Starting phenix.real_space_refine on Fri Sep 27 20:06:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xgc_22180/09_2024/6xgc_22180.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xgc_22180/09_2024/6xgc_22180.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xgc_22180/09_2024/6xgc_22180.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xgc_22180/09_2024/6xgc_22180.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xgc_22180/09_2024/6xgc_22180.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xgc_22180/09_2024/6xgc_22180.cif" } resolution = 4.1 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= 0.003 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 69 5.16 5 C 10668 2.51 5 N 2916 2.21 5 O 3387 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 17040 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2528 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 18, 'TRANS': 304} Chain: "B" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1339 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 1, 'TRANS': 162} Chain: "I" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 925 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "J" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 790 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: C, E, D, F, K, O, H, M, L, N Time building chain proxies: 9.08, per 1000 atoms: 0.53 Number of scatterers: 17040 At special positions: 0 Unit cell: (124.962, 131.316, 150.378, 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 69 16.00 O 3387 8.00 N 2916 7.00 C 10668 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.08 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 285 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 77 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 146 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 313 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 29 " - pdb=" SG CYS N 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 403 " - " ASN A 286 " " NAG A 404 " - " ASN A 297 " " NAG A 405 " - " ASN A 33 " " NAG A 406 " - " ASN A 21 " " NAG B 301 " - " ASN B 154 " " NAG C 403 " - " ASN C 286 " " NAG C 404 " - " ASN C 297 " " NAG C 405 " - " ASN C 33 " " NAG C 406 " - " ASN C 21 " " NAG D 301 " - " ASN D 154 " " NAG E 403 " - " ASN E 286 " " NAG E 404 " - " ASN E 297 " " NAG E 405 " - " ASN E 33 " " NAG E 406 " - " ASN E 21 " " NAG F 301 " - " ASN F 154 " " NAG G 1 " - " ASN A 97 " " NAG K 1 " - " ASN C 97 " " NAG O 1 " - " ASN E 97 " Time building additional restraints: 4.42 Conformation dependent library (CDL) restraints added in 2.2 seconds 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3924 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 54 sheets defined 19.9% alpha, 29.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.80 Creating SS restraints... Processing helix chain 'A' and resid 66 through 72 Processing helix chain 'A' and resid 74 through 78 Processing helix chain 'A' and resid 107 through 115 Processing helix chain 'A' and resid 194 through 203 Processing helix chain 'B' and resid 37 through 58 Processing helix chain 'B' and resid 74 through 127 Processing helix chain 'B' and resid 145 through 155 Processing helix chain 'B' and resid 158 through 171 removed outlier: 4.003A pdb=" N TYR B 162 " --> pdb=" O ASP B 158 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N GLU B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'N' and resid 32 through 37 removed outlier: 3.742A pdb=" N GLY N 37 " --> pdb=" O SER N 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 72 Processing helix chain 'C' and resid 74 through 78 Processing helix chain 'C' and resid 107 through 115 Processing helix chain 'C' and resid 194 through 203 Processing helix chain 'D' and resid 37 through 58 Processing helix chain 'D' and resid 74 through 127 Processing helix chain 'D' and resid 145 through 155 Processing helix chain 'D' and resid 158 through 171 removed outlier: 4.002A pdb=" N TYR D 162 " --> pdb=" O ASP D 158 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU D 164 " --> pdb=" O PRO D 160 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N GLU D 165 " --> pdb=" O LYS D 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 32 through 37 removed outlier: 3.744A pdb=" N GLY L 37 " --> pdb=" O SER L 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 72 Processing helix chain 'E' and resid 74 through 78 Processing helix chain 'E' and resid 107 through 115 Processing helix chain 'E' and resid 194 through 203 Processing helix chain 'F' and resid 37 through 58 Processing helix chain 'F' and resid 74 through 127 Processing helix chain 'F' and resid 145 through 155 Processing helix chain 'F' and resid 158 through 171 removed outlier: 4.002A pdb=" N TYR F 162 " --> pdb=" O ASP F 158 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLU F 164 " --> pdb=" O PRO F 160 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N GLU F 165 " --> pdb=" O LYS F 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'J' and resid 32 through 37 removed outlier: 3.743A pdb=" N GLY J 37 " --> pdb=" O SER J 33 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 36 removed outlier: 4.104A pdb=" N GLY B 23 " --> pdb=" O GLY A 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 53 removed outlier: 5.930A pdb=" N LEU A 51 " --> pdb=" O HIS A 283 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N CYS A 285 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 60 through 61 removed outlier: 6.553A pdb=" N LEU A 60 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE A 89 " --> pdb=" O ILE A 276 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 122 through 124 removed outlier: 8.041A pdb=" N LEU A 186 " --> pdb=" O PRO A 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 122 through 124 Processing sheet with id=AA9, first strand: chain 'A' and resid 143 through 148 removed outlier: 4.649A pdb=" N CYS A 146 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 171 through 176 Processing sheet with id=AB2, first strand: chain 'A' and resid 289 through 290 removed outlier: 3.686A pdb=" N CYS A 289 " --> pdb=" O ILE A 296 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 310 through 311 removed outlier: 3.882A pdb=" N THR B 64 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AB5, first strand: chain 'M' and resid 10 through 11 removed outlier: 6.438A pdb=" N GLY M 10 " --> pdb=" O THR M 124 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 100 through 104 removed outlier: 3.670A pdb=" N GLY M 100 " --> pdb=" O ASN M 111 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 16 through 18 removed outlier: 6.417A pdb=" N TRP N 43 " --> pdb=" O LEU N 55 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 16 through 18 Processing sheet with id=AB9, first strand: chain 'N' and resid 25 through 30 Processing sheet with id=AC1, first strand: chain 'D' and resid 31 through 