Starting phenix.real_space_refine on Mon May 19 07:58:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yef_39193/05_2025/8yef_39193.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yef_39193/05_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_39193/05_2025/8yef_39193.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yef_39193/05_2025/8yef_39193.map" model { file = "/net/cci-nas-00/data/ceres_data/8yef_39193/05_2025/8yef_39193.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yef_39193/05_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 10.42, per 1000 atoms: 0.58 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: 4.12 Conformation dependent library (CDL) restraints added in 2.2 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: 2.48 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: 5.74 Time building geometry restraints manager: 4.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5793 1.34 - 1.46: 4316 1.46 - 1.58: 8281 1.58 - 1.70: 0 1.70 - 1.82: 150 Bond restraints: 18540 Sorted by residual: bond pdb=" CB ASN J 121 " pdb=" CG ASN J 121 " ideal model delta sigma weight residual 1.516 1.566 -0.050 2.50e-02 1.60e+03 3.93e+00 bond pdb=" CA ASN J 166 " pdb=" CB ASN J 166 " ideal model delta sigma weight residual 1.530 1.557 -0.027 1.69e-02 3.50e+03 2.51e+00 bond pdb=" CB GLU C 242 " pdb=" CG GLU C 242 " ideal model delta sigma weight residual 1.520 1.566 -0.046 3.00e-02 1.11e+03 2.30e+00 bond pdb=" CA ASN J 121 " pdb=" CB ASN J 121 " ideal model delta sigma weight residual 1.533 1.557 -0.023 1.66e-02 3.63e+03 1.99e+00 bond pdb=" CB GLN C 142 " pdb=" CG GLN C 142 " ideal model delta sigma weight residual 1.520 1.478 0.042 3.00e-02 1.11e+03 1.98e+00 ... (remaining 18535 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 24552 2.59 - 5.18: 570 5.18 - 7.77: 69 7.77 - 10.36: 14 10.36 - 12.95: 4 Bond angle restraints: 25209 Sorted by residual: angle pdb=" C THR J 165 " pdb=" N ASN J 166 " pdb=" CA ASN J 166 " ideal model delta sigma weight residual 121.54 130.19 -8.65 1.91e+00 2.74e-01 2.05e+01 angle pdb=" C TRP J 390 " pdb=" N ASN J 391 " pdb=" CA ASN J 391 " ideal model delta sigma weight residual 122.82 129.21 -6.39 1.42e+00 4.96e-01 2.03e+01 angle pdb=" CB MET H 352 " pdb=" CG MET H 352 " pdb=" SD MET H 352 " ideal model delta sigma weight residual 112.70 99.75 12.95 3.00e+00 1.11e-01 1.86e+01 angle pdb=" CB LYS H 304 " pdb=" CG LYS H 304 " pdb=" CD LYS H 304 " ideal model delta sigma weight residual 111.30 121.22 -9.92 2.30e+00 1.89e-01 1.86e+01 angle pdb=" C ALA J 47 " pdb=" N ASN J 48 " pdb=" CA ASN J 48 " ideal model delta sigma weight residual 121.54 129.67 -8.13 1.91e+00 2.74e-01 1.81e+01 ... (remaining 25204 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 9911 17.83 - 35.65: 847 35.65 - 53.48: 124 53.48 - 71.31: 35 71.31 - 89.14: 18 Dihedral angle restraints: 10935 sinusoidal: 4291 harmonic: 6644 Sorted by residual: dihedral pdb=" CB CYS B 23 " pdb=" SG CYS B 23 " pdb=" SG CYS B 88 " pdb=" CB CYS B 88 " ideal model delta sinusoidal sigma weight residual 93.00 149.62 -56.62 1 1.00e+01 1.00e-02 4.32e+01 dihedral pdb=" CB CYS A 22 " pdb=" SG CYS A 22 " pdb=" SG CYS A 96 " pdb=" CB CYS A 96 " ideal model delta sinusoidal sigma weight residual 93.00 144.05 -51.05 1 1.00e+01 1.00e-02 3.57e+01 dihedral pdb=" CA GLN C 243 " pdb=" C GLN C 243 " pdb=" N MET C 244 " pdb=" CA MET C 244 " ideal model delta harmonic sigma weight residual -180.00 -152.69 -27.31 0 5.00e+00 4.00e-02 2.98e+01 ... (remaining 10932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2087 0.061 - 0.121: 555 0.121 - 0.182: 82 0.182 - 0.243: 8 0.243 - 0.304: 5 Chirality restraints: 2737 Sorted by residual: chirality pdb=" CA TYR J 116 " pdb=" N TYR J 116 " pdb=" C TYR J 116 " pdb=" CB TYR J 116 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CB THR J 50 " pdb=" CA THR J 50 " pdb=" OG1 THR J 50 " pdb=" CG2 THR J 50 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CB THR K 50 " pdb=" CA THR K 50 " pdb=" OG1 THR K 50 " pdb=" CG2 THR K 50 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 2734 not shown) Planarity restraints: 3281 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP J 390 " 0.034 2.00e-02 2.50e+03 3.82e-02 3.64e+01 pdb=" CG TRP J 390 " -0.099 2.00e-02 2.50e+03 pdb=" CD1 TRP J 390 " 0.057 2.00e-02 2.50e+03 pdb=" CD2 TRP J 390 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP J 390 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP J 390 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP J 390 " 0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 390 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 390 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP J 390 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP I 390 " 0.026 2.00e-02 2.50e+03 2.78e-02 1.93e+01 pdb=" CG TRP I 390 " -0.075 2.00e-02 2.50e+03 pdb=" CD1 TRP I 390 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP I 390 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP I 390 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP I 390 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP I 390 " 0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 390 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 390 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP I 390 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 390 " 0.024 2.00e-02 2.50e+03 2.50e-02 1.56e+01 pdb=" CG TRP C 390 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 TRP C 390 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP C 390 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 390 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 