Starting phenix.real_space_refine on Sun Jun 22 23:09:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u44_41874/06_2025/8u44_41874.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u44_41874/06_2025/8u44_41874.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u44_41874/06_2025/8u44_41874.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u44_41874/06_2025/8u44_41874.map" model { file = "/net/cci-nas-00/data/ceres_data/8u44_41874/06_2025/8u44_41874.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u44_41874/06_2025/8u44_41874.cif" } resolution = 3.41 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= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 11763 atoms to isotropic. 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 81 5.16 5 C 10683 2.51 5 N 2922 2.21 5 O 3342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17028 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2527 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 20, 'TRANS': 301} Chain: "B" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1394 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 1, 'TRANS': 171} Chain: "S" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 898 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "T" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: G, H, I, J, U, V, W, X Time building chain proxies: 8.02, per 1000 atoms: 0.47 Number of scatterers: 17028 At special positions: 0 Unit cell: (130.625, 124.355, 146.3, 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 81 16.00 O 3342 8.00 N 2922 7.00 C 10683 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 21 " " NAG A 502 " - " ASN A 129 " " NAG A 503 " - " ASN A 289 " " NAG G 501 " - " ASN G 21 " " NAG G 502 " - " ASN G 129 " " NAG G 503 " - " ASN G 289 " " NAG H 501 " - " ASN H 21 " " NAG H 502 " - " ASN H 129 " " NAG H 503 " - " ASN H 289 " Time building additional restraints: 4.10 Conformation dependent library (CDL) restraints added in 2.1 seconds 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3954 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 42 sheets defined 18.8% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'V' and resid 85 through 89 Processing helix chain 'A' and resid 65 through 71 Processing helix chain 'A' and resid 73 through 77 removed outlier: 3.688A pdb=" N GLU A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 187 through 195 removed outlier: 3.750A pdb=" N GLN A 191 " --> pdb=" O ASN A 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 58 Processing helix chain 'B' and resid 74 through 127 Processing helix chain 'B' and resid 134 through 136 No H-bonds generated for 'chain 'B' and resid 134 through 136' Processing helix chain 'B' and resid 145 through 154 removed outlier: 4.226A pdb=" N MET B 149 " --> pdb=" O ASN B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 170 removed outlier: 4.395A pdb=" N GLU B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLU B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) Processing helix chain 'S' and resid 85 through 89 Processing helix chain 'G' and resid 65 through 71 Processing helix chain 'G' and resid 73 through 77 removed outlier: 3.688A pdb=" N GLU G 77 " --> pdb=" O PRO G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 112 Processing helix chain 'G' and resid 187 through 195 removed outlier: 3.750A pdb=" N GLN G 191 " --> pdb=" O ASN G 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 58 Processing helix chain 'I' and resid 74 through 127 Processing helix chain 'I' and resid 134 through 136 No H-bonds generated for 'chain 'I' and resid 134 through 136' Processing helix chain 'I' and resid 145 through 154 removed outlier: 4.226A pdb=" N MET I 149 " --> pdb=" O ASN I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 170 removed outlier: 4.395A pdb=" N GLU I 164 " --> pdb=" O PRO I 160 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLU I 165 " --> pdb=" O LYS I 161 " (cutoff:3.500A) Processing helix chain 'U' and resid 85 through 89 Processing helix chain 'H' and resid 65 through 71 Processing helix chain 'H' and resid 73 through 77 removed outlier: 3.688A pdb=" N GLU H 77 " --> pdb=" O PRO H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 112 Processing helix chain 'H' and resid 187 through 195 removed outlier: 3.750A pdb=" N GLN H 191 " --> pdb=" O ASN H 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 58 Processing helix chain 'J' and resid 74 through 127 Processing helix chain 'J' and resid 134 through 136 No H-bonds generated for 'chain 'J' and resid 134 through 136' Processing helix chain 'J' and resid 145 through 154 removed outlier: 4.226A pdb=" N MET J 149 " --> pdb=" O ASN J 145 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 170 removed outlier: 4.395A pdb=" N GLU J 164 " --> pdb=" O PRO J 160 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLU J 165 " --> pdb=" O LYS J 161 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'V' and resid 5 through 6 removed outlier: 4.203A pdb=" N ALA V 77 " --> pdb=" O CYS V 22 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR V 76 " --> pdb=" O ASP V 71 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASP V 71 " --> pdb=" O THR V 76 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR V 69 " --> pdb=" O TYR V 78 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'V' and resid 10 through 12 removed outlier: 3.953A pdb=" N THR V 118 " --> pdb=" O GLU V 10 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS V 12 " --> pdb=" O THR V 118 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'V' and resid 47 through 49 Processing sheet with id=AA4, first strand: chain 'X' and resid 4 through 7 removed outlier: 4.545A pdb=" N VAL X 19 " --> pdb=" O ILE X 75 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE X 75 " --> pdb=" O VAL X 19 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE X 21 " --> pdb=" O LEU X 73 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N CYS X 23 " --> pdb=" O PHE X 71 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE X 71 " --> pdb=" O CYS X 23 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP X 70 " --> pdb=" O SER X 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'X' and resid 53 through 54 removed outlier: 6.647A pdb=" N TRP X 35 " --> pdb=" O LEU X 47 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR X 85 " --> pdb=" O HIS X 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA7, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA8, first strand: chain 'A' and resid 88 through 89 Processing sheet with id=AA9, first strand: chain 'A' and resid 100 through 102 removed outlier: 7.305A pdb=" N HIS