36 removed outlier: 4.170A pdb=" N GLY D 23 " --> pdb=" O GLY C 16 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AC3, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AC4, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AC5, first strand: chain 'C' and resid 51 through 53 removed outlier: 5.930A pdb=" N LEU C 51 " --> pdb=" O HIS C 283 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N CYS C 285 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 60 through 61 removed outlier: 6.552A pdb=" N LEU C 60 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE C 89 " --> pdb=" O ILE C 276 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 122 through 124 removed outlier: 8.039A pdb=" N LEU C 186 " --> pdb=" O PRO C 261 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 122 through 124 Processing sheet with id=AC9, first strand: chain 'C' and resid 143 through 148 removed outlier: 4.649A pdb=" N CYS C 146 " --> pdb=" O SER C 153 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 171 through 176 Processing sheet with id=AD2, first strand: chain 'C' and resid 289 through 290 removed outlier: 3.686A pdb=" N CYS C 289 " --> pdb=" O ILE C 296 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 310 through 311 removed outlier: 3.972A pdb=" N THR D 64 " --> pdb=" O GLY C 311 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD5, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.439A pdb=" N GLY H 10 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 100 through 104 removed outlier: 3.668A pdb=" N GLY H 100 " --> pdb=" O ASN H 111 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 16 through 18 removed outlier: 6.416A pdb=" N TRP L 43 " --> pdb=" O LEU L 55 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 16 through 18 Processing sheet with id=AD9, first strand: chain 'L' and resid 25 through 30 Processing sheet with id=AE1, first strand: chain 'F' and resid 31 through 36 removed outlier: 4.086A pdb=" N GLY F 23 " --> pdb=" O GLY E 16 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 25 through 26 Processing sheet with id=AE3, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AE4, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AE5, first strand: chain 'E' and resid 51 through 53 removed outlier: 5.931A pdb=" N LEU E 51 " --> pdb=" O HIS E 283 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N CYS E 285 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 60 through 61 removed outlier: 6.552A pdb=" N LEU E 60 " --> pdb=" O VAL E 90 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE E 89 " --> pdb=" O ILE E 276 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'E' and resid 122 through 124 removed outlier: 8.041A pdb=" N LEU E 186 " --> pdb=" O PRO E 261 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 122 through 124 Processing sheet with id=AE9, first strand: chain 'E' and resid 143 through 148 removed outlier: 4.649A pdb=" N CYS E 146 " --> pdb=" O SER E 153 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 171 through 176 Processing sheet with id=AF2, first strand: chain 'E' and resid 289 through 290 removed outlier: 3.687A pdb=" N CYS E 289 " --> pdb=" O ILE E 296 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 310 through 311 removed outlier: 3.868A pdb=" N THR F 64 " --> pdb=" O GLY E 311 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AF5, first strand: chain 'I' and resid 10 through 11 removed outlier: 6.438A pdb=" N GLY I 10 " --> pdb=" O THR I 124 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 100 through 104 removed outlier: 3.671A pdb=" N GLY I 100 " --> pdb=" O ASN I 111 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 16 through 18 removed outlier: 6.415A pdb=" N TRP J 43 " --> pdb=" O LEU J 55 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'J' and resid 16 through 18 Processing sheet with id=AF9, first strand: chain 'J' and resid 25 through 30 738 hydrogen bonds defined for protein. 1926 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.25 Time building geometry restraints manager: 5.14 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: 5547 1.34 - 1.46: 3563 1.46 - 1.58: 8218 1.58 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 17418 Sorted by residual: bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.23e+00 bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.19e+00 bond pdb=" C1 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.11e+00 bond pdb=" C1 NAG A 403 " pdb=" O5 NAG A 403 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.90e+00 bond pdb=" C1 NAG B 301 " pdb=" O5 NAG B 301 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.90e+00 ... (remaining 17413 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.94: 22761 0.94 - 1.88: 618 1.88 - 2.83: 189 2.83 - 3.77: 36 3.77 - 4.71: 12 Bond angle restraints: 23616 Sorted by residual: angle pdb=" C LEU F 126 " pdb=" N LYS F 127 " pdb=" CA LYS F 127 " ideal model delta sigma weight residual 121.54 126.11 -4.57 1.91e+00 2.74e-01 5.72e+00 angle pdb=" C LEU D 126 " pdb=" N LYS D 127 " pdb=" CA LYS D 127 " ideal model delta sigma weight residual 121.54 126.07 -4.53 1.91e+00 2.74e-01 5.62e+00 angle pdb=" C LEU B 126 " pdb=" N LYS B 127 " pdb=" CA LYS B 127 " ideal model delta sigma weight residual 121.54 126.00 -4.46 1.91e+00 2.74e-01 5.45e+00 angle pdb=" C GLY E 165 " pdb=" N ASN E 166 " pdb=" CA ASN E 166 " ideal model delta sigma weight residual 121.54 125.25 -3.71 1.91e+00 2.74e-01 3.78e+00 angle pdb=" C GLY C 165 " pdb=" N ASN C 166 " pdb=" CA ASN C 166 " ideal model delta sigma weight residual 121.54 125.24 -3.70 1.91e+00 2.74e-01 3.75e+00 ... (remaining 23611 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 10234 17.31 - 34.63: 256 34.63 - 51.94: 58 51.94 - 69.25: 3 69.25 - 86.57: 9 Dihedral angle restraints: 10560 sinusoidal: 4389 harmonic: 6171 Sorted by residual: dihedral pdb=" CB GLU C 109 " pdb=" CG GLU C 109 " pdb=" CD GLU C 109 " pdb=" OE1 GLU C 109 " ideal model delta sinusoidal sigma weight residual 0.00 -86.57 86.57 1 3.00e+01 1.11e-03 1.00e+01 dihedral pdb=" CB GLU A 109 " pdb=" CG GLU A 109 " pdb=" CD GLU A 109 " pdb=" OE1 GLU A 109 " ideal model delta sinusoidal sigma weight residual 0.00 -86.56 86.56 1 3.00e+01 1.11e-03 1.00e+01 dihedral pdb=" CB GLU E 109 " pdb=" CG GLU E 109 " pdb=" CD GLU E 109 " pdb=" OE1 GLU E 109 " ideal model delta sinusoidal sigma weight residual 0.00 -86.54 86.54 1 3.00e+01 1.11e-03 1.00e+01 ... (remaining 10557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1561 0.025 - 0.050: 664 0.050 - 0.076: 174 0.076 - 0.101: 108 0.101 - 0.126: 115 Chirality restraints: 2622 Sorted by residual: chirality pdb=" CA ILE A 176 " pdb=" N ILE A 176 " pdb=" C ILE A 176 " pdb=" CB ILE A 176 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.98e-01 chirality pdb=" C1 NAG C 406 " pdb=" ND2 ASN C 21 " pdb=" C2 NAG C 406 " pdb=" O5 NAG C 406 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-01 