390 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 390 " 0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 390 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 390 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 390 " 0.001 2.00e-02 2.50e+03 ... (remaining 3278 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 3236 2.77 - 3.30: 17777 3.30 - 3.83: 31794 3.83 - 4.37: 36002 4.37 - 4.90: 60404 Nonbonded interactions: 149213 Sorted by model distance: nonbonded pdb=" OE1 GLN K 142 " pdb=" OG1 THR K 325 " model vdw 2.234 3.040 nonbonded pdb=" O GLY C 172 " pdb=" OH TYR I 351 " model vdw 2.237 3.040 nonbonded pdb=" OG1 THR H 338 " pdb=" OD1 ASP H 347 " model vdw 2.262 3.040 nonbonded pdb=" ND1 HIS H 248 " pdb=" OE2 GLU J 120 " model vdw 2.270 3.120 nonbonded pdb=" O GLY C 193 " pdb=" OG1 THR I 329 " model vdw 2.278 3.040 ... (remaining 149208 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 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: 0.700 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 39.630 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.180 ------------------------------------------------------------------------------- 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 : 2.241 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: 0.2764 time to fit residues: 121.7025 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 : 2.043 ------------------------------------------------------------------------------- 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 = 32)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.047648 restraints weight = 87432.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.049730 restraints weight = 46327.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.051207 restraints weight = 29602.542| |-----------------------------------------------------------------------------| 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 6.75656 ( 1284) SS BOND : bond 0.00551 ( 2) SS BOND : angle 1.65549 ( 4) covalent geometry : bond 0.00247 (18540) covalent geometry : angle 0.58257 (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 : 2.054 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: 0.8899 (mm110) cc_final: 0.8494 (mm110) REVERT: A 66 ASP cc_start: 0.9454 (p0) cc_final: 0.9183 (p0) REVERT: B 31 ASN cc_start: 0.9153 (p0) cc_final: 0.8728 (p0) REVERT: B 37 GLN cc_start: 0.9004 (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: 0.9075 (m-10) cc_final: 0.8762 (m-10) REVERT: B 87 TYR cc_start: 0.8710 (m-80) cc_final: 0.8419 (m-80) REVERT: C 138 MET cc_start: 0.8278 (ppp) cc_final: 0.7932 (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: 0.9415 (pt) cc_final: 0.9055 (tp) REVERT: C 222 ASP cc_start: 0.7570 (p0) cc_final: 0.6938 (p0) REVERT: C 244 MET cc_start: 0.8662 (tpt) cc_final: 0.8380 (tpt) REVERT: C 292 GLU cc_start: 0.9058 (pm20) cc_final: 0.8805 (pm20) REVERT: C 321 THR cc_start: 0.8976 (m) cc_final: 0.8508 (m) REVERT: C 390 TRP cc_start: 0.8981 (m-90) cc_final: 0.8405 (m-90) REVERT: H 96 GLU cc_start: 0.7849 (tp30) cc_final: 0.7485 (tp30) REVERT: H 119 VAL cc_start: 0.9394 (OUTLIER) cc_final: 0.9005 (p) REVERT: H 188 ASP cc_start: 0.9137 (m-30) cc_final: 0.8767 (m-30) REVERT: H 197 MET cc_start: 0.9127 (ppp) cc_final: 0.8083 (ppp) REVERT: H 251 ASN cc_start: 0.8761 (p0) cc_final: 0.8263 (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: 0.7743 (mpp) cc_final: 0.7331 (mpp) REVERT: I 244 MET cc_start: 0.8915 (ppp) cc_final: 0.8267 (ppp) REVERT: I 446 GLU cc_start: 0.8767 (tp30) cc_final: 0.8315 (tp30) REVERT: I 448 ASP cc_start: 0.9622 (m-30) cc_final: 0.9397 (m-30) REVERT: J 27 TYR cc_start: 0.8693 (m-80) cc_final: 0.8391 (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: 0.6950 (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: 0.8430 (mmm) REVERT: J 197 MET cc_start: 0.7323 (mmp) cc_final: 0.6981 (mmp) REVERT: J 218 CYS cc_start: 0.8970 (m) cc_final: 0.8766 (m) REVERT: J 222 ASP cc_start: 0.7743 (t0) cc_final: 0.6029 (t0) REVERT: J 226 MET cc_start: 0.9344 (tpp) cc_final: 0.9113 (tpp) REVERT: J 248 HIS cc_start: 0.8553 (m90) cc_final: 0.8225 (m90) REVERT: J 313 CYS cc_start: 0.8753 (m) cc_final: 0.8526 (m) REVERT: K 115 LYS cc_start: 0.9494 (tptp) cc_final: 0.9100 (tptp) REVERT: K 145 LEU cc_start: 0.9351 (tp) cc_final: 0.8900 (tp) REVERT: K 147 MET cc_start: 0.9184 (mmm) cc_final: 0.8766 (mmm) REVERT: K 272 ARG cc_start: 0.4256 (mpt180) cc_final: 0.3829 (mmt-90) outliers start: 3 outliers final: 0 residues processed: 285 average time/residue: 0.2645 time to fit residues: 119.4258 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 : 2.078 ------------------------------------------------------------------------------- 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: 20.0000 chunk 111 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 166 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 chunk 106 optimal weight: 30.0000 chunk 133 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 chunk 161 optimal weight: 10.0000 chunk 168 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 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 J 354 HIS ** 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 = 0.3092 r_free = 0.3092 target = 0.055399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.043592 restraints weight = 92423.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.045459 restraints weight = 49773.