A 101 " --> pdb=" O TYR A 232 " (cutoff:3.500A) removed outlier: 8.943A pdb=" N TRP A 234 " --> pdb=" O HIS A 101 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 178 " --> pdb=" O THR A 235 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 151 through 152 Processing sheet with id=AB2, first strand: chain 'A' and resid 167 through 170 removed outlier: 3.797A pdb=" N ASP A 241 " --> pdb=" O ASN A 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 286 through 287 Processing sheet with id=AB4, first strand: chain 'A' and resid 294 through 295 removed outlier: 3.524A pdb=" N GLN A 295 " --> pdb=" O LYS A 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 130 through 132 Processing sheet with id=AB6, first strand: chain 'S' and resid 5 through 6 removed outlier: 4.202A pdb=" N ALA S 77 " --> pdb=" O CYS S 22 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR S 76 " --> pdb=" O ASP S 71 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASP S 71 " --> pdb=" O THR S 76 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR S 69 " --> pdb=" O TYR S 78 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.953A pdb=" N THR S 118 " --> pdb=" O GLU S 10 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS S 12 " --> pdb=" O THR S 118 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'S' and resid 47 through 49 Processing sheet with id=AB9, first strand: chain 'T' and resid 4 through 7 removed outlier: 4.546A pdb=" N VAL T 19 " --> pdb=" O ILE T 75 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE T 75 " --> pdb=" O VAL T 19 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE T 21 " --> pdb=" O LEU T 73 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N CYS T 23 " --> pdb=" O PHE T 71 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE T 71 " --> pdb=" O CYS T 23 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP T 70 " --> pdb=" O SER T 67 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'T' and resid 53 through 54 removed outlier: 6.646A pdb=" N TRP T 35 " --> pdb=" O LEU T 47 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR T 85 " --> pdb=" O HIS T 38 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 25 through 26 Processing sheet with id=AC3, first strand: chain 'G' and resid 39 through 41 Processing sheet with id=AC4, first strand: chain 'G' and resid 88 through 89 Processing sheet with id=AC5, first strand: chain 'G' and resid 100 through 102 removed outlier: 7.306A pdb=" N HIS G 101 " --> pdb=" O TYR G 232 " (cutoff:3.500A) removed outlier: 8.943A pdb=" N TRP G 234 " --> pdb=" O HIS G 101 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL G 178 " --> pdb=" O THR G 235 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 151 through 152 Processing sheet with id=AC7, first strand: chain 'G' and resid 167 through 170 removed outlier: 3.797A pdb=" N ASP G 241 " --> pdb=" O ASN G 170 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 286 through 287 Processing sheet with id=AC9, first strand: chain 'G' and resid 294 through 295 removed outlier: 3.525A pdb=" N GLN G 295 " --> pdb=" O LYS G 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'I' and resid 130 through 132 Processing sheet with id=AD2, first strand: chain 'U' and resid 5 through 6 removed outlier: 4.202A pdb=" N ALA U 77 " --> pdb=" O CYS U 22 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR U 76 " --> pdb=" O ASP U 71 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASP U 71 " --> pdb=" O THR U 76 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR U 69 " --> pdb=" O TYR U 78 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'U' and resid 10 through 12 removed outlier: 3.952A pdb=" N THR U 118 " --> pdb=" O GLU U 10 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS U 12 " --> pdb=" O THR U 118 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'U' and resid 47 through 49 Processing sheet with id=AD5, first strand: chain 'W' and resid 4 through 7 removed outlier: 4.545A pdb=" N VAL W 19 " --> pdb=" O ILE W 75 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE W 75 " --> pdb=" O VAL W 19 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE W 21 " --> pdb=" O LEU W 73 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N CYS W 23 " --> pdb=" O PHE W 71 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE W 71 " --> pdb=" O CYS W 23 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP W 70 " --> pdb=" O SER W 67 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'W' and resid 53 through 54 removed outlier: 6.646A pdb=" N TRP W 35 " --> pdb=" O LEU W 47 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR W 85 " --> pdb=" O HIS W 38 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 25 through 26 Processing sheet with id=AD8, first strand: chain 'H' and resid 39 through 41 Processing sheet with id=AD9, first strand: chain 'H' and resid 88 through 89 Processing sheet with id=AE1, first strand: chain 'H' and resid 100 through 102 removed outlier: 7.305A pdb=" N HIS H 101 " --> pdb=" O TYR H 232 " (cutoff:3.500A) removed outlier: 8.943A pdb=" N TRP H 234 " --> pdb=" O HIS H 101 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL H 178 " --> pdb=" O THR H 235 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 151 through 152 Processing sheet with id=AE3, first strand: chain 'H' and resid 167 through 170 removed outlier: 3.797A pdb=" N ASP H 241 " --> pdb=" O ASN H 170 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 286 through 287 Processing sheet with id=AE5, first strand: chain 'H' and resid 294 through 295 removed outlier: 3.525A pdb=" N GLN H 295 " --> pdb=" O LYS H 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'J' and resid 130 through 132 492 hydrogen bonds defined for protein. 1314 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: 4.84 Time building geometry restraints manager: 4.