2.50e+01 3.96e-01 chirality pdb=" CA ILE E 176 " pdb=" N ILE E 176 " pdb=" C ILE E 176 " pdb=" CB ILE E 176 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.94e-01 ... (remaining 2619 not shown) Planarity restraints: 3045 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 291 " -0.022 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO A 292 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 292 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 292 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 291 " -0.022 5.00e-02 4.00e+02 3.38e-02 1.83e+00 pdb=" N PRO E 292 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO E 292 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 292 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 291 " 0.022 5.00e-02 4.00e+02 3.37e-02 1.82e+00 pdb=" N PRO C 292 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO C 292 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 292 " 0.019 5.00e-02 4.00e+02 ... (remaining 3042 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 131 2.55 - 3.13: 12817 3.13 - 3.72: 25829 3.72 - 4.31: 34997 4.31 - 4.90: 60182 Nonbonded interactions: 133956 Sorted by model distance: nonbonded pdb=" SG CYS C 14 " pdb=" SG CYS D 137 " model vdw 1.958 3.760 nonbonded pdb=" SG CYS C 289 " pdb=" SG CYS C 313 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS E 289 " pdb=" SG CYS E 313 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS C 65 " pdb=" SG CYS C 77 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS E 65 " pdb=" SG CYS E 77 " model vdw 2.030 3.760 ... (remaining 133951 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'O' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'N' } 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 39.630 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17418 Z= 0.146 Angle : 0.433 4.712 23616 Z= 0.235 Chirality : 0.040 0.126 2622 Planarity : 0.003 0.034 3027 Dihedral : 8.174 86.567 6612 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.16 % Allowed : 3.64 % Favored : 96.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.19), residues: 2133 helix: 4.15 (0.25), residues: 351 sheet: 1.15 (0.24), residues: 519 loop : -0.06 (0.17), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 133 HIS 0.004 0.000 HIS H 35 PHE 0.005 0.001 PHE A 121 TYR 0.007 0.001 TYR F 94 ARG 0.002 0.000 ARG I 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 742 time to evaluate : 1.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 LEU cc_start: 0.9253 (mt) cc_final: 0.8983 (mp) REVERT: A 300 LEU cc_start: 0.8719 (mt) cc_final: 0.8295 (mt) REVERT: B 17 MET cc_start: 0.8247 (ttp) cc_final: 0.8013 (ttp) REVERT: B 19 ASP cc_start: 0.8801 (p0) cc_final: 0.8547 (p0) REVERT: B 26 HIS cc_start: 0.7671 (p90) cc_final: 0.7433 (p90) REVERT: B 38 LEU cc_start: 0.8215 (mt) cc_final: 0.7929 (mt) REVERT: B 90 ASP cc_start: 0.6534 (m-30) cc_final: 0.6107 (m-30) REVERT: B 99 LEU cc_start: 0.8449 (tp) cc_final: 0.8242 (tp) REVERT: B 147 THR cc_start: 0.8874 (m) cc_final: 0.8636 (p) REVERT: M 36 TRP cc_start: 0.8377 (m100) cc_final: 0.7694 (m100) REVERT: M 47 TRP cc_start: 0.8490 (t60) cc_final: 0.8280 (t60) REVERT: M 48 ILE cc_start: 0.8494 (mm) cc_final: 0.6760 (mm) REVERT: N 105 ASN cc_start: 0.7580 (m-40) cc_final: 0.7189 (m110) REVERT: C 204 ASN cc_start: 0.8741 (m-40) cc_final: 0.8500 (m-40) REVERT: C 230 VAL cc_start: 0.8622 (t) cc_final: 0.8416 (p) REVERT: C 262 ARG cc_start: 0.8385 (ttt180) cc_final: 0.8144 (ttt-90) REVERT: C 263 TYR cc_start: 0.7903 (m-80) cc_final: 0.7635 (m-80) REVERT: D 26 HIS cc_start: 0.7970 (p90) cc_final: 0.7302 (p90) REVERT: D 138 PHE cc_start: 0.8338 (m-80) cc_final: 0.8077 (m-80) REVERT: D 147 THR cc_start: 0.8975 (m) cc_final: 0.8541 (p) REVERT: H 36 TRP cc_start: 0.8464 (m100) cc_final: 0.8224 (m100) REVERT: H 48 ILE cc_start: 0.8495 (mm) cc_final: 0.8277 (mm) REVERT: H 94 TYR cc_start: 0.7169 (m-80) cc_final: 0.6966 (m-10) REVERT: L 93 ASP cc_start: 0.8351 (m-30) cc_final: 0.8081 (m-30) REVERT: L 113 ARG cc_start: 0.6793 (tpp80) cc_final: 0.6521 (tpp-160) REVERT: E 204 ASN cc_start: 0.8576 (m-40) cc_final: 0.8361 (m110) REVERT: F 26 HIS cc_start: 0.8135 (p90) cc_final: 0.7558 (p90) REVERT: F 27 GLN cc_start: 0.8415 (tt0) cc_final: 0.8215 (tm-30) REVERT: F 99 LEU cc_start: 0.8120 (tp) cc_final: 0.7503 (tt) REVERT: F 114 ASN cc_start: 0.8663 (m-40) cc_final: 0.8396 (m110) REVERT: I 34 MET cc_start: 0.7986 (mmm) cc_final: 0.7439 (mmt) REVERT: I 47 TRP cc_start: 0.8378 (t60) cc_final: 0.8111 (t60) outliers start: 3 outliers final: 3 residues processed: 745 average time/residue: 0.2974 time to fit residues: 323.7227 Evaluate side-chains 406 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 403 time to evaluate : 1.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.0370 chunk 159 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 107 optimal weight: 0.5980 chunk 85 optimal weight: 0.1980 chunk 164 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 190 optimal weight: 1.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 HIS A 238 ASN A 290 GLN ** B 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 GLN M 39 GLN N 40 HIS N 45 GLN N 58 ASN N 87 GLN C 148 HIS C 238 ASN C 257 ASN C 290 GLN D 114 ASN ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 45 GLN ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 238 ASN E 290 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 GLN J 46 GLN ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 17418 Z= 0.178 Angle : 0.552 7.116 23616 Z= 0.286 Chirality : 0.043 0.141 2622 Planarity : 0.004 0.049 3027 Dihedral : 5.520 56.032 2760 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.16 % Allowed : 1.63 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.14 (0.18), residues: 2133 helix: 3.36 (0.25), residues: 360 sheet: 1.34 (0.25), residues: 435 loop : -0.18 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP N 43 HIS 0.011 0.001 HIS I 35 PHE 0.019 0.001 PHE A 210 TYR 0.019 0.001 TYR M 94 ARG 0.014 0.001 ARG E 112 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 518 time to evaluate : 1.989 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: B 19 ASP cc_start: 0.8922 (p0) cc_final: 0.8695 (p0) REVERT: B 147 THR cc_start: 0.9021 (m) cc_final: 0.8566 (p) REVERT: M 36 TRP cc_start: 0.8381 (m100) cc_final: 0.7200 (m100) REVERT: M 46 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7279 (tm-30) REVERT: M 47 TRP cc_start: 0.8535 (t60) cc_final: 0.8270 (t60) REVERT: M 82 GLN cc_start: 0.7049 (tp40) cc_final: 0.6759 (tm-30) REVERT: M 87 ARG cc_start: 0.7260 (ptp-110) cc_final: 0.6981 (mtm-85) REVERT: M 90 ASP cc_start: 0.8143 (m-30) cc_final: 0.7837 (m-30) REVERT: N 105 ASN cc_start: 0.7760 (m-40) cc_final: 0.7412 (m-40) REVERT: C 77 CYS cc_start: 0.7918 (m) cc_final: 0.7598 (m) REVERT: C 155 TYR cc_start: 0.8024 (m-80) cc_final: 0.7691 (m-80) REVERT: C 204 ASN