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.046778 restraints weight = 32361.642| |-----------------------------------------------------------------------------| r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 18542 Z= 0.274 Angle : 0.675 9.361 25213 Z= 0.355 Chirality : 0.044 0.169 2737 Planarity : 0.005 0.060 3281 Dihedral : 5.110 20.418 2491 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.22 % Favored : 93.74 % Rotamer: Outliers : 0.05 % Allowed : 5.73 % Favored : 94.22 % 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: -0.88 (0.37), residues: 190 sheet: -0.43 (0.19), residues: 699 loop : -1.25 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP J 158 HIS 0.010 0.002 HIS H 354 PHE 0.018 0.002 PHE K 296 TYR 0.027 0.002 TYR J 116 ARG 0.008 0.001 ARG H 272 Details of bonding type rmsd hydrogen bonds : bond 0.03966 ( 476) hydrogen bonds : angle 6.59488 ( 1284) SS BOND : bond 0.00212 ( 2) SS BOND : angle 1.37267 ( 4) covalent geometry : bond 0.00579 (18540) covalent geometry : angle 0.67480 (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 246 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 245 time to evaluate : 2.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8844 (mm110) cc_final: 0.8467 (mm110) REVERT: A 66 ASP cc_start: 0.9483 (p0) cc_final: 0.9260 (p0) REVERT: A 108 GLU cc_start: 0.7367 (mm-30) cc_final: 0.7135 (mm-30) REVERT: B 31 ASN cc_start: 0.9091 (p0) cc_final: 0.8642 (p0) REVERT: B 37 GLN cc_start: 0.9013 (pp30) cc_final: 0.8651 (pp30) REVERT: B 78 LEU cc_start: 0.9398 (mt) cc_final: 0.9093 (mt) REVERT: B 83 PHE cc_start: 0.9126 (m-10) cc_final: 0.8794 (m-10) REVERT: B 87 TYR cc_start: 0.8714 (m-80) cc_final: 0.8423 (m-80) REVERT: C 120 GLU cc_start: 0.8432 (mm-30) cc_final: 0.7805 (mm-30) REVERT: C 138 MET cc_start: 0.8438 (ppp) cc_final: 0.7976 (ppp) REVERT: C 140 TYR cc_start: 0.8386 (m-80) cc_final: 0.8185 (m-10) REVERT: C 183 VAL cc_start: 0.9170 (m) cc_final: 0.8941 (p) REVERT: C 213 ILE cc_start: 0.9416 (pt) cc_final: 0.9049 (tp) REVERT: C 222 ASP cc_start: 0.7685 (p0) cc_final: 0.6450 (p0) REVERT: C 244 MET cc_start: 0.8635 (tpt) cc_final: 0.8426 (tpt) REVERT: H 34 LEU cc_start: 0.9396 (tp) cc_final: 0.9015 (tt) REVERT: H 188 ASP cc_start: 0.9226 (m-30) cc_final: 0.8720 (m-30) REVERT: H 197 MET cc_start: 0.9353 (ppp) cc_final: 0.8541 (ppp) REVERT: H 244 MET cc_start: 0.8046 (tmm) cc_final: 0.7750 (tmm) REVERT: H 251 ASN cc_start: 0.8820 (p0) cc_final: 0.8502 (p0) REVERT: H 359 ASP cc_start: 0.7093 (m-30) cc_final: 0.6774 (m-30) REVERT: I 197 MET cc_start: 0.7728 (mpp) cc_final: 0.7353 (mpp) REVERT: I 244 MET cc_start: 0.8998 (ppp) cc_final: 0.8319 (ppp) REVERT: I 296 PHE cc_start: 0.8875 (m-10) cc_final: 0.8639 (m-10) REVERT: J 27 TYR cc_start: 0.8887 (m-80) cc_final: 0.8364 (m-10) REVERT: J 110 HIS cc_start: 0.9320 (t-90) cc_final: 0.8896 (t-90) REVERT: J 138 MET cc_start: 0.9233 (pmm) cc_final: 0.8767 (pmm) REVERT: J 140 TYR cc_start: 0.7884 (m-80) cc_final: 0.7638 (m-80) REVERT: J 147 MET cc_start: 0.8529 (mmp) cc_final: 0.8247 (mmm) REVERT: J 218 CYS cc_start: 0.9355 (m) cc_final: 0.8850 (t) REVERT: J 222 ASP cc_start: 0.8029 (t0) cc_final: 0.6582 (t0) REVERT: J 226 MET cc_start: 0.9434 (tpp) cc_final: 0.9232 (tpp) REVERT: K 138 MET cc_start: 0.9049 (mmm) cc_final: 0.8721 (mmm) REVERT: K 147 MET cc_start: 0.9136 (mmm) cc_final: 0.8690 (mmm) REVERT: K 212 ASP cc_start: 0.9201 (p0) cc_final: 0.8963 (p0) REVERT: K 272 ARG cc_start: 0.4883 (mpt180) cc_final: 0.4435 (mmt-90) outliers start: 1 outliers final: 0 residues processed: 246 average time/residue: 0.2849 time to fit residues: 109.6771 Evaluate side-chains 201 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 2.354 ------------------------------------------------------------------------------- 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: 5.9990 chunk 80 optimal weight: 4.9990 chunk 172 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 134 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 26 optimal weight: 20.0000 chunk 209 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 4 optimal weight: 0.0980 overall best weight: 3.3786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 361 GLN ** 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** K 308 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.056377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.044549 restraints weight = 91413.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.046449 restraints weight = 48799.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.047823 restraints weight = 31738.113| |-----------------------------------------------------------------------------| r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18542 Z= 0.194 Angle : 0.598 7.815 25213 Z= 0.314 Chirality : 0.044 0.180 2737 Planarity : 0.005 0.082 3281 Dihedral : 4.910 19.806 2491 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.52 % Favored : 94.44 % 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: -1.42 (0.17), residues: 2283 helix: -0.88 (0.37), residues: 190 sheet: -0.42 (0.19), residues: 695 loop : -1.23 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP J 390 HIS 0.010 0.001 HIS I 28 PHE 0.011 0.001 PHE K 296 TYR 0.016 0.002 TYR H 58 ARG 0.013 0.001 ARG J 133 Details of bonding type rmsd hydrogen bonds : bond 0.03579 ( 476) hydrogen bonds : angle 6.34583 ( 1284) SS BOND : bond 0.00579 ( 2) SS BOND : angle 1.66359 ( 4) covalent geometry : bond 0.00415 (18540) covalent geometry : angle 0.59802 (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 256 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 2.152 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: 0.8888 (mm110) cc_final: 0.8476 (mm110) REVERT: A 66 ASP cc_start: 0.9489 (p0) cc_final: 0.9258 (p0) REVERT: B 31 ASN cc_start: 0.8988 (p0) cc_final: 0.8509 (p0) REVERT: B 37 GLN cc_start: 0.8987 (pp30) cc_final: 0.8637 (pp30) REVERT: B 78 LEU cc_start: 0.9421 (mt) cc_final: 0.9167 (mt) REVERT: B 83 PHE cc_start: 0.9115 (m-10) cc_final: 0.8791 (m-10) REVERT: C 138 MET cc_start: 0.8514 (ppp) cc_final: 0.7985 (ppp) REVERT: C 140 TYR cc_start: 0.8168 (m-80) cc_final: 0.7937 (m-10) REVERT: C 183 VAL cc_start: 0.9167 (m) cc_final: 0.8903 (p) REVERT: C 213 ILE cc_start: 0.9446 (pt) cc_final: 0.9138 (tp) REVERT: C 222 ASP cc_start: 0.7663 (p0) cc_final: 0.6883 (p0) REVERT: C 244 MET cc_start: 0.8751 (tpt) cc_final: 0.8524 (tpt) REVERT: C 321 THR cc_start: 0.8739 (m) cc_final: 0.8502 (m) REVERT: H 34 LEU cc_start: 0.9316 (tp) cc_final: 0.9081 (tt) REVERT: H 96 GLU cc_start: 0.7723 (tp30) cc_final: 0.7393 (tp30) REVERT: H 188 ASP cc_start: 0.9168 (m-30) cc_final: 0.8706 (m-30) REVERT: H 197 MET cc_start: 0.9420 (ppp) cc_final: 0.8504 (ppp) REVERT: H 244 MET cc_start: 0.8051 (tmm) cc_final: 0.7670 (tmm) REVERT: H 251 ASN cc_start: 0.8748 (p0) cc_final: 0.8426 (p0) REVERT: H 352 MET cc_start: 0.8614 (mmm) cc_final: 0.8296 (mmm) REVERT: I 197 MET cc_start: 0.7744 (mpp) cc_final: 0.7440 (mpp) REVERT: I 244 MET cc_start: 0.9013 (ppp) cc_final: 0.8283 (ppp) REVERT: J 27 TYR cc_start: 0.8865 (m-80) cc_final: 0.8505 (m-80) REVERT: J 58 TYR cc_start: 0.8865 (m-80) cc_final: 0.8476 (m-10) REVERT: J 110 HIS cc_start: 0.9362 (t-90) cc_final: 0.8879 (t-90) REVERT: J 116 TYR cc_start: 0.4471 (m-10) cc_final: 0.4240 (m-80) REVERT: J 138 MET cc_start: 0.9282 (pmm) cc_final: 0.8855 (pmm) REVERT: J 140 TYR cc_start: 0.7769 (m-80) cc_final: 0.7438 (m-80) REVERT: J 222 ASP cc_start: 0.8032 (t0) cc_final: 0.6533 (t0) REVERT: J 226 MET cc_start: 0.9400 (tpp) cc_final: 0.9180 (tpp) REVERT: K 147 MET cc_start: 0.9093 (mmm) cc_final: 0.8475 (mmm) REVERT: K 212 ASP cc_start: 0.9223 (p0) cc_final: 0.8918 (p0) REVERT: K 244 MET cc_start: 0.8549 (tmm) cc_final: 0.8154 (tmm) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.2845 time to fit residues: 112.1734 Evaluate side-chains 205 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 1.992 ------------------------------------------------------------------------------- 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: 0.9990 chunk 115 optimal weight: 0.6980 chunk 222 optimal weight: 10.0000 chunk 188 optimal weight: 9.9990 chunk 104 optimal weight: 9.9990 chunk 125 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 chunk 132 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- 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 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 248 HIS H 459 GLN I 157 HIS ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.056147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.044334 restraints weight = 91997.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.046224 restraints weight = 49195.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.047575 restraints weight = 32041.498| |-----------------------------------------------------------------------------| r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18542 Z= 0.202 Angle : 0.608 8.246 25213 Z= 0.317 Chirality : 0.044 0.174 2737 Planarity : 0.005 0.058 3281 Dihedral : 4.943 19.776 2491 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.87 % Favored : 94.09 % Rotamer: Outliers : 0.10 % Allowed : 2.74 % Favored : 97.16 % 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: -0.92 (0.37), residues: 190 sheet: -0.41 (0.19), residues: 695 loop : -1.27 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP J 390 HIS 0.010 0.001 HIS I 28 PHE 0.026 0.002 PHE K 245 TYR 0.021 0.002 TYR H 58 ARG 0.011 0.001 ARG H 272 Details of bonding type rmsd hydrogen bonds : bond 0.03588 ( 476) hydrogen bonds : angle 6.28803 ( 1284) SS BOND : bond 0.00460 ( 2) SS BOND : angle 1.51173 ( 4) covalent geometry : bond 0.00436 (18540) covalent geometry : angle 0.60782 (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 256 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 254 time to evaluate : 2.105 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: 0.8872 (mm110) cc_final: 0.8464 (mm110) REVERT: A 66 ASP cc_start: 0.9493 (p0) cc_final: 0.9289 (p0) REVERT: B 31 ASN cc_start: 0.8981 (p0) cc_final: 0.8499 (p0) REVERT: B 37 GLN cc_start: 0.9004 (pp30) cc_final: 0.8610 (pp30) REVERT: B 78 LEU cc_start: 0.9410 (mt) cc_final: 0.9132 (mt) REVERT: B 83 PHE cc_start: 0.9131 (m-10) cc_final: 0.8812 (m-10) REVERT: C 120 GLU cc_start: 0.8474 (mm-30) cc_final: 0.7597 (mm-30) REVERT: C 138 MET cc_start: 0.8502 (ppp) cc_final: 0.7949 (ppp) REVERT: C 183 VAL cc_start: 0.9187 (m) cc_final: 0.8918 (p) REVERT: C 222 ASP cc_start: 0.7554 (p0) cc_final: 0.6420 (p0) REVERT: C 243 GLN cc_start: 0.8583 (tp-100) cc_final: 0.8355 (tp-100) REVERT: C 244 MET cc_start: 0.8791 (tpt) cc_final: 0.8450 (tpt) REVERT: H 96 GLU cc_start: 0.7848 (tp30) cc_final: 0.7481 (tp30) REVERT: H 188 ASP cc_start: 0.9210 (m-30) cc_final: 0.8747 (m-30) REVERT: H 197 MET cc_start: 0.9458 (ppp) cc_final: 0.8496 (ppp) REVERT: H 244 MET cc_start: 0.8117 (tmm) cc_final: 0.7733 (tmm) REVERT: H 251 ASN cc_start: 0.8789 (p0) cc_final: 0.8468 (p0) REVERT: H 352 MET cc_start: 0.8685 (mmm) cc_final: 0.8408 (mmm) REVERT: I 197 MET cc_start: 0.7625 (mpp) cc_final: 0.7398 (mpp) REVERT: I 244 MET cc_start: 0.9059 (ppp) cc_final: 0.8288 (ppp) REVERT: J 27 TYR cc_start: 0.8944 (m-80) cc_final: 0.8552 (m-80) REVERT: J 58 TYR cc_start: 0.8896 (m-80) cc_final: 0.8521 (m-10) REVERT: J 110 HIS cc_start: 0.9385 (t-90) cc_final: 0.8893 (t-90) REVERT: J 116 TYR cc_start: 0.4868 (m-10) cc_final: 0.3159 (m-10) REVERT: J 