m) REVERT: J 390 TRP cc_start: 0.7586 (m-90) cc_final: 0.7213 (m-90) REVERT: K 147 MET cc_start: 0.9059 (mmm) cc_final: 0.8529 (mmm) REVERT: K 212 ASP cc_start: 0.9246 (p0) cc_final: 0.8959 (p0) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.2812 time to fit residues: 108.1109 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 : 4.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 144 optimal weight: 0.0470 chunk 168 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 182 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 146 optimal weight: 8.9990 overall best weight: 1.8086 ------------------------------------------------------------------------------- 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 144 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.057151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.045099 restraints weight = 90132.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.047021 restraints weight = 48480.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.048408 restraints weight = 31546.984| |-----------------------------------------------------------------------------| r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18542 Z= 0.134 Angle : 0.602 8.599 25213 Z= 0.307 Chirality : 0.045 0.182 2737 Planarity : 0.005 0.069 3281 Dihedral : 4.778 19.588 2491 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.17), residues: 2283 helix: -0.68 (0.38), residues: 189 sheet: -0.54 (0.19), residues: 708 loop : -1.12 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP J 158 HIS 0.008 0.001 HIS I 28 PHE 0.019 0.001 PHE I 456 TYR 0.019 0.001 TYR H 58 ARG 0.011 0.000 ARG J 133 Details of bonding type rmsd hydrogen bonds : bond 0.03380 ( 476) hydrogen bonds : angle 6.27570 ( 1284) SS BOND : bond 0.00572 ( 2) SS BOND : angle 1.27996 ( 4) covalent geometry : bond 0.00293 (18540) covalent geometry : angle 0.60172 (25209) *********************** 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 257 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 1.990 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: A 3 GLN cc_start: 0.8923 (mm110) cc_final: 0.8474 (mm110) REVERT: A 66 ASP cc_start: 0.9407 (p0) cc_final: 0.9186 (p0) REVERT: B 4 MET cc_start: 0.8460 (pmm) cc_final: 0.7882 (pmm) REVERT: B 31 ASN cc_start: 0.9002 (p0) cc_final: 0.8507 (p0) REVERT: B 37 GLN cc_start: 0.8924 (pp30) cc_final: 0.8493 (tm-30) REVERT: B 83 PHE cc_start: 0.9070 (m-10) cc_final: 0.8715 (m-10) REVERT: C 120 GLU cc_start: 0.8498 (mm-30) cc_final: 0.7692 (mm-30) REVERT: C 147 MET cc_start: 0.8111 (ppp) cc_final: 0.7854 (ppp) REVERT: C 183 VAL cc_start: 0.9183 (m) cc_final: 0.8910 (p) REVERT: C 212 ASP cc_start: 0.9298 (p0) cc_final: 0.9077 (p0) REVERT: C 222 ASP cc_start: 0.7244 (p0) cc_final: 0.6094 (p0) REVERT: C 243 GLN cc_start: 0.8632 (tp-100) cc_final: 0.8284 (tp-100) REVERT: C 249 PHE cc_start: 0.9199 (m-80) cc_final: 0.8856 (m-10) REVERT: C 300 TYR cc_start: 0.8117 (m-80) cc_final: 0.7368 (m-10) REVERT: C 310 ASN cc_start: 0.7936 (t0) cc_final: 0.7329 (t0) REVERT: H 96 GLU cc_start: 0.7965 (tp30) cc_final: 0.7598 (tp30) REVERT: H 188 ASP cc_start: 0.9198 (m-30) cc_final: 0.8772 (t0) REVERT: H 197 MET cc_start: 0.9118 (ppp) cc_final: 0.8584 (ppp) REVERT: H 244 MET cc_start: 0.8018 (tmm) cc_final: 0.7697 (tmm) REVERT: H 251 ASN cc_start: 0.8868 (p0) cc_final: 0.8494 (p0) REVERT: H 317 GLN cc_start: 0.9296 (pm20) cc_final: 0.9055 (pm20) REVERT: H 352 MET cc_start: 0.8902 (mmm) cc_final: 0.8339 (mmm) REVERT: I 197 MET cc_start: 0.7599 (mpp) cc_final: 0.7289 (mpp) REVERT: J 27 TYR cc_start: 0.8915 (m-80) cc_final: 0.8527 (m-80) REVERT: J 58 TYR cc_start: 0.8838 (m-80) cc_final: 0.8532 (m-10) REVERT: J 110 HIS cc_start: 0.9439 (t-90) cc_final: 