cc_start: 0.8942 (m-40) cc_final: 0.8563 (m-40) REVERT: D 114 ASN cc_start: 0.8745 (m-40) cc_final: 0.8255 (m-40) REVERT: D 147 THR cc_start: 0.9101 (m) cc_final: 0.8543 (p) REVERT: H 34 MET cc_start: 0.7682 (mmt) cc_final: 0.7346 (mtp) REVERT: H 36 TRP cc_start: 0.8379 (m100) cc_final: 0.8054 (m100) REVERT: H 76 LYS cc_start: 0.8471 (mtmt) cc_final: 0.8146 (ptpt) REVERT: H 83 MET cc_start: 0.7760 (mtt) cc_final: 0.7164 (mtt) REVERT: H 87 ARG cc_start: 0.7925 (mtp85) cc_final: 0.7664 (mtm-85) REVERT: H 94 TYR cc_start: 0.7319 (m-80) cc_final: 0.7005 (m-10) REVERT: H 99 ASP cc_start: 0.7931 (m-30) cc_final: 0.7677 (m-30) REVERT: L 43 TRP cc_start: 0.7897 (m100) cc_final: 0.7593 (m-10) REVERT: L 81 LEU cc_start: 0.8999 (tt) cc_final: 0.8041 (tt) REVERT: F 26 HIS cc_start: 0.8393 (p90) cc_final: 0.7454 (p90) REVERT: F 114 ASN cc_start: 0.8783 (m-40) cc_final: 0.8387 (m110) REVERT: I 6 GLU cc_start: 0.8486 (mp0) cc_final: 0.8180 (mp0) REVERT: I 22 CYS cc_start: 0.7576 (t) cc_final: 0.6263 (t) REVERT: I 34 MET cc_start: 0.8069 (mmm) cc_final: 0.7691 (mmt) REVERT: I 47 TRP cc_start: 0.8493 (t60) cc_final: 0.7938 (t60) REVERT: I 48 ILE cc_start: 0.8778 (mm) cc_final: 0.7936 (mt) REVERT: I 82 GLN cc_start: 0.7213 (tp40) cc_final: 0.6861 (tm-30) REVERT: J 43 TRP cc_start: 0.8078 (m100) cc_final: 0.7591 (m100) REVERT: J 93 ASP cc_start: 0.8626 (m-30) cc_final: 0.7493 (p0) outliers start: 3 outliers final: 0 residues processed: 520 average time/residue: 0.2830 time to fit residues: 226.1165 Evaluate side-chains 362 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 362 time to evaluate : 1.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 158 optimal weight: 0.9990 chunk 129 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 191 optimal weight: 4.9990 chunk 206 optimal weight: 8.9990 chunk 170 optimal weight: 0.9980 chunk 189 optimal weight: 9.9990 chunk 65 optimal weight: 0.0030 chunk 153 optimal weight: 5.9990 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS A 290 GLN ** B 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 GLN B 142 HIS ** N 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 HIS C 290 GLN ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** L 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 45 GLN ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 105 ASN ** E 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 238 ASN E 257 ASN E 283 HIS E 290 GLN F 62 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 GLN ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 105 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17418 Z= 0.180 Angle : 0.534 6.579 23616 Z= 0.283 Chirality : 0.042 0.163 2622 Planarity : 0.004 0.049 3027 Dihedral : 5.340 53.510 2760 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.05 % Allowed : 2.66 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.05 (0.18), residues: 2133 helix: 3.07 (0.26), residues: 357 sheet: 1.50 (0.25), residues: 435 loop : -0.24 (0.16), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 133 HIS 0.012 0.001 HIS I 35 PHE 0.030 0.002 PHE A 210 TYR 0.028 0.001 TYR H 112 ARG 0.006 0.001 ARG M 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 472 time to evaluate : 1.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 MET cc_start: 0.8432 (ttp) cc_final: 0.7989 (ttp) REVERT: B 19 ASP cc_start: 0.8820 (p0) cc_final: 0.8519 (p0) REVERT: B 27 GLN cc_start: 0.8315 (tp40) cc_final: 0.8100 (tp-100) REVERT: B 147 THR cc_start: 0.9089 (m) cc_final: 0.8722 (p) REVERT: M 36 TRP cc_start: 0.8143 (m100) cc_final: 0.7402 (m100) REVERT: M 38 ARG cc_start: 0.8021 (ptt90) cc_final: 0.7811 (ptt90) REVERT: M 47 TRP cc_start: 0.8627 (t60) cc_final: 0.8354 (t60) REVERT: M 48 ILE cc_start: 0.8626 (mm) cc_final: 0.8284 (mm) REVERT: M 82 GLN cc_start: 0.7205 (tp40) cc_final: 0.6842 (tm-30) REVERT: M 83 MET cc_start: 0.7073 (mtt) cc_final: 0.6792 (mtt) REVERT: M 90 ASP cc_start: 0.8071 (m-30) cc_final: 0.7580 (m-30) REVERT: N 46 GLN cc_start: 0.8384 (tt0) cc_final: 0.7984 (tt0) REVERT: C 108 TYR cc_start: 0.7378 (t80) cc_final: 0.7169 (t80) REVERT: C 155 TYR cc_start: 0.8022 (m-80) cc_final: 0.7729 (m-80) REVERT: C 204 ASN cc_start: 0.8992 (m-40) cc_final: 0.8654 (m-40) REVERT: D 78 GLU cc_start: 0.7756 (tp30) cc_final: 0.7448 (tp30) REVERT: D 105 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7520 (mm-30) REVERT: D 114 ASN cc_start: 0.8814 (m-40) cc_final: 0.8251 (m-40) REVERT: D 147 THR cc_start: 0.9300 (m) cc_final: 0.8651 (p) REVERT: H 36 TRP cc_start: 0.8513 (m100) cc_final: 0.8081 (m100) REVERT: H 68 PHE cc_start: 0.8352 (m-10) cc_final: 0.8112 (m-10) REVERT: H 76 LYS cc_start: 0.8547 (mtmt) cc_final: 0.8265 (ptpt) REVERT: H 90 ASP cc_start: 0.8067 (m-30) cc_final: 0.7729 (m-30) REVERT: L 27 ILE cc_start: 0.8984 (mt) cc_final: 0.8651 (mt) REVERT: L 43 TRP cc_start: 0.7962 (m100) cc_final: 0.7625 (m-10) REVERT: L 46 GLN cc_start: 0.8375 (tp40) cc_final: 0.7720 (tp40) REVERT: L 81 LEU cc_start: 0.9003 (tt) cc_final: 0.7977 (tt) REVERT: F 26 HIS cc_start: 0.8367 (p90) cc_final: 0.7710 (p90) REVERT: F 32 SER cc_start: 0.8393 (p) cc_final: 0.8031 (p) REVERT: F 114 ASN cc_start: 0.8809 (m-40) cc_final: 0.8353 (m110) REVERT: I 34 MET cc_start: 0.8303 (mmm) cc_final: 0.7908 (mmt) REVERT: I 46 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7500 (tm-30) REVERT: I 47 TRP cc_start: 0.8489 (t60) cc_final: 0.8203 (t60) REVERT: I 48 ILE cc_start: 0.8849 (mm) cc_final: 0.8156 (mm) REVERT: I 82 GLN cc_start: 0.7261 (tp40) cc_final: 0.6840 (tm-30) REVERT: I 87 ARG cc_start: 0.7645 (mtm180) cc_final: 0.7380 (mtm180) REVERT: I 90 ASP cc_start: 0.8036 (m-30) cc_final: 0.7754 (m-30) REVERT: J 43 TRP cc_start: 0.8078 (m100) cc_final: 0.7567 (m100) outliers start: 1 outliers final: 0 residues processed: 472 average time/residue: 0.2476 time to fit residues: 183.6303 Evaluate side-chains 341 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 341 time to evaluate : 1.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 99 optimal weight: 0.3980 chunk 21 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 chunk 191 optimal weight: 5.9990 chunk 202 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 181 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 ASN A 290 GLN B 125 GLN ** N 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 105 ASN C 257 ASN C 290 GLN D 125 GLN ** L 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 HIS E 290 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17418 Z= 0.224 Angle : 0.555 6.219 23616 Z= 0.294 Chirality : 0.043 0.159 2622 Planarity : 0.004 0.059 3027 Dihedral : 5.064 51.574 2760 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.11 % Allowed : 2.33 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.77 (0.18), residues: 2133 helix: 2.44 (0.26), residues: 357 sheet: 1.32 (0.23), residues: 507 loop : -0.41 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 47 HIS 0.003 0.001 HIS C 148 PHE 0.020 0.002 PHE E 105 TYR 0.034 0.002 TYR I 112 ARG 0.005 0.001 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 460 time to evaluate : 1.