Starting phenix.real_space_refine on Thu Mar 5 00:26:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o8t_70236/03_2026/9o8t_70236.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o8t_70236/03_2026/9o8t_70236.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9o8t_70236/03_2026/9o8t_70236.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o8t_70236/03_2026/9o8t_70236.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9o8t_70236/03_2026/9o8t_70236.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o8t_70236/03_2026/9o8t_70236.map" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 81 5.16 5 C 10749 2.51 5 N 2910 2.21 5 O 3402 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17142 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2528 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 18, 'TRANS': 304} Chain: "B" Number of atoms: 1355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1355 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 1, 'TRANS': 165} Chain: "H" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 971 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 2, 'TRANS': 125} Chain: "L" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 790 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: C, D, E, F, G, I, J, K, N, O Time building chain proxies: 3.13, per 1000 atoms: 0.18 Number of scatterers: 17142 At special positions: 0 Unit cell: (129.05, 125.425, 142.825, 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 3402 8.00 N 2910 7.00 C 10749 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.02 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.02 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 98 " - pdb=" SG CYS H 100C" distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS E 137 " distance=2.02 Simple disulfide: pdb=" SG CYS D 14 " - pdb=" SG CYS F 137 " distance=2.02 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS D 52 " - pdb=" SG CYS D 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.02 Simple disulfide: pdb=" SG CYS D 97 " - pdb=" SG CYS D 139 " distance=2.02 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS D 281 " - pdb=" SG CYS D 305 " distance=2.03 Simple disulfide: pdb=" SG CYS E 144 " - pdb=" SG CYS E 148 " distance=2.02 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 98 " - pdb=" SG CYS G 100C" distance=2.02 Simple disulfide: pdb=" SG CYS I 98 " - pdb=" SG CYS I 100C" distance=2.02 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 401 " - " ASN A 33 " " NAG A 402 " - " ASN A 278 " " NAG B 301 " - " ASN B 154 " " NAG C 401 " - " ASN C 33 " " NAG C 402 " - " ASN C 278 " " NAG D 401 " - " ASN D 33 " " NAG D 402 " - " ASN D 278 " " NAG E 301 " - " ASN E 154 " " NAG F 301 " - " ASN F 154 " " NAG M 1 " - " ASN A 94 " " NAG N 1 " - " ASN C 94 " " NAG O 1 " - " ASN D 94 " Time building additional restraints: 1.68 Conformation dependent library (CDL) restraints added in 768.9 milliseconds 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: 3966 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 51 sheets defined 19.6% alpha, 24.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 125 through 127 removed outlier: 4.534A pdb=" N TRP A 127 " --> pdb=" O LYS A 125A" (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 removed outlier: 3.517A pdb=" N GLN A 191 " --> pdb=" O THR A 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 58 Processing helix chain 'B' and resid 71 through 73 No H-bonds generated for 'chain 'B' and resid 71 through 73' Processing helix chain 'B' and resid 74 through 126 Processing helix chain 'B' and resid 145 through 155 removed outlier: 3.504A pdb=" N ASN B 154 " --> pdb=" O GLU B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 161 Processing helix chain 'B' and resid 162 through 169 Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.614A pdb=" N LYS H 64 " --> pdb=" O ASP H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 125 through 127 removed outlier: 4.531A pdb=" N TRP C 127 " --> pdb=" O LYS C 125A" (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 removed outlier: 3.515A pdb=" N GLN C 191 " --> pdb=" O THR C 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 58 Processing helix chain 'E' and resid 71 through 73 No H-bonds generated for 'chain 'E' and resid 71 through 73' Processing helix chain 'E' and resid 74 through 126 Processing helix chain 'E' and resid 145 through 155 removed outlier: 3.501A pdb=" N ASN E 154 " --> pdb=" O GLU E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 161 Processing helix chain 'E' and resid 162 through 169 Processing helix chain 'G' and resid 61 through 64 removed outlier: 3.612A pdb=" N LYS G 64 " --> pdb=" O ASP G 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 61 through 64' Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'D' and resid 65 through 72 Processing helix chain 'D' and resid 104 through 112 Processing helix