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5580 1.35 - 1.47: 4354 1.47 - 1.59: 7364 1.59 - 1.72: 0 1.72 - 1.84: 114 Bond restraints: 17412 Sorted by residual: bond pdb=" N GLY B 1 " pdb=" CA GLY B 1 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 6.03e+00 bond pdb=" N GLY I 1 " pdb=" CA GLY I 1 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 6.03e+00 bond pdb=" N GLY J 1 " pdb=" CA GLY J 1 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 6.02e+00 bond pdb=" N GLU V 1 " pdb=" CA GLU V 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.99e+00 bond pdb=" N GLU S 1 " pdb=" CA GLU S 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 ... (remaining 17407 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 22620 2.32 - 4.65: 813 4.65 - 6.97: 132 6.97 - 9.30: 18 9.30 - 11.62: 3 Bond angle restraints: 23586 Sorted by residual: angle pdb=" CA TYR A 256 " pdb=" CB TYR A 256 " pdb=" CG TYR A 256 " ideal model delta sigma weight residual 113.90 121.94 -8.04 1.80e+00 3.09e-01 1.99e+01 angle pdb=" CA TYR G 256 " pdb=" CB TYR G 256 " pdb=" CG TYR G 256 " ideal model delta sigma weight residual 113.90 121.94 -8.04 1.80e+00 3.09e-01 1.99e+01 angle pdb=" CA TYR H 256 " pdb=" CB TYR H 256 " pdb=" CG TYR H 256 " ideal model delta sigma weight residual 113.90 121.93 -8.03 1.80e+00 3.09e-01 1.99e+01 angle pdb=" CB LEU J 99 " pdb=" CG LEU J 99 " pdb=" CD1 LEU J 99 " ideal model delta sigma weight residual 110.70 122.32 -11.62 3.00e+00 1.11e-01 1.50e+01 angle pdb=" CB LEU B 99 " pdb=" CG LEU B 99 " pdb=" CD1 LEU B 99 " ideal model delta sigma weight residual 110.70 122.32 -11.62 3.00e+00 1.11e-01 1.50e+01 ... (remaining 23581 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 9267 16.96 - 33.91: 923 33.91 - 50.87: 166 50.87 - 67.82: 39 67.82 - 84.78: 33 Dihedral angle restraints: 10428 sinusoidal: 4221 harmonic: 6207 Sorted by residual: dihedral pdb=" CA PHE G 124 " pdb=" C PHE G 124 " pdb=" N PRO G 125 " pdb=" CA PRO G 125 " ideal model delta harmonic sigma weight residual 180.00 155.20 24.80 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA PHE H 124 " pdb=" C PHE H 124 " pdb=" N PRO H 125 " pdb=" CA PRO H 125 " ideal model delta harmonic sigma weight residual 180.00 155.22 24.78 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA PHE A 124 " pdb=" C PHE A 124 " pdb=" N PRO A 125 " pdb=" CA PRO A 125 " ideal model delta harmonic sigma weight residual 180.00 155.23 24.77 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 10425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1656 0.047 - 0.094: 625 0.094 - 0.141: 210 0.141 - 0.189: 62 0.189 - 0.236: 9 Chirality restraints: 2562 Sorted by residual: chirality pdb=" CA GLU J 103 " pdb=" N GLU J 103 " pdb=" C GLU J 103 " pdb=" CB GLU J 103 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA GLU I 103 " pdb=" N GLU I 103 " pdb=" C GLU I 103 " pdb=" CB GLU I 103 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA GLU B 103 " pdb=" N GLU B 103 " pdb=" C GLU B 103 " pdb=" CB GLU B 103 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.24 2.00e-01 2.50e+01 1.38e+00 ... (remaining 2559 not shown) Planarity restraints: 3066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE H 124 " 0.050 5.00e-02 4.00e+02 7.63e-02 9.32e+00 pdb=" N PRO H 125 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO H 125 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO H 125 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 124 " -0.050 5.00e-02 4.00e+02 7.62e-02 9.29e+00 pdb=" N PRO A 125 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 125 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 125 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE G 124 " 0.050 5.00e-02 4.00e+02 7.62e-02 9.28e+00 pdb=" N PRO G 125 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO G 125 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO G 125 " 0.041 5.00e-02 4.00e+02 ... (remaining 3063 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 264 2.60 - 3.18: 15032 3.18 - 3.75: 26823 3.75 - 4.33: 36839 4.33 - 4.90: 62065 Nonbonded interactions: 141023 Sorted by model distance: nonbonded pdb=" SG CYS X 23 " pdb=" SG CYS X 88 " model vdw 2.027 3.760 nonbonded pdb=" SG CYS W 23 " pdb=" SG CYS W 88 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS T 23 " pdb=" SG CYS T 88 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS H 64 " pdb=" SG CYS H 76 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS G 64 " pdb=" SG CYS G 76 " model vdw 2.029 3.760 ... (remaining 141018 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'S' selection = chain 'U' selection = chain 'V' } ncs_group { reference = chain 'T' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.010 Extract box with map and model: 0.710 Check model and map are aligned: 0.110 Set scattering table: 0.180 Process input model: 36.470 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 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 : 0.006 0.056 17421 Z= 0.256 Angle : 1.010 11.622 23613 Z= 0.529 Chirality : 0.058 0.236 2562 Planarity : 0.006 0.076 3057 Dihedral : 14.786 84.781 6474 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -2.70 (0.17), residues: 2145 helix: 0.11 (0.26), residues: 378 sheet: -2.20 (0.23), residues: 510 loop : -2.29 (0.16), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP G 69 HIS 0.005 0.001 HIS J 142 PHE 0.024 0.003 PHE B 70 TYR 0.027 0.002 TYR V 92 ARG 0.023 0.001 ARG V 36 Details of bonding type rmsd link_NAG-ASN : bond 0.00363 ( 9) link_NAG-ASN : angle 1.80758 ( 27) hydrogen bonds : bond 0.15114 ( 492) hydrogen bonds : angle 8.66761 ( 1314) covalent geometry : bond 0.00603 (17412) covalent geometry : angle 1.00882 (23586) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 355 time to evaluate : 2.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 113 GLN cc_start: 0.7953 (pt0) cc_final: 0.7612 (pm20) REVERT: X 55 GLN cc_start: 0.8407 (tp-100) cc_final: 0.8043 (tp-100) REVERT: X 100 GLN cc_start: 0.7988 (mm110) cc_final: 0.7343 (mp10) REVERT: B 17 MET cc_start: 0.6903 (mmm) cc_final: 0.6164 (tpp) REVERT: S 113 GLN cc_start: 0.8062 (pt0) cc_final: 0.7581 (pp30) REVERT: T 53 ASN cc_start: 0.8697 (m-40) cc_final: 0.8476 (m110) REVERT: T 55 GLN cc_start: 0.8438 (tp-100) cc_final: 0.8022 (tp-100) REVERT: T 100 GLN cc_start: 0.8130 (mm110) cc_final: 0.7607 (mp10) REVERT: I 42 GLN cc_start: 0.7949 (tp-100) cc_final: 0.7723 (tp40) REVERT: U 113 GLN cc_start: 0.8025 (pt0) cc_final: 0.7667 (pm20) REVERT: W 100 GLN cc_start: 0.7911 (mm110) cc_final: 0.7330 (mp10) REVERT: J 17 MET cc_start: 0.6739 (mmm) cc_final: 0.6306 (tpp) outliers start: 0 outliers final: 0 residues processed: 355 average time/residue: 0.2896 time to fit residues: 152.8501 Evaluate side-chains 199 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 2.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 179 optimal weight: 9.9990 chunk 161 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 108 optimal weight: 0.1980 chunk 86 optimal weight: 8.9990 chunk 166 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 101 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 193 optimal weight: 6.