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 MET cc_start: 0.8549 (ttp) cc_final: 0.8116 (ttp) REVERT: B 19 ASP cc_start: 0.8905 (p0) cc_final: 0.8556 (p0) REVERT: B 32 SER cc_start: 0.8964 (p) cc_final: 0.8679 (p) REVERT: M 36 TRP cc_start: 0.8116 (m100) cc_final: 0.7426 (m100) REVERT: M 38 ARG cc_start: 0.8189 (ptt90) cc_final: 0.7955 (ptt90) REVERT: M 46 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7396 (tm-30) REVERT: M 47 TRP cc_start: 0.8601 (t60) cc_final: 0.8273 (t60) REVERT: M 48 ILE cc_start: 0.8795 (mm) cc_final: 0.8013 (mm) REVERT: M 82 GLN cc_start: 0.7273 (tp40) cc_final: 0.6884 (tm-30) REVERT: M 83 MET cc_start: 0.7656 (mtt) cc_final: 0.7353 (mtt) REVERT: M 87 ARG cc_start: 0.8087 (mtp85) cc_final: 0.7627 (mtm-85) REVERT: M 90 ASP cc_start: 0.8154 (m-30) cc_final: 0.7699 (m-30) REVERT: N 56 ILE cc_start: 0.8555 (mm) cc_final: 0.8343 (tp) REVERT: N 105 ASN cc_start: 0.7013 (m110) cc_final: 0.6678 (m110) REVERT: C 108 TYR cc_start: 0.7619 (t80) cc_final: 0.7375 (t80) REVERT: C 204 ASN cc_start: 0.8970 (m-40) cc_final: 0.8611 (m-40) REVERT: C 262 ARG cc_start: 0.8556 (ttt180) cc_final: 0.8226 (ttt-90) REVERT: C 283 HIS cc_start: 0.7375 (m170) cc_final: 0.7055 (m170) REVERT: D 78 GLU cc_start: 0.7921 (tp30) cc_final: 0.7677 (tp30) REVERT: D 114 ASN cc_start: 0.8873 (m-40) cc_final: 0.8343 (m-40) REVERT: D 147 THR cc_start: 0.9156 (m) cc_final: 0.8660 (p) REVERT: H 36 TRP cc_start: 0.8149 (m100) cc_final: 0.7924 (m100) REVERT: H 90 ASP cc_start: 0.8276 (m-30) cc_final: 0.7762 (m-30) REVERT: L 27 ILE cc_start: 0.9114 (mt) cc_final: 0.8794 (mt) REVERT: L 43 TRP cc_start: 0.7972 (m100) cc_final: 0.7548 (m-10) REVERT: L 46 GLN cc_start: 0.8415 (tp40) cc_final: 0.7851 (tp40) REVERT: L 81 LEU cc_start: 0.9053 (tt) cc_final: 0.7954 (tt) REVERT: E 122 GLU cc_start: 0.7946 (mp0) cc_final: 0.7712 (mp0) REVERT: F 26 HIS cc_start: 0.8417 (p90) cc_final: 0.7607 (p90) REVERT: F 27 GLN cc_start: 0.8261 (tp40) cc_final: 0.7935 (tp-100) REVERT: F 28 ASN cc_start: 0.8974 (p0) cc_final: 0.8625 (p0) REVERT: I 34 MET cc_start: 0.8342 (mmm) cc_final: 0.8093 (mmt) REVERT: I 46 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7818 (tm-30) REVERT: I 47 TRP cc_start: 0.8560 (t60) cc_final: 0.8326 (t60) REVERT: I 48 ILE cc_start: 0.8825 (mm) cc_final: 0.8509 (mt) REVERT: I 68 PHE cc_start: 0.7949 (m-10) cc_final: 0.7416 (m-10) REVERT: I 82 GLN cc_start: 0.7432 (tp40) cc_final: 0.6874 (tm-30) REVERT: I 87 ARG cc_start: 0.7858 (mtm180) cc_final: 0.7297 (mtm-85) REVERT: J 43 TRP cc_start: 0.8172 (m100) cc_final: 0.7464 (m100) outliers start: 2 outliers final: 0 residues processed: 460 average time/residue: 0.2485 time to fit residues: 178.5663 Evaluate side-chains 334 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 334 time to evaluate : 2.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 83 optimal weight: 0.0050 chunk 173 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 chunk 0 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 182 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 overall best weight: 2.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN B 125 GLN N 13 GLN C 290 GLN ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 HIS ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 13 GLN L 40 HIS ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 ASN E 290 GLN F 125 GLN F 142 HIS I 35 HIS ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 17418 Z= 0.374 Angle : 0.659 7.363 23616 Z= 0.347 Chirality : 0.045 0.187 2622 Planarity : 0.005 0.069 3027 Dihedral : 5.269 39.810 2760 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.25 (0.17), residues: 2133 helix: 1.75 (0.25), residues: 357 sheet: 1.02 (0.22), residues: 516 loop : -0.69 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 241 HIS 0.008 0.002 HIS I 35 PHE 0.023 0.002 PHE C 124 TYR 0.028 0.002 TYR I 112 ARG 0.006 0.001 ARG C 215 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 413 time to evaluate : 2.001 Fit side-chains revert: symmetry clash REVERT: B 17 MET cc_start: 0.8622 (ttp) cc_final: 0.8111 (ttp) REVERT: B 19 ASP cc_start: 0.8845 (p0) cc_final: 0.8534 (p0) REVERT: M 36 TRP cc_start: 0.8229 (m100) cc_final: 0.7739 (m100) REVERT: M 46 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7714 (tm-30) REVERT: M 47 TRP cc_start: 0.8606 (t60) cc_final: 0.8269 (t60) REVERT: M 48 ILE cc_start: 0.8776 (mm) cc_final: 0.8190 (mt) REVERT: M 82 GLN cc_start: 0.7607 (tp40) cc_final: 0.7084 (tm-30) REVERT: M 83 MET cc_start: 0.8037 (mtt) cc_final: 0.7624 (mtt) REVERT: M 87 ARG cc_start: 0.8049 (mtp85) cc_final: 0.7693 (mtm-85) REVERT: M 90 ASP cc_start: 0.8266 (m-30) cc_final: 0.7901 (m-30) REVERT: N 46 GLN cc_start: 0.8326 (tt0) cc_final: 0.7895 (tp40) REVERT: N 56 ILE cc_start: 0.8510 (mm) cc_final: 0.8304 (tp) REVERT: N 99 TRP cc_start: 0.7899 (t-100) cc_final: 0.7123 (t-100) REVERT: N 105 ASN cc_start: 0.7351 (m-40) cc_final: 0.6696 (m110) REVERT: C 204 ASN cc_start: 0.9093 (m-40) cc_final: 0.8771 (m-40) REVERT: C 241 TRP cc_start: 0.9105 (p-90) cc_final: 0.8886 (p-90) REVERT: D 17 MET cc_start: 0.8790 (tmm) cc_final: 0.8576 (tmm) REVERT: D 37 ASP cc_start: 0.8464 (m-30) cc_final: 0.7576 (m-30) REVERT: D 60 ASN cc_start: 0.8656 (m-40) cc_final: 0.8420 (m-40) REVERT: D 147 THR cc_start: 0.9162 (m) cc_final: 0.8684 (p) REVERT: H 36 TRP cc_start: 0.8197 (m100) cc_final: 0.7904 (m100) REVERT: H 87 ARG cc_start: 0.7865 (mtm-85) cc_final: 0.7407 (mtm-85) REVERT: H 90 ASP cc_start: 0.8397 (m-30) cc_final: 0.7905 (m-30) REVERT: L 43 TRP cc_start: 0.7768 (m100) cc_final: 0.6364 (m100) REVERT: L 46 GLN cc_start: 0.8693 (tp40) cc_final: 0.7939 (tp40) REVERT: E 77 CYS cc_start: 0.7987 (m) cc_final: 0.7341 (m) REVERT: E 104 ASP cc_start: 0.6803 (p0) cc_final: 0.6557 (p0) REVERT: E 108 TYR cc_start: 0.7590 (t80) cc_final: 0.7310 (t80) REVERT: E 122 GLU cc_start: 0.8208 (mp0) cc_final: 0.7889 (mp0) REVERT: E 146 CYS cc_start: 0.7173 (m) cc_final: 0.6711 (t) REVERT: E 241 TRP cc_start: 0.9193 (p-90) cc_final: 0.8936 (p-90) REVERT: E 269 ARG cc_start: 0.8290 (mtm110) cc_final: 0.8087 (mtm110) REVERT: F 28 ASN cc_start: 0.9064 (p0) cc_final: 0.8665 (p0) REVERT: F 90 ASP cc_start: 0.7357 (m-30) cc_final: 0.7066 (m-30) REVERT: F 133 ILE cc_start: 0.9062 (mt) cc_final: 0.8607 (mm) REVERT: I 31 THR cc_start: 0.9115 (m) cc_final: 0.8905 (t) REVERT: I 32 TYR cc_start: 0.8507 (m-10) cc_final: 0.8250 (m-10) REVERT: I 36 TRP cc_start: 0.8760 (m100) cc_final: 0.8474 (m100) REVERT: I 46 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7695 (tm-30) REVERT: I 48 ILE cc_start: 0.8860 (mm) cc_final: 0.8602 (mt) REVERT: I 82 GLN cc_start: 0.7661 (tp40) cc_final: 0.6925 (tm-30) REVERT: I 83 MET cc_start: 0.7442 (mtp) cc_final: 0.7016 (mtm) REVERT: I 87 ARG cc_start: 0.7730 (mtm180) cc_final: 0.7521 (mtm-85) REVERT: I 90 ASP cc_start: 0.8331 (m-30) cc_final: 0.8020 (m-30) REVERT: J 43 TRP cc_start: 0.8066 (m100) cc_final: 0.7538 (m100) outliers start: 0 outliers final: 0 residues processed: 413 average time/residue: 0.2401 time to fit residues: 157.3011 Evaluate side-chains 326 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 326 time to evaluate : 1.