chain 'D' and resid 125 through 127 removed outlier: 4.532A pdb=" N TRP D 127 " --> pdb=" O LYS D 125A" (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 195 removed outlier: 3.515A pdb=" N GLN D 191 " --> pdb=" O THR D 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 58 Processing helix chain 'F' and resid 71 through 73 No H-bonds generated for 'chain 'F' and resid 71 through 73' Processing helix chain 'F' and resid 74 through 126 Processing helix chain 'F' and resid 145 through 155 removed outlier: 3.506A pdb=" N ASN F 154 " --> pdb=" O GLU F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 161 Processing helix chain 'F' and resid 162 through 169 Processing helix chain 'I' and resid 61 through 64 removed outlier: 3.615A pdb=" N LYS I 64 " --> pdb=" O ASP I 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 61 through 64' Processing helix chain 'K' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 17 Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 removed outlier: 4.077A pdb=" N ASP A 24 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 removed outlier: 5.914A pdb=" N LEU A 51 " --> pdb=" O HIS A 275 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N CYS A 277 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 59 through 62 removed outlier: 6.451A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 119 through 121 Processing sheet with id=AA8, first strand: chain 'A' and resid 136 through 141 removed outlier: 4.228A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AB1, first strand: chain 'A' and resid 167 through 169 Processing sheet with id=AB2, first strand: chain 'A' and resid 281 through 282 removed outlier: 3.596A pdb=" N THR B 64 " --> pdb=" O GLY A 303 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 130 through 132 Processing sheet with id=AB4, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.536A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.146A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL H 89 " --> pdb=" O GLN H 39 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.146A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL H 102 " --> pdb=" O LYS H 94 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.551A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AB9, first strand: chain 'C' and resid 12 through 17 Processing sheet with id=AC1, first strand: chain 'C' and resid 24 through 26 removed outlier: 4.079A pdb=" N ASP C 24 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AC3, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AC4, first strand: chain 'C' and resid 51 through 54 removed outlier: 5.916A pdb=" N LEU C 51 " --> pdb=" O HIS C 275 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N CYS C 277 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 59 through 62 removed outlier: 6.460A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 119 through 121 Processing sheet with id=AC7, first strand: chain 'C' and resid 136 through 141 removed outlier: 4.229A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 151 through 153 Processing sheet with id=AC9, first strand: chain 'C' and resid 167 through 169 Processing sheet with id=AD1, first strand: chain 'C' and resid 281 through 282 removed outlier: 3.596A pdb=" N THR E 64 " --> pdb=" O GLY C 303 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 130 through 132 Processing sheet with id=AD3, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.536A pdb=" N GLN G 3 " --> pdb=" O SER G 25 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER G 25 " --> pdb=" O GLN G 3 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 10 through 11 removed outlier: 6.145A pdb=" N GLY G 10 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL G 89 " --> pdb=" O GLN G 39 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 10 through 11 removed outlier: 6.145A pdb=" N GLY G 10 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL G 102 " --> pdb=" O LYS G 94 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.552A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 19 through 24 Processing sheet with id=AD8, first strand: chain 'D' and resid 12 through 17 Processing sheet with id=AD9, first strand: chain 'D' and resid 24 through 26 removed outlier: 4.082A pdb=" N ASP D 24 " --> pdb=" O VAL D 36 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 39 through 41 Processing sheet with id=AE2, first strand: chain 'D' and resid 43 through 44 Processing sheet with id=AE3, first strand: chain 'D' and resid 51 through 54 removed outlier: 5.916A pdb=" N LEU D 51 " --> pdb=" O HIS D 275 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N CYS D 277 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 59 through 62 removed outlier: 6.455A pdb=" N LEU D 59 " --> pdb=" O VAL D 88 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 119 through 121 Processing sheet with id=AE6, first strand: chain 