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 6 GLN ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 ASN B 114 ASN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 ASN ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 50 ASN I 114 ASN I 125 GLN I 169 ASN W 6 GLN ** J 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 114 ASN ** J 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 169 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.078236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.067057 restraints weight = 66294.342| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 3.50 r_work: 0.3466 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17421 Z= 0.228 Angle : 0.675 10.358 23613 Z= 0.357 Chirality : 0.049 0.173 2562 Planarity : 0.005 0.051 3057 Dihedral : 5.693 55.679 2523 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 1.24 % Allowed : 10.84 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -2.46 (0.18), residues: 2145 helix: 0.56 (0.27), residues: 366 sheet: -2.19 (0.24), residues: 450 loop : -2.16 (0.16), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP U 45 HIS 0.004 0.001 HIS X 38 PHE 0.023 0.002 PHE U 53 TYR 0.014 0.002 TYR W 86 ARG 0.005 0.001 ARG A 82 Details of bonding type rmsd link_NAG-ASN : bond 0.00260 ( 9) link_NAG-ASN : angle 1.61115 ( 27) hydrogen bonds : bond 0.04694 ( 492) hydrogen bonds : angle 6.76533 ( 1314) covalent geometry : bond 0.00509 (17412) covalent geometry : angle 0.67324 (23586) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 216 time to evaluate : 2.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 78 TYR cc_start: 0.7168 (m-80) cc_final: 0.6910 (m-80) REVERT: X 55 GLN cc_start: 0.8879 (tp-100) cc_final: 0.8644 (tp40) REVERT: A 274 MET cc_start: 0.7741 (tpp) cc_final: 0.7512 (tpp) REVERT: B 17 MET cc_start: 0.7090 (mmm) cc_final: 0.6866 (tpp) REVERT: B 27 GLN cc_start: 0.8184 (tm-30) cc_final: 0.7757 (tm-30) REVERT: S 13 LYS cc_start: 0.7706 (tptt) cc_final: 0.7379 (tptt) REVERT: T 55 GLN cc_start: 0.8938 (tp-100) cc_final: 0.8432 (tp-100) REVERT: U 13 LYS cc_start: 0.7887 (tptt) cc_final: 0.7473 (tptt) REVERT: U 53 PHE cc_start: 0.7104 (OUTLIER) cc_final: 0.6597 (m-80) REVERT: U 85 ARG cc_start: 0.7525 (mtm110) cc_final: 0.7091 (ptp-170) REVERT: H 38 HIS cc_start: 0.8293 (m-70) cc_final: 0.8001 (m-70) outliers start: 23 outliers final: 13 residues processed: 234 average time/residue: 0.2826 time to fit residues: 102.1316 Evaluate side-chains 189 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 175 time to evaluate : 2.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 256 TYR Chi-restraints excluded: chain U residue 53 PHE Chi-restraints excluded: chain H residue 158 ASN Chi-restraints excluded: chain H residue 256 TYR Chi-restraints excluded: chain H residue 260 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 21 optimal weight: 10.0000 chunk 127 optimal weight: 6.9990 chunk 71 optimal weight: 20.0000 chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 145 optimal weight: 1.9990 chunk 142 optimal weight: 20.0000 chunk 206 optimal weight: 0.8980 chunk 92 optimal weight: 8.9990 chunk 79 optimal weight: 0.5980 chunk 6 optimal weight: 8.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 199 ASN ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 6 GLN ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 GLN G 183 HIS G 199 ASN H 199 ASN ** J 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 50 ASN ** J 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.075249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.063720 restraints weight = 67934.956| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 3.70 r_work: 0.3341 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 17421 Z= 0.250 Angle : 0.677 9.012 23613 Z= 0.356 Chirality : 0.048 0.177 2562 Planarity : 0.005 0.047 3057 Dihedral : 5.671 45.412 2523 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 2.00 % Allowed : 16.07 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -2.29 (0.18), residues: 2145 helix: 0.55 (0.27), residues: 366 sheet: -1.91 (0.26), residues: 423 loop : -2.07 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 153 HIS 0.004 0.001 HIS H 184 PHE 0.021 0.002 PHE U 53 TYR 0.013 0.002 TYR U 92 ARG 0.004 0.001 ARG A 82 Details of bonding type rmsd link_NAG-ASN : bond 0.00236 ( 9) link_NAG-ASN : angle 1.52292 ( 27) hydrogen bonds : bond 0.04636 ( 492) hydrogen bonds : angle 6.50338 ( 1314) covalent geometry : bond 0.00554 (17412) covalent geometry : angle 0.67549 (23586) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 206 time to evaluate : 1.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 108 MET cc_start: 0.7300 (tpp) cc_final: 0.6871 (tpp) REVERT: B 17 MET cc_start: 0.7141 (mmm) cc_final: 0.6900 (tpp) REVERT: B 27 GLN cc_start: 0.8273 (tm-30) cc_final: 0.7670 (tm-30) REVERT: B 98 LEU cc_start: 0.9000 (mm) cc_final: 0.8724 (mm) REVERT: S 53 PHE cc_start: 0.7456 (OUTLIER) cc_final: 0.6077 (m-80) REVERT: S 67 THR cc_start: 0.8696 (OUTLIER) cc_final: 0.8477 (p) REVERT: G 268 ILE cc_start: 0.6993 (OUTLIER) cc_final: 0.6609 (tt) REVERT: I 27 GLN cc_start: 0.8080 (tm-30) cc_final: 0.7653 (tm-30) REVERT: W 32 TYR cc_start: 0.7881 (m-80) cc_final: 0.7653 (m-80) REVERT: H 258 PHE cc_start: 0.8216 (m-10) cc_final: 0.7872 (m-10) REVERT: J 27 GLN cc_start: 0.8086 (tm-30) cc_final: 0.7670 (tm-30) outliers start: 37 outliers final: 17 residues processed: 237 average time/residue: 0.2646 time to fit residues: 98.7514 Evaluate side-chains 196 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 1.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 89 THR Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain S residue 53 PHE Chi-restraints excluded: chain S residue 67 THR Chi-restraints excluded: chain S residue 89 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 204 VAL Chi-restraints excluded: chain G residue 256 TYR Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain U residue 89 THR Chi-restraints excluded: chain H residue 256 TYR Chi-restraints excluded: chain H residue 260 LEU Chi-restraints excluded: chain H residue 268 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 59 optimal weight: 5.9990 chunk 172 optimal weight: 9.9990 chunk 138 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 chunk 173 optimal weight: 0.0970 chunk 178 optimal weight: 2.9990 chunk 199 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 197 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 chunk 71 optimal weight: 20.0000 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 GLN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 169 ASN ** W 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 111 GLN ** J 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 169 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.074082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.062495 restraints weight = 68213.834| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 3.68 r_work: 0.3304 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 17421 Z= 0.290 Angle : 0.713 8.525 23613 Z= 0.374 Chirality : 0.049 0.190 2562 Planarity : 0.005 0.042 3057 Dihedral : 5.581 37.749 2523 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 2.64 % Allowed : 18.55 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -2.17 (0.18), residues: 2145 helix: 0.47 (0.26), residues: 366 sheet: -1.75 (0.25), residues: 465 loop : -1.95 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP V 111 HIS 0.005 0.002 HIS G 184 PHE 0.018 0.002 PHE B 140 TYR 0.015 0.002 TYR U 92 ARG 0.004 0.001 ARG A 82 Details of bonding type rmsd link_NAG-ASN : bond 0.00306 ( 9) link_NAG-ASN : angle 1.72420 ( 27) hydrogen bonds : bond 0.04804 ( 492) hydrogen bonds : angle 6.43893 ( 1314) covalent geometry : bond 0.00645 (17412) covalent geometry : angle 0.71061 (23586) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 185 time to evaluate : 2.