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 1.9990 chunk 182 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 119 optimal weight: 9.9990 chunk 50 optimal weight: 0.9990 chunk 203 optimal weight: 0.9980 chunk 168 optimal weight: 0.6980 chunk 94 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 67 optimal weight: 10.0000 chunk 106 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 ASN A 290 GLN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 GLN ** N 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN C 257 ASN C 290 GLN ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 13 GLN ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 87 GLN E 74 ASN E 136 HIS E 290 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 40 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 17418 Z= 0.191 Angle : 0.591 11.581 23616 Z= 0.307 Chirality : 0.044 0.157 2622 Planarity : 0.004 0.051 3027 Dihedral : 4.750 34.681 2760 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.33 (0.17), residues: 2133 helix: 1.91 (0.26), residues: 357 sheet: 1.11 (0.22), residues: 516 loop : -0.70 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 133 HIS 0.007 0.001 HIS H 35 PHE 0.019 0.001 PHE A 210 TYR 0.024 0.001 TYR I 112 ARG 0.004 0.001 ARG C 215 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 408 time to evaluate : 1.954 Fit side-chains revert: symmetry clash REVERT: A 124 PHE cc_start: 0.8112 (t80) cc_final: 0.7843 (t80) REVERT: B 19 ASP cc_start: 0.8861 (p0) cc_final: 0.8602 (p0) REVERT: B 90 ASP cc_start: 0.7514 (m-30) cc_final: 0.6396 (m-30) REVERT: M 36 TRP cc_start: 0.8044 (m100) cc_final: 0.7489 (m100) REVERT: M 46 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7622 (tm-30) REVERT: M 47 TRP cc_start: 0.8563 (t60) cc_final: 0.8060 (t60) REVERT: M 82 GLN cc_start: 0.7579 (tp40) cc_final: 0.7045 (tm-30) REVERT: M 83 MET cc_start: 0.7868 (mtt) cc_final: 0.7491 (mtt) REVERT: M 87 ARG cc_start: 0.8254 (mtp85) cc_final: 0.7794 (mtm-85) REVERT: M 90 ASP cc_start: 0.8321 (m-30) cc_final: 0.7821 (m-30) REVERT: N 99 TRP cc_start: 0.7991 (t-100) cc_final: 0.6997 (t-100) REVERT: N 105 ASN cc_start: 0.7367 (m-40) cc_final: 0.6755 (m110) REVERT: C 108 TYR cc_start: 0.7564 (t80) cc_final: 0.7293 (t80) REVERT: C 204 ASN cc_start: 0.8991 (m-40) cc_final: 0.8747 (m-40) REVERT: C 241 TRP cc_start: 0.8962 (p-90) cc_final: 0.8761 (p-90) REVERT: D 17 MET cc_start: 0.8782 (tmm) cc_final: 0.8493 (tmm) REVERT: D 147 THR cc_start: 0.9192 (m) cc_final: 0.8741 (p) REVERT: H 36 TRP cc_start: 0.8036 (m100) cc_final: 0.7674 (m100) REVERT: H 90 ASP cc_start: 0.8368 (m-30) cc_final: 0.7827 (m-30) REVERT: H 99 ASP cc_start: 0.8122 (m-30) cc_final: 0.7835 (m-30) REVERT: L 43 TRP cc_start: 0.7571 (m100) cc_final: 0.6342 (m100) REVERT: L 46 GLN cc_start: 0.8719 (tp40) cc_final: 0.8026 (tp40) REVERT: L 55 LEU cc_start: 0.8916 (mt) cc_final: 0.8639 (mp) REVERT: E 108 TYR cc_start: 0.7390 (t80) cc_final: 0.6991 (t80) REVERT: E 122 GLU cc_start: 0.8166 (mp0) cc_final: 0.7857 (mp0) REVERT: E 155 TYR cc_start: 0.8385 (m-80) cc_final: 0.8070 (m-80) REVERT: E 241 TRP cc_start: 0.9114 (p-90) cc_final: 0.8840 (p-90) REVERT: E 269 ARG cc_start: 0.8282 (mtm110) cc_final: 0.7969 (mtm110) REVERT: F 133 ILE cc_start: 0.8988 (mt) cc_final: 0.8580 (mm) REVERT: I 36 TRP cc_start: 0.8672 (m100) cc_final: 0.8452 (m100) REVERT: I 46 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7050 (tm-30) REVERT: I 48 ILE cc_start: 0.8951 (mm) cc_final: 0.8252 (mm) REVERT: I 82 GLN cc_start: 0.7612 (tp40) cc_final: 0.6859 (tm-30) REVERT: I 87 ARG cc_start: 0.7801 (mtm180) cc_final: 0.7441 (mtm-85) REVERT: I 90 ASP cc_start: 0.8231 (m-30) cc_final: 0.7911 (m-30) REVERT: J 43 TRP cc_start: 0.7538 (m100) cc_final: 0.7135 (m100) outliers start: 0 outliers final: 0 residues processed: 408 average time/residue: 0.2404 time to fit residues: 154.8656 Evaluate side-chains 332 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 332 time to evaluate : 1.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 1.9990 chunk 22 optimal weight: 0.0770 chunk 115 optimal weight: 2.9990 chunk 148 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 171 optimal weight: 6.9990 chunk 113 optimal weight: 0.6980 chunk 202 optimal weight: 9.9990 chunk 126 optimal weight: 9.9990 chunk 123 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.2942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 GLN C 290 GLN ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN L 13 GLN ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 87 GLN E 290 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 17418 Z= 0.231 Angle : 0.590 9.130 23616 Z= 0.310 Chirality : 0.044 0.164 2622 Planarity : 0.004 0.045 3027 Dihedral : 4.696 36.084 2760 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.28 (0.17), residues: 2133 helix: 1.84 (0.26), residues: 357 sheet: 1.11 (0.22), residues: 516 loop : -0.73 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 133 HIS 0.009 0.001 HIS H 35 PHE 0.034 0.002 PHE A 210 TYR 0.021 0.002 TYR I 112 ARG 0.005 0.001 ARG I 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 391 time to evaluate : 2.183 Fit side-chains REVERT: A 124 PHE cc_start: 0.8227 (t80) cc_final: 0.7947 (t80) REVERT: B 19 ASP cc_start: 0.8855 (p0) cc_final: 0.8626 (p0) REVERT: B 90 ASP cc_start: 0.7123 (m-30) cc_final: 0.6657 (m-30) REVERT: M 36 TRP cc_start: 0.8043 (m100) cc_final: 0.7504 (m100) REVERT: M 46 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7384 (tm-30) REVERT: M 47 TRP cc_start: 0.8546 (t60) cc_final: 0.8068 (t60) REVERT: M 48 ILE cc_start: 0.8811 (mm) cc_final: 0.7655 (mm) REVERT: M 82 GLN cc_start: 0.7576 (tp40) cc_final: 0.7035 (tm-30) REVERT: M 83 MET cc_start: 0.7932 (mtt) cc_final: 0.7531 (mtt) REVERT: M 87 ARG cc_start: 0.8292 (mtp85) cc_final: 0.7826 (mtm-85) REVERT: M 90 ASP cc_start: 0.8401 (m-30) cc_final: 0.7914 (m-30) REVERT: M 112 TYR cc_start: 0.7981 (m-80) cc_final: 0.7241 (m-10) REVERT: N 99 TRP cc_start: 0.8130 (t-100) cc_final: 0.7368 (t-100) REVERT: N 105 ASN cc_start: 0.7616 (m-40) cc_final: 0.6972 (m-40) REVERT: C 108 TYR cc_start: 0.7639 (t80) cc_final: 0.7319 (t80) REVERT: C 204 ASN cc_start: 0.9009 (m-40) cc_final: 0.8639 (m-40) REVERT: C 241 TRP cc_start: 0.9017 (p-90) cc_final: 0.8808 (p-90) REVERT: D 17 MET cc_start: 0.8796 (tmm) cc_final: 0.8517 (tmm) REVERT: D 147 THR cc_start: 0.9167 (m) cc_final: 0.8713 (p) REVERT: H 87 ARG cc_start: 0.7729 (mtm-85) cc_final: 0.7305 (mtm-85) REVERT: H 90 ASP cc_start: 0.8414 (m-30) cc_final: 