0.8899 (t-90) REVERT: J 116 TYR cc_start: 0.3313 (m-10) cc_final: 0.3109 (m-10) REVERT: J 138 MET cc_start: 0.9283 (pmm) cc_final: 0.8865 (pmm) REVERT: J 140 TYR cc_start: 0.7799 (m-80) cc_final: 0.7345 (m-80) REVERT: J 147 MET cc_start: 0.8597 (mmp) cc_final: 0.7979 (mmp) REVERT: J 218 CYS cc_start: 0.9182 (m) cc_final: 0.8906 (m) REVERT: K 147 MET cc_start: 0.9038 (mmm) cc_final: 0.8528 (mmm) REVERT: K 212 ASP cc_start: 0.9295 (p0) cc_final: 0.8973 (p0) outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.3116 time to fit residues: 126.7391 Evaluate side-chains 208 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 2.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 209 optimal weight: 5.9990 chunk 187 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 125 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 310 ASN ** C 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 308 HIS ** J 144 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** ** K 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.054960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.043264 restraints weight = 95018.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.045080 restraints weight = 51253.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.046392 restraints weight = 33552.615| |-----------------------------------------------------------------------------| r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 18542 Z= 0.251 Angle : 0.678 9.953 25213 Z= 0.350 Chirality : 0.045 0.211 2737 Planarity : 0.005 0.063 3281 Dihedral : 5.071 20.626 2491 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 20.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.17), residues: 2283 helix: -0.91 (0.36), residues: 190 sheet: -0.70 (0.18), residues: 754 loop : -1.23 (0.17), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP J 390 HIS 0.011 0.002 HIS I 28 PHE 0.022 0.002 PHE I 456 TYR 0.029 0.002 TYR H 58 ARG 0.011 0.001 ARG J 133 Details of bonding type rmsd hydrogen bonds : bond 0.03660 ( 476) hydrogen bonds : angle 6.44456 ( 1284) SS BOND : bond 0.00343 ( 2) SS BOND : angle 1.30802 ( 4) covalent geometry : bond 0.00535 (18540) covalent geometry : angle 0.67774 (25209) *********************** 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 238 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 2.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8881 (mm110) cc_final: 0.8431 (mm110) REVERT: A 65 GLU cc_start: 0.9396 (pp20) cc_final: 0.9171 (pm20) REVERT: A 108 GLU cc_start: 0.7413 (mm-30) cc_final: 0.7143 (mm-30) REVERT: B 4 MET cc_start: 0.8395 (pmm) cc_final: 0.7855 (pmm) REVERT: B 31 ASN cc_start: 0.9066 (p0) cc_final: 0.8619 (p0) REVERT: B 37 GLN cc_start: 0.8997 (pp30) cc_final: 0.8456 (tm-30) REVERT: B 78 LEU cc_start: 0.9333 (mt) cc_final: 0.9010 (mt) REVERT: B 83 PHE cc_start: 0.9073 (m-10) cc_final: 0.8695 (m-10) REVERT: B 87 TYR cc_start: 0.8805 (m-80) cc_final: 0.8597 (m-80) REVERT: C 120 GLU cc_start: 0.8624 (mm-30) cc_final: 0.7824 (mm-30) REVERT: C 183 VAL cc_start: 0.9262 (m) cc_final: 0.9010 (p) REVERT: C 222 ASP cc_start: 0.7393 (p0) cc_final: 0.6346 (p0) REVERT: C 243 GLN cc_start: 0.8654 (tp-100) cc_final: 0.8309 (tp-100) REVERT: C 249 PHE cc_start: 0.9338 (m-80) cc_final: 0.9003 (m-10) REVERT: C 300 TYR cc_start: 0.8257 (m-80) cc_final: 0.7498 (m-10) REVERT: C 310 ASN cc_start: 0.7906 (t160) cc_final: 0.7579 (t0) REVERT: H 96 GLU cc_start: 0.7826 (tp30) cc_final: 0.7500 (tp30) REVERT: H 188 ASP cc_start: 0.9249 (m-30) cc_final: 0.8845 (t0) REVERT: H 197 MET cc_start: 0.9193 (ppp) cc_final: 0.8565 (ppp) REVERT: H 251 ASN cc_start: 0.8794 (p0) cc_final: 0.8413 (p0) REVERT: H 317 GLN cc_start: 0.9331 (pm20) cc_final: 0.9114 (pm20) REVERT: H 352 