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 53 PHE cc_start: 0.7622 (OUTLIER) cc_final: 0.6390 (m-80) REVERT: V 108 MET cc_start: 0.7327 (tpp) cc_final: 0.6825 (tpp) REVERT: B 27 GLN cc_start: 0.8270 (tm-30) cc_final: 0.7649 (tm-30) REVERT: B 98 LEU cc_start: 0.8989 (mm) cc_final: 0.8747 (mm) REVERT: S 53 PHE cc_start: 0.7657 (OUTLIER) cc_final: 0.6075 (m-80) REVERT: G 268 ILE cc_start: 0.7101 (OUTLIER) cc_final: 0.6746 (tt) REVERT: I 27 GLN cc_start: 0.8134 (tm-30) cc_final: 0.7624 (tm-30) REVERT: U 53 PHE cc_start: 0.7464 (OUTLIER) cc_final: 0.5699 (m-80) REVERT: J 27 GLN cc_start: 0.8193 (tm-30) cc_final: 0.7672 (tm-30) outliers start: 49 outliers final: 31 residues processed: 231 average time/residue: 0.2545 time to fit residues: 93.7388 Evaluate side-chains 198 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 163 time to evaluate : 1.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 53 PHE Chi-restraints excluded: chain V residue 67 THR Chi-restraints excluded: chain V residue 89 THR Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain B residue 50 ASN Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain S residue 53 PHE Chi-restraints excluded: chain S residue 89 THR Chi-restraints excluded: chain T residue 90 GLN Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 204 VAL Chi-restraints excluded: chain G residue 256 TYR Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain U residue 53 PHE Chi-restraints excluded: chain U residue 67 THR Chi-restraints excluded: chain U residue 89 THR Chi-restraints excluded: chain W residue 90 GLN Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 256 TYR Chi-restraints excluded: chain H residue 260 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 14 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 135 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 167 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 179 optimal weight: 0.0070 chunk 160 optimal weight: 20.0000 overall best weight: 1.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 ASN A 111 GLN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 ASN ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 95 ASN G 111 GLN I 169 ASN ** W 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 ASN H 111 GLN ** J 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 169 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.077572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.065804 restraints weight = 67554.429| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 3.83 r_work: 0.3395 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17421 Z= 0.129 Angle : 0.589 7.789 23613 Z= 0.308 Chirality : 0.046 0.172 2562 Planarity : 0.004 0.052 3057 Dihedral : 4.803 31.877 2523 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.56 % Allowed : 20.12 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -1.88 (0.18), residues: 2145 helix: 0.74 (0.27), residues: 384 sheet: -1.36 (0.30), residues: 360 loop : -1.91 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP V 111 HIS 0.005 0.001 HIS B 142 PHE 0.015 0.001 PHE X 49 TYR 0.012 0.001 TYR G 17 ARG 0.003 0.000 ARG H 82 Details of bonding type rmsd link_NAG-ASN : bond 0.00186 ( 9) link_NAG-ASN : angle 1.30536 ( 27) hydrogen bonds : bond 0.04043 ( 492) hydrogen bonds : angle 5.90922 ( 1314) covalent geometry : bond 0.00284 (17412) covalent geometry : angle 0.58747 (23586) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 223 time to evaluate : 1.879 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: V 53 PHE cc_start: 0.7293 (OUTLIER) cc_final: 0.6173 (m-80) REVERT: V 108 MET cc_start: 0.7347 (tpp) cc_final: 0.6561 (tpp) REVERT: X 89 GLN cc_start: 0.8012 (tt0) cc_final: 0.7784 (pp30) REVERT: B 27 GLN cc_start: 0.8288 (tm-30) cc_final: 0.7973 (tm-30) REVERT: B 98 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8804 (mm) REVERT: S 43 LEU cc_start: 0.8152 (mm) cc_final: 0.7928 (mt) REVERT: G 268 ILE cc_start: 0.6749 (OUTLIER) cc_final: 0.6537 (tt) REVERT: G 274 MET cc_start: 0.8249 (tpp) cc_final: 0.7973 (tpp) REVERT: I 17 MET cc_start: 0.7263 (tpp) cc_final: 0.6644 (mpp) REVERT: I 27 GLN cc_start: 0.8212 (tm-30) cc_final: 0.7601 (tm-30) REVERT: U 108 MET cc_start: 0.7172 (tpp) cc_final: 0.6288 (tpp) REVERT: W 105 GLU cc_start: 0.4186 (tp30) cc_final: 0.3909 (tp30) REVERT: J 17 MET cc_start: 0.7239 (tpp) cc_final: 0.7028 (tpp) REVERT: J 27 GLN cc_start: 0.8175 (tm-30) cc_final: 0.7575 (tm-30) outliers start: 29 outliers final: 17 residues processed: 248 average time/residue: 0.2565 time to fit residues: 99.8308 Evaluate side-chains 209 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 189 time to evaluate : 2.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 53 PHE Chi-restraints excluded: chain V residue 67 THR Chi-restraints excluded: chain X residue 82 ASP Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain S residue 67 THR Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 256 TYR Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain U residue 67 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 256 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 44 optimal weight: 8.9990 chunk 184 optimal weight: 5.9990 chunk 5 optimal weight: 0.0570 chunk 150 optimal weight: 3.9990 chunk 156 optimal weight: 7.9990 chunk 128 optimal weight: 9.9990 chunk 155 optimal weight: 20.0000 chunk 125 optimal weight: 8.9990 chunk 75 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 overall best weight: 3.