0.7923 (m-30) REVERT: H 99 ASP cc_start: 0.8005 (m-30) cc_final: 0.7700 (m-30) REVERT: L 13 GLN cc_start: 0.7903 (pt0) cc_final: 0.7522 (pt0) REVERT: L 43 TRP cc_start: 0.7637 (m100) cc_final: 0.6525 (m100) REVERT: L 46 GLN cc_start: 0.8803 (tp40) cc_final: 0.8081 (tp40) REVERT: E 108 TYR cc_start: 0.7510 (t80) cc_final: 0.7076 (t80) REVERT: E 122 GLU cc_start: 0.8213 (mp0) cc_final: 0.7902 (mp0) REVERT: E 146 CYS cc_start: 0.7013 (m) cc_final: 0.6624 (t) REVERT: E 155 TYR cc_start: 0.8327 (m-80) cc_final: 0.7984 (m-80) REVERT: E 241 TRP cc_start: 0.9118 (p-90) cc_final: 0.8840 (p-90) REVERT: E 269 ARG cc_start: 0.8218 (mtm110) cc_final: 0.7896 (mtm110) REVERT: F 19 ASP cc_start: 0.8391 (p0) cc_final: 0.8190 (p0) REVERT: F 59 MET cc_start: 0.9002 (tpt) cc_final: 0.8794 (tpt) REVERT: F 133 ILE cc_start: 0.8994 (mt) cc_final: 0.8602 (mm) REVERT: I 34 MET cc_start: 0.7701 (mmt) cc_final: 0.7447 (mmt) REVERT: I 46 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7725 (tm-30) REVERT: I 48 ILE cc_start: 0.8742 (mm) cc_final: 0.8069 (mm) REVERT: I 82 GLN cc_start: 0.7676 (tp40) cc_final: 0.6910 (tm-30) REVERT: I 87 ARG cc_start: 0.7880 (mtm180) cc_final: 0.7527 (mtm-85) REVERT: J 13 GLN cc_start: 0.8092 (mt0) cc_final: 0.7881 (pt0) REVERT: J 43 TRP cc_start: 0.7540 (m100) cc_final: 0.7172 (m100) outliers start: 0 outliers final: 0 residues processed: 391 average time/residue: 0.2574 time to fit residues: 158.7710 Evaluate side-chains 328 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 328 time to evaluate : 1.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 128 optimal weight: 0.8980 chunk 137 optimal weight: 5.9990 chunk 100 optimal weight: 0.4980 chunk 18 optimal weight: 0.8980 chunk 159 optimal weight: 3.9990 chunk 184 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 GLN C 283 HIS C 290 GLN ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 13 GLN ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 ASN E 290 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.4331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17418 Z= 0.202 Angle : 0.588 7.358 23616 Z= 0.311 Chirality : 0.044 0.170 2622 Planarity : 0.004 0.043 3027 Dihedral : 4.578 33.974 2760 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.26 (0.17), residues: 2133 helix: 1.77 (0.26), residues: 357 sheet: 1.10 (0.22), residues: 516 loop : -0.74 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP N 43 HIS 0.008 0.001 HIS H 35 PHE 0.029 0.002 PHE A 210 TYR 0.021 0.001 TYR D 141 ARG 0.005 0.001 ARG J 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 395 time to evaluate : 2.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 CYS cc_start: 0.5763 (m) cc_final: 0.5523 (m) REVERT: B 17 MET cc_start: 0.8725 (ttp) cc_final: 0.8242 (tmm) REVERT: B 19 ASP cc_start: 0.8796 (p0) cc_final: 0.8502 (p0) REVERT: M 36 TRP cc_start: 0.7917 (m100) cc_final: 0.7239 (m100) REVERT: M 46 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7508 (tm-30) REVERT: M 47 TRP cc_start: 0.8557 (t60) cc_final: 0.8022 (t60) REVERT: M 48 ILE cc_start: 0.8786 (mm) cc_final: 0.7950 (mm) REVERT: M 82 GLN cc_start: 0.7582 (tp40) cc_final: 0.7049 (tm-30) REVERT: M 83 MET cc_start: 0.7828 (mtt) cc_final: 0.7456 (mtt) REVERT: M 87 ARG cc_start: 0.8204 (mtp85) cc_final: 0.7797 (mtm-85) REVERT: M 90 ASP cc_start: 0.8351 (m-30) cc_final: 0.7879 (m-30) REVERT: M 112 TYR cc_start: 0.8024 (m-80) cc_final: 0.7306 (m-10) REVERT: N 46 GLN cc_start: 0.8571 (tp40) cc_final: 0.8310 (tp40) REVERT: N 99 TRP cc_start: 0.8147 (t-100) cc_final: 0.7337 (t-100) REVERT: N 105 ASN cc_start: 0.7609 (m-40) cc_final: 0.7041 (m-40) REVERT: C 108 TYR cc_start: 0.7667 (t80) cc_final: 0.7341 (t80) REVERT: C 204 ASN cc_start: 0.8992 (m-40) cc_final: 0.8651 (m-40) REVERT: D 17 MET cc_start: 0.8768 (tmm) cc_final: 0.8480 (tmm) REVERT: D 147 THR cc_start: 0.9218 (m) cc_final: 0.8950 (t) REVERT: H 34 MET cc_start: 0.7588 (ptp) cc_final: 0.7165 (ptt) REVERT: H 36 TRP cc_start: 0.8623 (m100) cc_final: 0.8270 (m100) REVERT: H 90 ASP cc_start: 0.8296 (m-30) cc_final: 0.7868 (m-30) REVERT: L 13 GLN cc_start: 0.7854 (pt0) cc_final: 0.6717 (pt0) REVERT: L 43 TRP cc_start: 0.7461 (m100) cc_final: 0.6544 (m100) REVERT: L 46 GLN cc_start: 0.8681 (tp40) cc_final: 0.8128 (tp40) REVERT: E 108 TYR cc_start: 0.7510 (t80) cc_final: 0.7049 (t80) REVERT: E 122 GLU cc_start: 0.8212 (mp0) cc_final: 0.7876 (mp0) REVERT: E 155 TYR cc_start: 0.8301 (m-80) cc_final: 0.7873 (m-80) REVERT: E 241 TRP cc_start: 0.9047 (p-90) cc_final: 0.8780 (p-90) REVERT: F 133 ILE cc_start: 0.8933 (mt) cc_final: 0.8515 (mm) REVERT: I 34 MET cc_start: 0.7622 (mmt) cc_final: 0.7405 (mmt) REVERT: I 82 GLN cc_start: 0.7554 (tp40) cc_final: 0.6916 (tm-30) REVERT: I 87 ARG cc_start: 0.7795 (mtm180) cc_final: 0.7515 (mtm-85) REVERT: I 90 ASP cc_start: 0.8330 (m-30) cc_final: 0.8028 (m-30) REVERT: J 43 TRP cc_start: 0.7451 (m100) cc_final: 0.7201 (m100) outliers start: 0 outliers final: 0 residues processed: 395 average time/residue: 0.2508 time to fit residues: 153.9849 Evaluate side-chains 316 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 316 time to evaluate : 2.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 3.9990 chunk 176 optimal weight: 0.9990 chunk 188 optimal weight: 5.9990 chunk 113 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 148 optimal weight: 0.9980 chunk 57 optimal weight: 7.9990 chunk 170 optimal weight: 0.8980 chunk 178 optimal weight: 0.5980 chunk 187 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 290 GLN ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 13 GLN ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 87 GLN E 290 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 46 GLN J 87 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17418 Z= 0.191 Angle : 0.585 7.216 23616 Z= 0.309 Chirality : 0.044 0.165 2622 Planarity : 0.004 0.042 3027 Dihedral : 4.507 32.767 2760 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.29 (0.17), residues: 2133 helix: 1.68 (0.26), residues: 357 sheet: 1.20 (0.23), residues: 501 loop : -0.69 (0.16), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 241 HIS 0.010 0.001 HIS H 35 PHE 0.030 0.001 PHE E 124 TYR 0.018 0.001 TYR H 112 ARG 0.008 0.001 ARG E 269 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 393 time to evaluate : 2.