138 MET cc_start: 0.9283 (pmm) cc_final: 0.8857 (pmm) REVERT: J 140 TYR cc_start: 0.7771 (m-80) cc_final: 0.7438 (m-80) REVERT: J 147 MET cc_start: 0.8519 (mmp) cc_final: 0.8243 (mmm) REVERT: J 390 TRP cc_start: 0.7710 (m-90) cc_final: 0.7228 (m-90) REVERT: K 147 MET cc_start: 0.9039 (mmm) cc_final: 0.8484 (mmm) REVERT: K 244 MET cc_start: 0.8401 (tmm) cc_final: 0.8029 (tmm) outliers start: 2 outliers final: 1 residues processed: 256 average time/residue: 0.2744 time to fit residues: 108.9918 Evaluate side-chains 208 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 207 time to evaluate : 1.976 ------------------------------------------------------------------------------- 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: 1.9990 chunk 85 optimal weight: 6.9990 chunk 189 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 146 optimal weight: 9.9990 chunk 127 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 chunk 214 optimal weight: 6.9990 chunk 167 optimal weight: 9.9990 chunk 174 optimal weight: 10.0000 overall best weight: 3.1986 ------------------------------------------------------------------------------- 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 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.055990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.044057 restraints weight = 92435.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.045971 restraints weight = 49451.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.047320 restraints weight = 32084.818| |-----------------------------------------------------------------------------| r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2353 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= 0.186 Angle : 0.598 7.480 25213 Z= 0.312 Chirality : 0.044 0.172 2737 Planarity : 0.005 0.057 3281 Dihedral : 4.888 22.173 2491 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % 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: -1.39 (0.17), residues: 2283 helix: -0.89 (0.37), residues: 190 sheet: -0.31 (0.19), residues: 711 loop : -1.27 (0.17), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.002 TRP I 390 HIS 0.010 0.001 HIS I 28 PHE 0.021 0.001 PHE I 456 TYR 0.021 0.001 TYR H 58 ARG 0.010 0.001 ARG H 272 Details of bonding type rmsd hydrogen bonds : bond 0.03480 ( 476) hydrogen bonds : angle 6.27211 ( 1284) SS BOND : bond 0.00472 ( 2) SS BOND : angle 1.42763 ( 4) covalent geometry : bond 0.00400 (18540) covalent geometry : angle 0.59798 (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 250 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 2.098 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: 0.8883 (mm110) cc_final: 0.8448 (mm110) REVERT: B 4 MET cc_start: 0.8418 (pmm) cc_final: 0.7853 (pmm) REVERT: B 31 ASN cc_start: 0.8956 (p0) cc_final: 0.8487 (p0) REVERT: B 37 GLN cc_start: 0.8965 (pp30) cc_final: 0.8607 (pp30) REVERT: B 78 LEU cc_start: 0.9386 (mt) cc_final: 0.9167 (mt) REVERT: B 83 PHE cc_start: 0.9117 (m-10) cc_final: 0.8809 (m-10) REVERT: C 120 GLU cc_start: 0.8531 (mm-30) cc_final: 0.7718 (mm-30) REVERT: C 147 MET cc_start: 0.8188 (ppp) cc_final: 0.7967 (ppp) REVERT: C 183 VAL cc_start: 0.9155 (m) cc_final: 0.8871 (p) REVERT: C 212 ASP cc_start: 0.9463 (p0) cc_final: 0.8857 (p0) REVERT: C 242 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8251 (mm-30) REVERT: C 244 MET cc_start: 0.8847 (tpt) cc_final: 0.8587 (tpt) REVERT: C 300 TYR cc_start: 0.8075 (m-80) cc_final: 0.7407 (m-10) REVERT: H 96 GLU cc_start: 0.7898 (tp30) cc_final: 0.7525 (tp30) REVERT: H 188 ASP cc_start: 0.9219 (m-30) cc_final: 0.8752 (m-30) REVERT: H 197 MET cc_start: 0.9425 (ppp) cc_final: 0.8469 (ppp) REVERT: H 244 MET cc_start: 0.8071 (tmm) cc_final: 0.7671 (tmm) REVERT: H 251 ASN cc_start: 0.8783 (p0) cc_final: 0.8400 (p0) REVERT: H 352 MET cc_start: 0.8817 (mmm) cc_final: 0.8444 (mmm) REVERT: I 197 MET cc_start: 0.7619 (mpp) cc_final: 0.7346 (mpp) REVERT: I 244 MET cc_start: 0.9069 (ppp) cc_final: 0.8314 (ppp) REVERT: J 27 TYR cc_start: 0.8956 (m-80) cc_final: 0.8614 (m-80) REVERT: J 58 TYR cc_start: 0.8910 (m-80) cc_final: 0.8576 (m-10) REVERT: J 110 HIS cc_start: 0.9391 (t-90) cc_final: 0.8865 (t-90) REVERT: J 116 TYR cc_start: 0.4212 (m-10) cc_final: 0.3972 (m-80) REVERT: J 138 MET cc_start: 0.9243 (pmm) cc_final: 0.8821 (pmm) REVERT: J 140 TYR cc_start: 0.7768 (m-80) cc_final: 0.7435 (m-80) REVERT: J 218 CYS cc_start: 0.9093 (m) cc_final: 0.8872 (m) REVERT: K 147 MET cc_start: 0.9045 (mmm) cc_final: 0.8511 (mmm) REVERT: K 212 ASP cc_start: 0.9193 (p0) cc_final: 0.8979 (p0) outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 0.2803 time to fit residues: 109.6827 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 : 2.102 ------------------------------------------------------------------------------- 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: 0.8980 chunk 98 optimal weight: 10.0000 chunk 140 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 81 optimal weight: 9.9990 chunk 143 optimal weight: 0.8980 chunk 209 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.056102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.044257 restraints weight = 90273.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.046170 restraints weight = 48334.