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 GLN A 183 HIS ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 GLN ** W 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 55 GLN ** W 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 111 GLN ** J 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.074781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.063085 restraints weight = 68385.213| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 3.74 r_work: 0.3321 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 17421 Z= 0.254 Angle : 0.688 10.901 23613 Z= 0.356 Chirality : 0.047 0.210 2562 Planarity : 0.005 0.044 3057 Dihedral : 5.143 34.336 2523 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 2.70 % Allowed : 20.82 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -1.82 (0.18), residues: 2145 helix: 0.83 (0.27), residues: 366 sheet: -1.37 (0.26), residues: 450 loop : -1.82 (0.16), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP V 111 HIS 0.005 0.001 HIS H 184 PHE 0.019 0.002 PHE I 140 TYR 0.018 0.002 TYR V 92 ARG 0.004 0.001 ARG H 120 Details of bonding type rmsd link_NAG-ASN : bond 0.00264 ( 9) link_NAG-ASN : angle 1.48206 ( 27) hydrogen bonds : bond 0.04466 ( 492) hydrogen bonds : angle 6.15891 ( 1314) covalent geometry : bond 0.00569 (17412) covalent geometry : angle 0.68702 (23586) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 180 time to evaluate : 1.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 53 PHE cc_start: 0.7572 (OUTLIER) cc_final: 0.6138 (m-80) REVERT: V 108 MET cc_start: 0.7275 (tpp) cc_final: 0.6694 (tpp) REVERT: B 27 GLN cc_start: 0.8265 (tm-30) cc_final: 0.7941 (tm-30) REVERT: B 98 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8772 (mm) REVERT: S 53 PHE cc_start: 0.7538 (OUTLIER) cc_final: 0.6394 (m-80) REVERT: G 268 ILE cc_start: 0.6977 (OUTLIER) cc_final: 0.6657 (tt) REVERT: I 27 GLN cc_start: 0.8200 (tm-30) cc_final: 0.7582 (tm-30) REVERT: U 1 GLU cc_start: 0.2735 (OUTLIER) cc_final: 0.2354 (tp30) REVERT: U 116 MET cc_start: 0.7215 (mmm) cc_final: 0.6885 (mmm) REVERT: W 55 GLN cc_start: 0.8858 (tp-100) cc_final: 0.8603 (tp-100) REVERT: H 258 PHE cc_start: 0.8256 (m-10) cc_final: 0.7832 (m-10) REVERT: J 27 GLN cc_start: 0.8181 (tm-30) cc_final: 0.7544 (tm-30) REVERT: J 150 GLU cc_start: 0.6724 (OUTLIER) cc_final: 0.6469 (tm-30) outliers start: 50 outliers final: 34 residues processed: 224 average time/residue: 0.2347 time to fit residues: 84.2580 Evaluate side-chains 208 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 168 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 53 PHE Chi-restraints excluded: chain V residue 67 THR Chi-restraints excluded: chain V residue 89 THR Chi-restraints excluded: chain X residue 21 ILE Chi-restraints excluded: chain X residue 82 ASP Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain B residue 50 ASN Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain S residue 53 PHE Chi-restraints excluded: chain S residue 67 THR Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 256 TYR Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain U residue 1 GLU Chi-restraints excluded: chain U residue 67 THR Chi-restraints excluded: chain W residue 21 ILE Chi-restraints excluded: chain W residue 82 ASP Chi-restraints excluded: chain W residue 89 GLN Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 256 TYR Chi-restraints excluded: chain J residue 150 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 200 optimal weight: 0.7980 chunk 4 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 208 optimal weight: 10.0000 chunk 211 optimal weight: 0.1980 chunk 146 optimal weight: 6.9990 chunk 132 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 156 optimal weight: 8.9990 chunk 77 optimal weight: 9.9990 chunk 177 optimal weight: 10.0000 overall best weight: 3.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.074962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.063239 restraints weight = 68005.577| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 3.74 r_work: 0.3327 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.4769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17421 Z= 0.228 Angle : 0.672 10.582 23613 Z= 0.346 Chirality : 0.047 0.173 2562 Planarity : 0.004 0.055 3057 Dihedral : 5.154 33.994 2523 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 3.07 % Allowed : 21.20 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -1.85 (0.18), residues: 2145 helix: 0.58 (0.26), residues: 384 sheet: -1.37 (0.27), residues: 450 loop : -1.81 (0.16), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP V 111 HIS 0.005 0.001 HIS H 184 PHE 0.017 0.002 PHE I 140 TYR 0.013 0.002 TYR V 92 ARG 0.003 0.000 ARG H 82 Details of bonding type rmsd link_NAG-ASN : bond 0.00208 ( 9) link_NAG-ASN : angle 1.42490 ( 27) hydrogen bonds : bond 0.04403 ( 492) hydrogen bonds : angle 6.13156 ( 1314) covalent geometry : bond 0.00510 (17412) covalent geometry : angle 0.67067 (23586) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 173 time to evaluate : 2.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 1 GLU cc_start: 0.2986 (OUTLIER) cc_final: 0.2364 (tp30) REVERT: V 53 PHE cc_start: 0.7627 (OUTLIER) cc_final: 0.6286 (m-80) REVERT: V 61 LYS cc_start: 0.8903 (tmtt) cc_final: 0.8637 (ptmm) REVERT: B 27 GLN cc_start: 0.8255 (tm-30) cc_final: 0.7930 (tm-30) REVERT: S 53 PHE cc_start: 0.7551 (OUTLIER) cc_final: 0.6419 (m-80) REVERT: G 69 TRP cc_start: 0.8851 (OUTLIER) cc_final: 0.8562 (p-90) REVERT: G 268 ILE cc_start: 0.7000 (OUTLIER) cc_final: 0.6697 (tt) REVERT: G 274 MET cc_start: 0.8376 (tpp) cc_final: 0.8134 (tpp) REVERT: I 27 GLN cc_start: 0.8233 (tm-30) cc_final: 0.7602 (tm-30) REVERT: U 116 MET cc_start: 0.7061 (mmm) cc_final: 0.6578 (mmm) REVERT: H 258 PHE cc_start: 0.8229 (m-10) cc_final: 0.7823 (m-10) REVERT: J 27 GLN cc_start: 0.8168 (tm-30) cc_final: 0.7507 (tm-30) REVERT: J 150 GLU cc_start: 0.6774 (OUTLIER) cc_final: 0.6516 (tm-30) outliers start: 57 outliers final: 41 residues processed: 221 average time/residue: 0.2541 time to fit residues: 91.4159 Evaluate side-chains 210 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 163 time to evaluate : 2.