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 19 ASP cc_start: 0.8833 (p0) cc_final: 0.8602 (p0) REVERT: M 36 TRP cc_start: 0.7946 (m100) cc_final: 0.7251 (m100) REVERT: M 46 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7678 (tm-30) REVERT: M 47 TRP cc_start: 0.8498 (t60) cc_final: 0.8127 (t60) REVERT: M 48 ILE cc_start: 0.8777 (mm) cc_final: 0.7871 (mm) REVERT: M 82 GLN cc_start: 0.7588 (tp40) cc_final: 0.7049 (tm-30) REVERT: M 83 MET cc_start: 0.7828 (mtt) cc_final: 0.7450 (mtt) REVERT: M 87 ARG cc_start: 0.8202 (mtp85) cc_final: 0.7810 (mtm-85) REVERT: M 90 ASP cc_start: 0.8334 (m-30) cc_final: 0.7872 (m-30) REVERT: M 112 TYR cc_start: 0.8073 (m-80) cc_final: 0.7337 (m-10) REVERT: N 99 TRP cc_start: 0.8135 (t-100) cc_final: 0.7316 (t-100) REVERT: N 105 ASN cc_start: 0.7607 (m-40) cc_final: 0.7009 (m-40) REVERT: C 108 TYR cc_start: 0.7698 (t80) cc_final: 0.7330 (t80) REVERT: C 204 ASN cc_start: 0.8976 (m-40) cc_final: 0.8626 (m-40) REVERT: D 17 MET cc_start: 0.8760 (tmm) cc_final: 0.8530 (tmm) REVERT: D 19 ASP cc_start: 0.8351 (p0) cc_final: 0.8133 (p0) REVERT: D 145 ASP cc_start: 0.8881 (p0) cc_final: 0.8230 (p0) REVERT: D 147 THR cc_start: 0.9160 (m) cc_final: 0.8890 (p) REVERT: H 36 TRP cc_start: 0.8627 (m100) cc_final: 0.8177 (m100) REVERT: H 87 ARG cc_start: 0.7700 (mtm-85) cc_final: 0.7237 (mtm-85) REVERT: H 90 ASP cc_start: 0.8246 (m-30) cc_final: 0.7882 (m-30) REVERT: L 43 TRP cc_start: 0.7421 (m100) cc_final: 0.6233 (m100) REVERT: L 46 GLN cc_start: 0.8754 (tp40) cc_final: 0.8098 (tp40) REVERT: E 108 TYR cc_start: 0.7493 (t80) cc_final: 0.7175 (t80) REVERT: E 122 GLU cc_start: 0.8209 (mp0) cc_final: 0.7900 (mp0) REVERT: E 155 TYR cc_start: 0.8251 (m-80) cc_final: 0.7844 (m-80) REVERT: E 241 TRP cc_start: 0.9092 (p-90) cc_final: 0.8826 (p-90) REVERT: F 133 ILE cc_start: 0.8890 (mt) cc_final: 0.8462 (mm) REVERT: I 46 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7842 (tm-30) REVERT: I 82 GLN cc_start: 0.7498 (tp40) cc_final: 0.6885 (tm-30) REVERT: I 87 ARG cc_start: 0.7888 (mtm180) cc_final: 0.7575 (mtm-85) REVERT: I 90 ASP cc_start: 0.8338 (m-30) cc_final: 0.8001 (m-30) REVERT: J 108 PHE cc_start: 0.7991 (m-80) cc_final: 0.7710 (m-10) outliers start: 0 outliers final: 0 residues processed: 393 average time/residue: 0.2473 time to fit residues: 153.9249 Evaluate side-chains 324 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 324 time to evaluate : 2.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 209 optimal weight: 0.9980 chunk 192 optimal weight: 0.8980 chunk 166 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 128 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS C 290 GLN ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 13 GLN ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 87 GLN ** E 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 290 GLN F 50 ASN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 46 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 17418 Z= 0.242 Angle : 0.620 7.451 23616 Z= 0.328 Chirality : 0.044 0.160 2622 Planarity : 0.004 0.038 3027 Dihedral : 4.599 32.690 2760 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.05 % Allowed : 0.33 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.12 (0.17), residues: 2133 helix: 1.42 (0.26), residues: 357 sheet: 1.00 (0.22), residues: 516 loop : -0.73 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP N 43 HIS 0.005 0.001 HIS B 26 PHE 0.030 0.002 PHE E 124 TYR 0.020 0.001 TYR I 112 ARG 0.008 0.001 ARG E 215 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 385 time to evaluate : 1.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 17 MET cc_start: 0.8919 (tmm) cc_final: 0.8522 (tmm) REVERT: B 19 ASP cc_start: 0.8782 (p0) cc_final: 0.8577 (p0) REVERT: B 90 ASP cc_start: 0.7117 (m-30) cc_final: 0.6793 (m-30) REVERT: M 36 TRP cc_start: 0.7930 (m100) cc_final: 0.7358 (m100) REVERT: M 46 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7624 (tm-30) REVERT: M 47 TRP cc_start: 0.8538 (t60) cc_final: 0.8172 (t60) REVERT: M 48 ILE cc_start: 0.8770 (mm) cc_final: 0.7904 (mm) REVERT: M 82 GLN cc_start: 0.7708 (tp40) cc_final: 0.7135 (tm-30) REVERT: M 83 MET cc_start: 0.7880 (mtt) cc_final: 0.7480 (mtt) REVERT: M 87 ARG cc_start: 0.8210 (mtp85) cc_final: 0.7815 (mtm-85) REVERT: M 90 ASP cc_start: 0.8387 (m-30) cc_final: 0.7910 (m-30) REVERT: M 112 TYR cc_start: 0.8051 (m-80) cc_final: 0.7273 (m-10) REVERT: N 99 TRP cc_start: 0.8186 (t-100) cc_final: 0.7351 (t-100) REVERT: N 105 ASN cc_start: 0.7709 (m-40) cc_final: 0.7088 (m110) REVERT: C 108 TYR cc_start: 0.7755 (t80) cc_final: 0.7278 (t80) REVERT: C 204 ASN cc_start: 0.8996 (m-40) cc_final: 0.8690 (m-40) REVERT: H 36 TRP cc_start: 0.8523 (m100) cc_final: 0.8246 (m100) REVERT: H 90 ASP cc_start: 0.8300 (m-30) cc_final: 0.7901 (m-30) REVERT: L 13 GLN cc_start: 0.7849 (pt0) cc_final: 0.7308 (pt0) REVERT: L 43 TRP cc_start: 0.7577 (m100) cc_final: 0.6390 (m100) REVERT: L 46 GLN cc_start: 0.8736 (tp40) cc_final: 0.8047 (tp40) REVERT: E 108 TYR cc_start: 0.7649 (t80) cc_final: 0.7252 (t80) REVERT: E 122 GLU cc_start: 0.8248 (mp0) cc_final: 0.7903 (mp0) REVERT: E 155 TYR cc_start: 0.8305 (m-80) cc_final: 0.7949 (m-80) REVERT: E 241 TRP cc_start: 0.9141 (p-90) cc_final: 0.8872 (p-90) REVERT: F 133 ILE cc_start: 0.8930 (mt) cc_final: 0.8577 (mm) REVERT: F 145 ASP cc_start: 0.8880 (p0) cc_final: 0.7968 (p0) REVERT: I 82 GLN cc_start: 0.7605 (tp40) cc_final: 0.6924 (tm-30) REVERT: I 87 ARG cc_start: 0.7889 (mtm180) cc_final: 0.7607 (mtm-85) REVERT: I 90 ASP cc_start: 0.8328 (m-30) cc_final: 0.8025 (m-30) REVERT: J 43 TRP cc_start: 0.7065 (m100) cc_final: 0.6798 (m100) REVERT: J 46 GLN cc_start: 0.8076 (tt0) cc_final: 0.7794 (tt0) REVERT: J 99 TRP cc_start: 0.7616 (t-100) cc_final: 0.7194 (t-100) outliers start: 1 outliers final: 0 residues processed: 385 average time/residue: 0.2515 time to fit residues: 153.3691 Evaluate side-chains 312 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 312 time to evaluate : 1.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 153 optimal weight: 0.0010 chunk 24 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 166 optimal weight: 0.5980 chunk 69 optimal weight: 0.0030 chunk 171 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 146 optimal weight: 0.7980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 290 GLN ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 13 GLN ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 HIS E 290 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 87 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.109181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.089786 restraints weight = 35918.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.091849 restraints weight = 24321.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.093394 restraints weight = 16601.277| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17418 Z= 0.165 Angle : 0.604 7.701 23616 Z= 0.317 Chirality : 0.044 0.165 2622 Planarity : 0.004 0.040 3027 Dihedral : 4.414 30.708 2760 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.26 (0.17), residues: 2133 helix: 1.70 (0.26), residues: 357 sheet: 1.14 (0.22), residues: 501 loop : -0.70 (0.16), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP J 43 HIS 0.004 0.001 HIS B 26 PHE 0.032 0.001 PHE E 124 TYR 0.016 0.001 TYR H 112 ARG 0.007 0.001 ARG E 215 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3966.20 seconds wall clock time: 71 minutes 40.12 seconds (4300.12 seconds total)