MET cc_start: 0.8880 (mmm) cc_final: 0.8310 (mmm) REVERT: I 197 MET cc_start: 0.7713 (mpp) cc_final: 0.7476 (mpp) REVERT: I 244 MET cc_start: 0.9064 (ppp) cc_final: 0.8440 (ppp) REVERT: J 27 TYR cc_start: 0.8940 (m-80) cc_final: 0.8603 (m-80) REVERT: J 54 LYS cc_start: 0.8601 (mmtm) cc_final: 0.8398 (tppt) REVERT: J 58 TYR cc_start: 0.8901 (m-80) cc_final: 0.8615 (m-10) REVERT: J 110 HIS cc_start: 0.9405 (t-90) cc_final: 0.9006 (t-90) REVERT: J 116 TYR cc_start: 0.4143 (m-10) cc_final: 0.3626 (m-80) REVERT: J 138 MET cc_start: 0.9244 (pmm) cc_final: 0.8862 (pmm) REVERT: J 140 TYR cc_start: 0.8006 (m-80) cc_final: 0.7559 (m-80) REVERT: J 147 MET cc_start: 0.8530 (mmp) cc_final: 0.8196 (mmm) REVERT: J 191 ASP cc_start: 0.8924 (p0) cc_final: 0.8711 (p0) REVERT: J 218 CYS cc_start: 0.9219 (m) cc_final: 0.8885 (m) REVERT: J 390 TRP cc_start: 0.7592 (m-90) cc_final: 0.7388 (m-90) REVERT: K 147 MET cc_start: 0.9074 (mmm) cc_final: 0.8575 (mmm) REVERT: K 212 ASP cc_start: 0.9180 (p0) cc_final: 0.8929 (p0) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.2745 time to fit residues: 102.6229 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 : 2.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 148 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 chunk 158 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 46 optimal weight: 0.0040 chunk 157 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 196 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 overall best weight: 2.7998 ------------------------------------------------------------------------------- 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** H 361 GLN ** J 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 = 0.3098 r_free = 0.3098 target = 0.055642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.043764 restraints weight = 91374.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.045634 restraints weight = 49003.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.046980 restraints weight = 31945.162| |-----------------------------------------------------------------------------| r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18542 Z= 0.172 Angle : 0.629 9.888 25213 Z= 0.321 Chirality : 0.045 0.202 2737 Planarity : 0.005 0.064 3281 Dihedral : 4.914 20.033 2491 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.17), residues: 2283 helix: -0.70 (0.37), residues: 190 sheet: -0.65 (0.19), residues: 716 loop : -1.15 (0.17), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP J 390 HIS 0.010 0.001 HIS I 28 PHE 0.015 0.001 PHE C 296 TYR 0.019 0.001 TYR H 58 ARG 0.010 0.001 ARG H 272 Details of bonding type rmsd hydrogen bonds : bond 0.03401 ( 476) hydrogen bonds : angle 6.34360 ( 1284) SS BOND : bond 0.00467 ( 2) SS BOND : angle 1.26864 ( 4) covalent geometry : bond 0.00373 (18540) covalent geometry : angle 0.62907 (25209) ********************** 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 240 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 2.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8891 (mm110) cc_final: 0.8440 (mm110) REVERT: A 66 ASP cc_start: 0.9348 (p0) cc_final: 0.9011 (p0) REVERT: A 108 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7224 (mm-30) REVERT: B 4 MET cc_start: 0.8499 (pmm) cc_final: 0.7847 (pmm) REVERT: B 31 ASN cc_start: 0.9044 (p0) cc_final: 0.8538 (p0) REVERT: B 37 GLN cc_start: 0.9020 (pp30) cc_final: 0.8503 (tm-30) REVERT: B 78 LEU cc_start: 0.9322 (mt) cc_final: 0.9003 (mt) REVERT: B 83 PHE cc_start: 0.9073 (m-10) cc_final: 0.8719 (m-10) REVERT: B 87 TYR cc_start: 0.8782 (m-80) cc_final: 0.8567 (m-80) REVERT: C 120 GLU cc_start: 0.8609 (mm-30) cc_final: 0.7738 (mm-30) REVERT: C 138 MET cc_start: 0.9332 (pmm) cc_final: 0.9119 (pmm) REVERT: C 140 TYR cc_start: 0.8424 (m-80) cc_final: 0.8003 (m-80) REVERT: C 147 MET cc_start: 0.8240 (ppp) cc_final: 0.7963 (ppp) REVERT: C 183 VAL cc_start: 0.9199 (m) cc_final: 0.8933 (p) REVERT: C 222 ASP cc_start: 0.7434 (p0) cc_final: 0.6466 (p0) REVERT: C 243 GLN cc_start: 0.8585 (tp-100) cc_final: 0.8180 (tp-100) REVERT: C 249 PHE cc_start: 0.9244 (m-80) cc_final: 0.8955 (m-10) REVERT: C 300 TYR cc_start: 0.8112 (m-80) cc_final: 0.7339 (m-10) REVERT: H 96 GLU cc_start: 0.7939 (tp30) cc_final: 0.7583 (tp30) REVERT: H 188 ASP cc_start: 0.9252 (m-30) cc_final: 0.8837 (t0) REVERT: H 197 MET cc_start: 0.9182 (ppp) cc_final: 0.8587 (ppp) REVERT: H 244 MET cc_start: 0.7918 (tmm) cc_final: 0.7640 (tmm) REVERT: H 251 ASN cc_start: 0.8844 (p0) cc_final: 0.8475 (p0) REVERT: H 317 GLN cc_start: 0.9290 (pm20) cc_final: 0.9045 (pm20) REVERT: H 331 MET cc_start: 0.8367 (mmm) cc_final: 0.7417 (mmt) REVERT: H 352 MET cc_start: 0.8913 (mmm) cc_final: 0.8342 (mmm) REVERT: H 390 TRP cc_start: 0.8734 (m-10) cc_final: 0.7648 (m-90) REVERT: I 197 MET cc_start: 0.7640 (mpp) cc_final: 0.7265 (mpp) REVERT: I 244 MET cc_start: 0.9085 (ppp) cc_final: 0.8461 (ppp) REVERT: J 27 TYR cc_start: 0.8926 (m-80) cc_final: 0.8554 (m-80) REVERT: J 58 TYR cc_start: 0.8848 (m-80) cc_final: 0.8549 (m-10) REVERT: J 110 HIS cc_start: 0.9402 (t-90) cc_final: 0.8875 (t-90) REVERT: J 116 TYR cc_start: 0.3688 (m-10) cc_final: 0.3307 (m-80) REVERT: J 138 MET cc_start: 0.9244 (pmm) cc_final: 0.8877 (pmm) REVERT: J 140 TYR cc_start: 0.7873 (m-80) cc_final: 0.7476 (m-80) REVERT: J 147 MET cc_start: 0.8583 (mmp) cc_final: 0.8225 (mmm) REVERT: J 218 CYS cc_start: 0.9191 (m) cc_final: 0.8900 (m) REVERT: K 147 MET cc_start: 0.9050 (mmm) cc_final: 0.8539 (mmm) REVERT: K 212 ASP cc_start: 0.9259 (p0) cc_final: 0.8963 (p0) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.2751 time to fit residues: 104.3065 Evaluate side-chains 196 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 2.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 126 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 chunk 95 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 210 optimal weight: 0.6980 chunk 121 optimal weight: 0.6980 chunk 8 optimal weight: 4.9990 chunk 193 optimal weight: 8.9990 chunk 203 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- 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 144 GLN ** 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 = 0.3087 r_free = 0.3087 target = 0.055452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.043668 restraints weight = 91925.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.045528 restraints weight = 49516.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.046899 restraints weight = 32231.087| |-----------------------------------------------------------------------------| r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 18542 Z= 0.199 Angle : 0.634 9.765 25213 Z= 0.326 Chirality : 0.045 0.190 2737 Planarity : 0.005 0.064 3281 Dihedral : 4.957 20.680 2491 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.17), residues: 2283 helix: -0.71 (0.37), residues: 190 sheet: -0.66 (0.19), residues: 712 loop : -1.17 (0.17), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP J 390 HIS 0.010 0.001 HIS I 28 PHE 0.022 0.002 PHE I 456 TYR 0.024 0.002 TYR H 58 ARG 0.009 0.001 ARG J 133 Details of bonding type rmsd hydrogen bonds : bond 0.03466 ( 476) hydrogen bonds : angle 6.37004 ( 1284) SS BOND : bond 0.00400 ( 2) SS BOND : angle 1.29897 ( 4) covalent geometry : bond 0.00428 (18540) covalent geometry : angle 0.63386 (25209) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4879.19 seconds wall clock time: 86 minutes 21.31 seconds (5181.31 seconds total)