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 1 GLU Chi-restraints excluded: chain V residue 53 PHE Chi-restraints excluded: chain V residue 67 THR Chi-restraints excluded: chain V residue 89 THR Chi-restraints excluded: chain X residue 21 ILE Chi-restraints excluded: chain X residue 82 ASP Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain B residue 50 ASN Chi-restraints excluded: chain S residue 53 PHE Chi-restraints excluded: chain S residue 67 THR Chi-restraints excluded: chain S residue 89 THR Chi-restraints excluded: chain T residue 21 ILE Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 256 TYR Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain U residue 67 THR Chi-restraints excluded: chain W residue 21 ILE Chi-restraints excluded: chain W residue 82 ASP Chi-restraints excluded: chain W residue 89 GLN Chi-restraints excluded: chain W residue 90 GLN Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 69 TRP Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 256 TYR Chi-restraints excluded: chain J residue 150 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 136 optimal weight: 4.9990 chunk 191 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 129 optimal weight: 0.8980 chunk 176 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 194 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 18 optimal weight: 20.0000 chunk 154 optimal weight: 9.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.075499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.063795 restraints weight = 67316.030| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 3.72 r_work: 0.3343 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17421 Z= 0.194 Angle : 0.656 11.453 23613 Z= 0.338 Chirality : 0.047 0.174 2562 Planarity : 0.004 0.055 3057 Dihedral : 5.050 32.514 2523 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 3.18 % Allowed : 21.52 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -1.84 (0.18), residues: 2145 helix: 0.60 (0.26), residues: 384 sheet: -1.45 (0.26), residues: 459 loop : -1.76 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP V 111 HIS 0.004 0.001 HIS H 184 PHE 0.014 0.002 PHE G 258 TYR 0.014 0.001 TYR T 87 ARG 0.003 0.000 ARG H 82 Details of bonding type rmsd link_NAG-ASN : bond 0.00174 ( 9) link_NAG-ASN : angle 1.33937 ( 27) hydrogen bonds : bond 0.04302 ( 492) hydrogen bonds : angle 6.00472 ( 1314) covalent geometry : bond 0.00436 (17412) covalent geometry : angle 0.65503 (23586) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 179 time to evaluate : 2.662 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: V 1 GLU cc_start: 0.3429 (OUTLIER) cc_final: 0.2583 (tt0) REVERT: V 53 PHE cc_start: 0.7534 (OUTLIER) cc_final: 0.6160 (m-80) REVERT: V 61 LYS cc_start: 0.8861 (tmtt) cc_final: 0.8614 (ptmm) REVERT: B 27 GLN cc_start: 0.8334 (tm-30) cc_final: 0.8012 (tm-30) REVERT: S 53 PHE cc_start: 0.7462 (OUTLIER) cc_final: 0.6298 (m-80) REVERT: G 274 MET cc_start: 0.8382 (tpp) cc_final: 0.8118 (tpp) REVERT: I 27 GLN cc_start: 0.8243 (tm-30) cc_final: 0.7610 (tm-30) REVERT: U 53 PHE cc_start: 0.7423 (OUTLIER) cc_final: 0.5512 (m-80) REVERT: W 55 GLN cc_start: 0.8899 (tp-100) cc_final: 0.8681 (tp40) REVERT: H 258 PHE cc_start: 0.8171 (m-10) cc_final: 0.7809 (m-10) REVERT: J 27 GLN cc_start: 0.8204 (tm-30) cc_final: 0.7498 (tm-30) REVERT: J 42 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.7907 (tp-100) REVERT: J 150 GLU cc_start: 0.6730 (OUTLIER) cc_final: 0.6495 (tm-30) outliers start: 59 outliers final: 43 residues processed: 233 average time/residue: 0.2822 time to fit residues: 105.9474 Evaluate side-chains 219 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 170 time to evaluate : 1.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 1 GLU Chi-restraints excluded: chain V residue 53 PHE Chi-restraints excluded: chain V residue 67 THR Chi-restraints excluded: chain V residue 89 THR Chi-restraints excluded: chain X residue 21 ILE Chi-restraints excluded: chain X residue 82 ASP Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain B residue 50 ASN Chi-restraints excluded: chain S residue 53 PHE Chi-restraints excluded: chain S residue 67 THR Chi-restraints excluded: chain S residue 80 GLU Chi-restraints excluded: chain S residue 89 THR Chi-restraints excluded: chain T residue 21 ILE Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 256 TYR Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain I residue 103 GLU Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain U residue 53 PHE Chi-restraints excluded: chain U residue 67 THR Chi-restraints excluded: chain U residue 89 THR Chi-restraints excluded: chain W residue 82 ASP Chi-restraints excluded: chain W residue 89 GLN Chi-restraints excluded: chain W residue 90 GLN Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 69 TRP Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 256 TYR Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain J residue 150 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 52 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 43 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 203 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 185 optimal weight: 0.9990 chunk 123 optimal weight: 5.9990 chunk 161 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 GLN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 GLN ** W 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 111 GLN ** J 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.077204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.065467 restraints weight = 67258.428| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 3.77 r_work: 0.3390 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.4799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17421 Z= 0.137 Angle : 0.633 11.889 23613 Z= 0.324 Chirality : 0.046 0.240 2562 Planarity : 0.004 0.056 3057 Dihedral : 4.776 29.304 2523 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.83 % Allowed : 22.76 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -1.78 (0.18), residues: 2145 helix: 0.64 (0.27), residues: 387 sheet: -1.34 (0.29), residues: 399 loop : -1.76 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 92 HIS 0.003 0.001 HIS I 142 PHE 0.016 0.001 PHE G 258 TYR 0.024 0.001 TYR B 94 ARG 0.003 0.000 ARG G 315 Details of bonding type rmsd link_NAG-ASN : bond 0.00194 ( 9) link_NAG-ASN : angle 1.18338 ( 27) hydrogen bonds : bond 0.04066 ( 492) hydrogen bonds : angle 5.78922 ( 1314) covalent geometry : bond 0.00310 (17412) covalent geometry : angle 0.63259 (23586) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 199 time to evaluate : 2.029 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: V 53 PHE cc_start: 0.7425 (OUTLIER) cc_final: 0.6185 (m-80) REVERT: V 57 ASN cc_start: 0.7606 (t0) cc_final: 0.7311 (t0) REVERT: V 61 LYS cc_start: 0.8897 (tmtt) cc_final: 0.8687 (ptmm) REVERT: V 108 MET cc_start: 0.7399 (tpp) cc_final: 0.6769 (tpp) REVERT: B 27 GLN cc_start: 0.8298 (tm-30) cc_final: 0.7961 (tm-30) REVERT: S 43 LEU cc_start: 0.8242 (mm) cc_final: 0.7961 (mt) REVERT: G 274 MET cc_start: 0.8353 (tpp) cc_final: 0.8075 (tpp) REVERT: I 6 ILE cc_start: 0.8504 (tt) cc_final: 0.8192 (pt) REVERT: I 27 GLN cc_start: 0.8236 (tm-30) cc_final: 0.7575 (tm-30) REVERT: U 116 MET cc_start: 0.7164 (mmm) cc_final: 0.6791 (mmm) REVERT: W 55 GLN cc_start: 0.8896 (tp-100) cc_final: 0.8671 (tp40) REVERT: W 105 GLU cc_start: 0.3790 (tp30) cc_final: 0.3569 (tp30) REVERT: H 258 PHE cc_start: 0.8092 (m-10) cc_final: 0.7736 (m-10) REVERT: J 27 GLN cc_start: 0.8198 (tm-30) cc_final: 0.7480 (tm-30) REVERT: J 42 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.8013 (mm-40) outliers start: 34 outliers final: 29 residues processed: 230 average time/residue: 0.2507 time to fit residues: 91.9643 Evaluate side-chains 215 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 184 time to evaluate : 2.