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.047535 restraints weight = 31311.202| |-----------------------------------------------------------------------------| r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18542 Z= 0.169 Angle : 0.602 9.253 25213 Z= 0.311 Chirality : 0.044 0.157 2737 Planarity : 0.005 0.085 3281 Dihedral : 4.842 20.039 2491 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % 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: -0.84 (0.37), residues: 190 sheet: -0.31 (0.19), residues: 710 loop : -1.27 (0.16), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP J 390 HIS 0.009 0.001 HIS I 28 PHE 0.021 0.001 PHE I 456 TYR 0.022 0.001 TYR I 358 ARG 0.016 0.001 ARG J 133 Details of bonding type rmsd hydrogen bonds : bond 0.03473 ( 476) hydrogen bonds : angle 6.29641 ( 1284) SS BOND : bond 0.00478 ( 2) SS BOND : angle 1.37813 ( 4) covalent geometry : bond 0.00366 (18540) covalent geometry : angle 0.60207 (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 258 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 2.052 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: 0.8883 (mm110) cc_final: 0.8449 (mm110) REVERT: A 66 ASP cc_start: 0.9443 (p0) cc_final: 0.9220 (p0) REVERT: B 4 MET cc_start: 0.8474 (pmm) cc_final: 0.7844 (pmm) REVERT: B 31 ASN cc_start: 0.8991 (p0) cc_final: 0.8459 (p0) REVERT: B 37 GLN cc_start: 0.8971 (pp30) cc_final: 0.8517 (tm-30) REVERT: B 78 LEU cc_start: 0.9389 (mt) cc_final: 0.9174 (mt) REVERT: B 83 PHE cc_start: 0.9074 (m-10) cc_final: 0.8726 (m-10) REVERT: C 120 GLU cc_start: 0.8619 (mm-30) cc_final: 0.7707 (mm-30) REVERT: C 147 MET cc_start: 0.8161 (ppp) cc_final: 0.7936 (ppp) REVERT: C 183 VAL cc_start: 0.9196 (m) cc_final: 0.8905 (p) REVERT: C 212 ASP cc_start: 0.9277 (p0) cc_final: 0.8721 (p0) REVERT: C 222 ASP cc_start: 0.7628 (p0) cc_final: 0.6620 (p0) REVERT: C 242 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8249 (mm-30) REVERT: C 243 GLN cc_start: 0.8622 (tp-100) cc_final: 0.8385 (tp-100) REVERT: C 300 TYR cc_start: 0.8180 (m-80) cc_final: 0.7475 (m-10) REVERT: H 96 GLU cc_start: 0.7879 (tp30) cc_final: 0.7527 (tp30) REVERT: H 188 ASP cc_start: 0.9186 (m-30) cc_final: 0.8736 (m-30) REVERT: H 244 MET cc_start: 0.8106 (tmm) cc_final: 0.7738 (tmm) REVERT: H 251 ASN cc_start: 0.8805 (p0) cc_final: 0.8430 (p0) REVERT: I 197 MET cc_start: 0.7573 (mpp) cc_final: 0.7260 (mpp) REVERT: I 244 MET cc_start: 0.9074 (ppp) cc_final: 0.8330 (ppp) REVERT: J 27 TYR cc_start: 0.8934 (m-80) cc_final: 0.8578 (m-80) REVERT: J 58 TYR cc_start: 0.8869 (m-80) cc_final: 0.8544 (m-10) REVERT: J 110 HIS cc_start: 0.9411 (t-90) cc_final: 0.8914 (t-90) REVERT: J 116 TYR cc_start: 0.3355 (m-10) cc_final: 0.2842 (m-10) REVERT: J 138 MET cc_start: 0.9250 (pmm) cc_final: 0.8852 (pmm) REVERT: J 140 TYR cc_start: 0.7795 (m-80) cc_final: 0.7334 (m-80) REVERT: J 147 MET cc_start: 0.8504 (mmp) cc_final: 0.8146 (mmm) REVERT: J 218 CYS cc_start: 0.9158 (m) cc_final: 0.8932 (m) REVERT: K 147 MET cc_start: 0.9060 (mmm) cc_final: 0.8552 (mmm) outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.2733 time to fit residues: 110.1780 Evaluate side-chains 211 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 2.168 ------------------------------------------------------------------------------- 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: 0.8980 chunk 168 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 135 optimal weight: 5.9990 chunk 146 optimal weight: 9.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 157 HIS H 248 HIS ** 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 132 ASN ** K 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.057887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.046003 restraints weight = 90400.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.047943 restraints weight = 48347.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.049339 restraints weight = 31303.736| |-----------------------------------------------------------------------------| r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18542 Z= 0.122 Angle : 0.604 8.368 25213 Z= 0.307 Chirality : 0.045 0.177 2737 Planarity : 0.004 0.060 3281 Dihedral : 4.698 19.740 2491 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % 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: -1.30 (0.17), residues: 2283 helix: -0.72 (0.38), residues: 189 sheet: -0.45 (0.19), residues: 689 loop : -1.10 (0.16), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP J 390 HIS 0.007 0.001 HIS I 28 PHE 0.013 0.001 PHE C 296 TYR 0.018 0.001 TYR H 58 ARG 0.011 0.000 ARG J 133 Details of bonding type rmsd hydrogen bonds : bond 0.03343 ( 476) hydrogen bonds : angle 6.25309 ( 1284) SS BOND : bond 0.00499 ( 2) SS BOND : angle 1.34380 ( 4) covalent geometry : bond 0.00268 (18540) covalent geometry : angle 0.60399 (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 264 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 2.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8933 (mm110) cc_final: 0.8514 (mm110) REVERT: A 66 ASP cc_start: 0.9373 (p0) cc_final: 0.9140 (p0) REVERT: B 4 MET cc_start: 0.8528 (pmm) cc_final: 0.7784 (pmm) REVERT: B 31 ASN cc_start: 0.9051 (p0) cc_final: 0.8549 (p0) REVERT: B 37 GLN cc_start: 0.8897 (pp30) cc_final: 0.8524 (tm-30) REVERT: B 78 LEU cc_start: 0.9376 (mt) cc_final: 0.9086 (mt) REVERT: B 83 PHE cc_start: 0.9084 (m-10) cc_final: 0.8720 (m-10) REVERT: C 120 GLU cc_start: 0.8382 (mm-30) cc_final: 0.7514 (mm-30) REVERT: C 183 VAL cc_start: 0.9144 (m) cc_final: 0.8870 (p) REVERT: C 212 ASP cc_start: 0.9128 (p0) cc_final: 0.8775 (p0) REVERT: C 222 ASP cc_start: 0.7341 (p0) cc_final: 0.6163 (p0) REVERT: C 243 GLN cc_start: 0.8621 (tp-100) cc_final: 0.8273 (tp-100) REVERT: C 300 TYR cc_start: 0.8063 (m-80) cc_final: 0.7321 (m-10) REVERT: H 96 GLU cc_start: 0.7967 (tp30) cc_final: 0.7587 (tp30) REVERT: H 188 ASP cc_start: 0.9180 (m-30) cc_final: 0.8759 (t0) REVERT: H 197 MET cc_start: 0.9138 (ppp) cc_final: 0.8487 (ppp) REVERT: H 