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 53 PHE Chi-restraints excluded: chain V residue 67 THR Chi-restraints excluded: chain X residue 82 ASP Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain B residue 50 ASN Chi-restraints excluded: chain S residue 67 THR Chi-restraints excluded: chain T residue 21 ILE Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 256 TYR Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain I residue 103 GLU Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain U residue 67 THR Chi-restraints excluded: chain W residue 82 ASP Chi-restraints excluded: chain W residue 90 GLN Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 69 TRP Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 256 TYR Chi-restraints excluded: chain J residue 42 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 5 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 chunk 147 optimal weight: 0.8980 chunk 54 optimal weight: 8.9990 chunk 93 optimal weight: 9.9990 chunk 154 optimal weight: 0.9990 chunk 137 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 60 ASN ** J 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.076763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.065073 restraints weight = 67206.782| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 3.76 r_work: 0.3380 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 17421 Z= 0.155 Angle : 0.643 11.030 23613 Z= 0.327 Chirality : 0.047 0.309 2562 Planarity : 0.004 0.049 3057 Dihedral : 4.738 28.202 2523 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.05 % Allowed : 22.71 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.18), residues: 2145 helix: 0.71 (0.27), residues: 387 sheet: -1.24 (0.27), residues: 432 loop : -1.69 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP V 111 HIS 0.003 0.001 HIS H 184 PHE 0.025 0.002 PHE T 83 TYR 0.015 0.001 TYR V 58 ARG 0.003 0.000 ARG H 255 Details of bonding type rmsd link_NAG-ASN : bond 0.00161 ( 9) link_NAG-ASN : angle 1.18422 ( 27) hydrogen bonds : bond 0.04016 ( 492) hydrogen bonds : angle 5.77276 ( 1314) covalent geometry : bond 0.00351 (17412) covalent geometry : angle 0.64178 (23586) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 188 time to evaluate : 1.864 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: V 53 PHE cc_start: 0.7452 (OUTLIER) cc_final: 0.6144 (m-80) REVERT: V 108 MET cc_start: 0.7387 (tpp) cc_final: 0.6766 (tpp) REVERT: B 27 GLN cc_start: 0.8325 (tm-30) cc_final: 0.7990 (tm-30) REVERT: G 274 MET cc_start: 0.8331 (tpp) cc_final: 0.8044 (tpp) REVERT: I 27 GLN cc_start: 0.8246 (tm-30) cc_final: 0.7581 (tm-30) REVERT: U 116 MET cc_start: 0.7209 (mmm) cc_final: 0.6772 (mmm) REVERT: W 55 GLN cc_start: 0.8906 (tp-100) cc_final: 0.8610 (tp-100) REVERT: W 105 GLU cc_start: 0.3845 (tp30) cc_final: 0.3628 (tp30) REVERT: H 258 PHE cc_start: 0.8089 (m-10) cc_final: 0.7703 (m-10) REVERT: J 27 GLN cc_start: 0.8218 (tm-30) cc_final: 0.7504 (tm-30) REVERT: J 42 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8135 (tp-100) outliers start: 38 outliers final: 33 residues processed: 222 average time/residue: 0.2553 time to fit residues: 89.4809 Evaluate side-chains 212 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 177 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 53 PHE Chi-restraints excluded: chain V residue 67 THR Chi-restraints excluded: chain X residue 21 ILE Chi-restraints excluded: chain X residue 82 ASP Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain B residue 50 ASN Chi-restraints excluded: chain S residue 67 THR Chi-restraints excluded: chain T residue 21 ILE Chi-restraints excluded: chain T residue 104 VAL Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 256 TYR Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain I residue 103 GLU Chi-restraints excluded: chain I residue 112 ASP Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain U residue 67 THR Chi-restraints excluded: chain W residue 82 ASP Chi-restraints excluded: chain W residue 89 GLN Chi-restraints excluded: chain W residue 90 GLN Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 69 TRP Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 256 TYR Chi-restraints excluded: chain J residue 42 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 203 optimal weight: 4.9990 chunk 109 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 141 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 118 optimal weight: 4.9990 chunk 198 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 202 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 57 ASN ** X 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 GLN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 GLN ** W 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 111 GLN ** J 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.075034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.063258 restraints weight = 67595.282| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 3.74 r_work: 0.3329 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.5098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17421 Z= 0.240 Angle : 0.706 12.425 23613 Z= 0.360 Chirality : 0.047 0.205 2562 Planarity : 0.005 0.046 3057 Dihedral : 5.128 30.440 2523 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 2.21 % Allowed : 22.65 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -1.75 (0.18), residues: 2145 helix: 0.81 (0.27), residues: 369 sheet: -1.33 (0.27), residues: 438 loop : -1.75 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP V 111 HIS 0.005 0.001 HIS H 184 PHE 0.026 0.002 PHE T 83 TYR 0.023 0.002 TYR V 58 ARG 0.005 0.000 ARG U 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00245 ( 9) link_NAG-ASN : angle 1.40850 ( 27) hydrogen bonds : bond 0.04383 ( 492) hydrogen bonds : angle 6.05049 ( 1314) covalent geometry : bond 0.00539 (17412) covalent geometry : angle 0.70494 (23586) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7115.69 seconds wall clock time: 124 minutes 43.97 seconds (7483.97 seconds total)