244 MET cc_start: 0.8053 (tmm) cc_final: 0.7666 (tmm) REVERT: H 251 ASN cc_start: 0.8853 (p0) cc_final: 0.8511 (p0) REVERT: H 300 TYR cc_start: 0.9248 (m-80) cc_final: 0.8745 (m-80) REVERT: H 352 MET cc_start: 0.8923 (mmm) cc_final: 0.8357 (mmm) REVERT: H 390 TRP cc_start: 0.8685 (m-10) cc_final: 0.7620 (m-90) REVERT: I 197 MET cc_start: 0.7470 (mpp) cc_final: 0.7176 (mpp) REVERT: J 27 TYR cc_start: 0.8856 (m-80) cc_final: 0.8481 (m-80) REVERT: J 54 LYS cc_start: 0.8501 (mmtm) cc_final: 0.8234 (tppt) REVERT: J 58 TYR cc_start: 0.8777 (m-80) cc_final: 0.8463 (m-10) REVERT: J 110 HIS cc_start: 0.9433 (t-90) cc_final: 0.8861 (t-90) REVERT: J 138 MET cc_start: 0.9236 (pmm) cc_final: 0.8803 (pmm) REVERT: J 140 TYR cc_start: 0.7694 (m-80) cc_final: 0.7266 (m-80) REVERT: J 147 MET cc_start: 0.8501 (mmp) cc_final: 0.8192 (mmm) REVERT: J 218 CYS cc_start: 0.9140 (m) cc_final: 0.8897 (m) REVERT: J 390 TRP cc_start: 0.7506 (m-90) cc_final: 0.7169 (m-90) REVERT: K 147 MET cc_start: 0.9025 (mmm) cc_final: 0.8495 (mmm) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.2732 time to fit residues: 113.0511 Evaluate side-chains 206 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 2.104 ------------------------------------------------------------------------------- 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: 10.0000 chunk 187 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 chunk 71 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 310 ASN ** C 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 308 HIS ** J 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 345 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 = 0.3051 r_free = 0.3051 target = 0.054057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.042478 restraints weight = 95867.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.044270 restraints weight = 51887.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.045581 restraints weight = 34005.321| |-----------------------------------------------------------------------------| r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 18542 Z= 0.329 Angle : 0.744 11.781 25213 Z= 0.385 Chirality : 0.046 0.211 2737 Planarity : 0.005 0.066 3281 Dihedral : 5.272 21.583 2491 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 23.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % 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: -1.68 (0.17), residues: 2283 helix: -1.01 (0.36), residues: 190 sheet: -0.75 (0.18), residues: 752 loop : -1.34 (0.17), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A 110 HIS 0.011 0.002 HIS I 28 PHE 0.025 0.002 PHE K 296 TYR 0.034 0.002 TYR H 58 ARG 0.012 0.001 ARG H 272 Details of bonding type rmsd hydrogen bonds : bond 0.03996 ( 476) hydrogen bonds : angle 6.57475 ( 1284) SS BOND : bond 0.00276 ( 2) SS BOND : angle 1.23232 ( 4) covalent geometry : bond 0.00695 (18540) covalent geometry : angle 0.74363 (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 232 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 2.112 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: 0.8903 (mm110) cc_final: 0.8486 (mm110) REVERT: A 66 ASP cc_start: 0.9477 (p0) cc_final: 0.9269 (p0) REVERT: B 4 MET cc_start: 0.8522 (pmm) cc_final: 0.7937 (pmm) REVERT: B 31 ASN cc_start: 0.9077 (p0) cc_final: 0.8645 (p0) REVERT: B 37 GLN cc_start: 0.9009 (pp30) cc_final: 0.8690 (pp30) REVERT: B 78 LEU cc_start: 0.9320 (mt) cc_final: 0.9037 (mt) REVERT: C 120 GLU cc_start: 0.8827 (mm-30) cc_final: 0.7836 (mm-30) REVERT: C 138 MET cc_start: 0.8172 (ppp) cc_final: 0.7771 (ppp) REVERT: C 183 VAL cc_start: 0.9262 (m) cc_final: 0.9027 (p) REVERT: C 212 ASP cc_start: 0.8996 (p0) cc_final: 0.8653 (p0) REVERT: C 222 ASP cc_start: 0.7400 (p0) cc_final: 0.6251 (p0) REVERT: C 244 MET cc_start: 0.8985 (tpt) cc_final: 0.8477 (tpt) REVERT: C 249 PHE cc_start: 0.9357 (m-10) cc_final: 0.9049 (m-10) REVERT: C 310 ASN cc_start: 0.7978 (t160) cc_final: 0.7619 (t0) REVERT: C 321 THR cc_start: 0.8813 (m) cc_final: 0.8556 (m) REVERT: H 96 GLU cc_start: 0.7933 (tp30) cc_final: 0.7552 (tp30) REVERT: H 188 ASP cc_start: 0.9291 (m-30) cc_final: 0.8858 (t0) REVERT: H 197 MET cc_start: 0.9268 (ppp) cc_final: 0.8600 (ppp) REVERT: H 251 ASN cc_start: 0.8782 (p0) cc_final: 0.8412 (p0) REVERT: H 352 MET cc_start: 0.8841 (mmm) cc_final: 0.8232 (mmm) REVERT: I 197 MET cc_start: 0.7586 (mpp) cc_final: 0.7372 (mpp) REVERT: I 244 MET cc_start: 0.9034 (ppp) cc_final: 0.8389 (ppp) REVERT: J 27 TYR cc_start: 0.8954 (m-80) cc_final: 0.8618 (m-80) REVERT: J 58 TYR cc_start: 0.8964 (m-80) cc_final: 0.8629 (m-10) REVERT: J 110 HIS cc_start: 0.9392 (t-90) cc_final: 0.8893 (t-90) REVERT: J 138 MET cc_start: 0.9219 (pmm) cc_final: 0.8835 (pmm) REVERT: J 140 TYR cc_start: 0.8095 (m-80) cc_final: 0.7679 (m-80) REVERT: J 147 MET cc_start: 0.8567 (mmp) cc_final: 0.8297 (mmm) REVERT: J 191 ASP cc_start: 0.8971 (p0) cc_final: 0.8676 (p0) REVERT: J 218 CYS cc_start: 0.9225 (m) cc_final: 0.8848 (m) REVERT: J 390 TRP cc_start: 0.7590 (m-90) cc_final: 0.7080 (m-90) REVERT: K 147 MET cc_start: 0.9087 (mmm) cc_final: 0.8601 (mmm) REVERT: K 244 MET cc_start: 0.8537 (tmm) cc_final: 0.8248 (tmm) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.2873 time to fit residues: 104.1277 Evaluate side-chains 179 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 2.114 ------------------------------------------------------------------------------- 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: 6.9990 chunk 44 optimal weight: 5.9990 chunk 158 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 157 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 196 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3080 r_free = 0.3080 target = 0.055164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.043476 restraints weight = 93255.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.045309 restraints weight = 50417.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.046640 restraints weight = 32951.832| |-----------------------------------------------------------------------------| r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2918 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= 0.223 Angle : 0.664 10.809 25213 Z= 0.342 Chirality : 0.045 0.197 2737 Planarity : 0.005 0.072 3281 Dihedral : 5.153 20.985 2491 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % 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: -1.60 (0.17), residues: 2283 helix: -0.87 (0.36), residues: 190 sheet: -0.73 (0.18), residues: 754 loop : -1.28 (0.17), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP J 390 HIS 0.010 0.001 HIS I 28 PHE 0.021 0.002 PHE I 456 TYR 0.025 0.002 TYR H 58 ARG 0.011 0.001 ARG J 133 Details of bonding type rmsd hydrogen bonds : bond 0.03626 ( 476) hydrogen bonds : angle 6.53188 ( 1284) SS BOND : bond 0.00381 ( 2) SS BOND : angle 1.25585 ( 4) covalent geometry : bond 0.00479 (18540) covalent geometry : angle 0.66426 (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 : 2.146 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: 0.8929 (mm110) cc_final: 0.8468 (mm110) REVERT: A 66 ASP cc_start: 0.9436 (p0) cc_final: 0.9233 (p0) REVERT: B 4 MET cc_start: 0.8557 (pmm) cc_final: 0.7887 (pmm) REVERT: B 31 ASN cc_start: 0.9055 (p0) cc_final: 0.8609 (p0) REVERT: B 37 GLN cc_start: 0.8969 (pp30) cc_final: 0.8648 (pp30) REVERT: B 78 LEU cc_start: 0.9355 (mt) cc_final: 0.9071 (mt) REVERT: C 120 GLU cc_start: 0.8828 (mm-30) cc_final: 0.7916 (mm-30) REVERT: C 138 MET cc_start: 0.8169 (ppp) cc_final: 0.7827 (ppp) REVERT: C 183 VAL cc_start: 0.9253 (m) cc_final: 0.8992 (p) REVERT: C 212 ASP cc_start: 0.9012 (p0) cc_final: 0.8742 (p0) REVERT: C 222 ASP cc_start: 0.7393 (p0) cc_final: 0.6365 (p0) REVERT: C 244 MET cc_start: 0.8989 (tpt) cc_final: 0.8660 (tpp) REVERT: C 249 PHE cc_start: 0.9311 (m-10) cc_final: 0.9040 (m-10) REVERT: C 331 MET cc_start: 0.8887 (tpp) cc_final: 0.8622 (tpp) REVERT: H 96 GLU cc_start: 0.7851 (tp30) cc_final: 0.7606 (tp30) REVERT: H 188 ASP cc_start: 0.9271 (m-30) cc_final: 0.8852 (t0) REVERT: H 197 MET cc_start: 0.9296 (ppp) cc_final: 0.8540 (ppp) REVERT: H 251 ASN cc_start: 0.8851 (p0) cc_final: 0.8466 (p0) REVERT: H 352 MET cc_start: 0.8864 (mmm) cc_final: 0.8261 (mmm) REVERT: H 390 TRP cc_start: 0.8768 (m-10) cc_final: 0.7697 (m-90) REVERT: I 197 MET cc_start: 0.7591 (mpp) cc_final: 0.7354 (mpp) REVERT: I 244 MET cc_start: 0.9076 (ppp) cc_final: 0.8411 (ppp) REVERT: J 27 TYR cc_start: 0.8893 (m-80) cc_final: 0.8540 (m-80) REVERT: J 110 HIS cc_start: 0.9388 (t-90) cc_final: 0.9038 (t-90) REVERT: J 138 MET cc_start: 0.9281 (pmm) cc_final: 0.8897 (pmm) REVERT: J 140 TYR cc_start: 0.7954 (m-80) cc_final: 0.7336 (m-80) REVERT: J 147 MET cc_start: 0.8580 (mmp) cc_final: 0.8288 (mmm) REVERT: J 218 CYS cc_start: 0.9292 (m) cc_final: 0.8973 (m) REVERT: J 390 TRP cc_start: 0.7681 (m-90) cc_final: 0.7237 (m-90) REVERT: K 147 MET cc_start: 0.9056 (mmm) cc_final: 0.8565 (mmm) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.2716 time to fit residues: 102.2809 Evaluate side-chains 191 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 1.946 ------------------------------------------------------------------------------- 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: 8.9990 chunk 79 optimal weight: 0.0030 chunk 97 optimal weight: 6.9990 chunk 95 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 210 optimal weight: 0.8980 chunk 121 optimal weight: 0.0980 chunk 8 optimal weight: 6.9990 chunk 193 optimal weight: 6.9990 chunk 203 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 overall best weight: 2.9994 ------------------------------------------------------------------------------- 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** ** J 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 345 ASN ** K 316 ASN ** 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 = 0.3094 r_free = 0.3094 target = 0.055744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.043939 restraints weight = 91257.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.045802 restraints weight = 49181.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.047167 restraints weight = 32090.826| |-----------------------------------------------------------------------------| r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2930 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= 0.179 Angle : 0.636 9.996 25213 Z= 0.325 Chirality : 0.045 0.191 2737 Planarity : 0.005 0.064 3281 Dihedral : 5.001 21.583 2491 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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: -1.45 (0.17), residues: 2283 helix: -0.72 (0.37), residues: 190 sheet: -0.58 (0.19), residues: 760 loop : -1.22 (0.17), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP J 390 HIS 0.009 0.001 HIS I 28 PHE 0.016 0.001 PHE C 296 TYR 0.022 0.002 TYR H 58 ARG 0.009 0.001 ARG J 133 Details of bonding type rmsd hydrogen bonds : bond 0.03454 ( 476) hydrogen bonds : angle 6.43663 ( 1284) SS BOND : bond 0.00501 ( 2) SS BOND : angle 1.23131 ( 4) covalent geometry : bond 0.00389 (18540) covalent geometry : angle 0.63591 (25209) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4577.58 seconds wall clock time: 82 minutes 0.68 seconds (4920.68 seconds total)