'D' and resid 136 through 141 removed outlier: 4.229A pdb=" N CYS D 139 " --> pdb=" O SER D 146 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 151 through 153 Processing sheet with id=AE8, first strand: chain 'D' and resid 167 through 169 Processing sheet with id=AE9, first strand: chain 'D' and resid 281 through 282 removed outlier: 3.600A pdb=" N THR F 64 " --> pdb=" O GLY D 303 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 130 through 132 Processing sheet with id=AF2, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.536A pdb=" N GLN I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER I 25 " --> pdb=" O GLN I 3 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 10 through 11 removed outlier: 6.145A pdb=" N GLY I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL I 89 " --> pdb=" O GLN I 39 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 10 through 11 removed outlier: 6.145A pdb=" N GLY I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL I 102 " --> pdb=" O LYS I 94 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.550A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 19 through 24 627 hydrogen bonds defined for protein. 1683 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.17 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5545 1.34 - 1.46: 4353 1.46 - 1.58: 7520 1.58 - 1.70: 3 1.70 - 1.82: 108 Bond restraints: 17529 Sorted by residual: bond pdb=" CB ASN D 278 " pdb=" CG ASN D 278 " ideal model delta sigma weight residual 1.516 1.591 -0.075 2.50e-02 1.60e+03 9.10e+00 bond pdb=" CB ASN A 278 " pdb=" CG ASN A 278 " ideal model delta sigma weight residual 1.516 1.591 -0.075 2.50e-02 1.60e+03 9.03e+00 bond pdb=" CB ASN C 278 " pdb=" CG ASN C 278 " ideal model delta sigma weight residual 1.516 1.590 -0.074 2.50e-02 1.60e+03 8.81e+00 bond pdb=" C1 NAG A 401 " pdb=" O5 NAG A 401 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.33e+00 bond pdb=" C1 NAG D 402 " pdb=" O5 NAG D 402 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.30e+00 ... (remaining 17524 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 23441 2.94 - 5.88: 305 5.88 - 8.82: 17 8.82 - 11.76: 0 11.76 - 14.69: 3 Bond angle restraints: 23766 Sorted by residual: angle pdb=" CA TYR H 100I" pdb=" CB TYR H 100I" pdb=" CG TYR H 100I" ideal model delta sigma weight residual 113.90 128.59 -14.69 1.80e+00 3.09e-01 6.66e+01 angle pdb=" CA TYR I 100I" pdb=" CB TYR I 100I" pdb=" CG TYR I 100I" ideal model delta sigma weight residual 113.90 128.56 -14.66 1.80e+00 3.09e-01 6.63e+01 angle pdb=" CA TYR G 100I" pdb=" CB TYR G 100I" pdb=" CG TYR G 100I" ideal model delta sigma weight residual 113.90 128.55 -14.65 1.80e+00 3.09e-01 6.63e+01 angle pdb=" CA ASN A 278 " pdb=" CB ASN A 278 " pdb=" CG ASN A 278 " ideal model delta sigma weight residual 112.60 116.61 -4.01 1.00e+00 1.00e+00 1.61e+01 angle pdb=" CA ASN D 278 " pdb=" CB ASN D 278 " pdb=" CG ASN D 278 " ideal model delta sigma weight residual 112.60 116.61 -4.01 1.00e+00 1.00e+00 1.61e+01 ... (remaining 23761 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 9552 17.83 - 35.67: 799 35.67 - 53.50: 173 53.50 - 71.33: 63 71.33 - 89.16: 21 Dihedral angle restraints: 10608 sinusoidal: 4368 harmonic: 6240 Sorted by residual: dihedral pdb=" CD ARG A 224 " pdb=" NE ARG A 224 " pdb=" CZ ARG A 224 " pdb=" NH1 ARG A 224 " ideal model delta sinusoidal sigma weight residual 0.00 -74.14 74.14 1 1.00e+01 1.00e-02 6.98e+01 dihedral pdb=" CD ARG D 224 " pdb=" NE ARG D 224 " pdb=" CZ ARG D 224 " pdb=" NH1 ARG D 224 " ideal model delta sinusoidal sigma weight residual 0.00 -74.13 74.13 1 1.00e+01 1.00e-02 6.97e+01 dihedral pdb=" CD ARG C 224 " pdb=" NE ARG C 224 " pdb=" CZ ARG C 224 " pdb=" NH1 ARG C 224 " ideal model delta sinusoidal sigma weight residual 0.00 -74.09 74.09 1 1.00e+01 1.00e-02 6.97e+01 ... (remaining 10605 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2217 0.063 - 0.126: 338 0.126 - 0.188: 52 0.188 - 0.251: 6 0.251 - 0.314: 3 Chirality restraints: 2616 Sorted by residual: chirality pdb=" C1 NAG C 401 " pdb=" ND2 ASN C 33 " pdb=" C2 NAG C 401 " pdb=" O5 NAG C 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" C1 NAG D 401 " pdb=" ND2 ASN D 33 " pdb=" C2 NAG D 401 " pdb=" O5 NAG D 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" C1 NAG A 401 " pdb=" ND2 ASN A 33 " pdb=" C2 NAG A 401 " pdb=" O5 NAG A 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.39e+00 ... (remaining 2613 not shown) Planarity restraints: 3066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 224 " -0.915 9.50e-02 1.11e+02 4.11e-01 1.11e+02 pdb=" NE ARG A 224 " 0.074 2.00e-02 2.50e+03 pdb=" CZ ARG A 224 " -0.040 2.00e-02 2.50e+03 pdb=" NH1 ARG A 224 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG A 224 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 224 " 0.915 9.50e-02 1.11e+02 4.11e-01 1.11e+02 pdb=" NE ARG C 224 " -0.074 2.00e-02 2.50e+03 pdb=" CZ ARG C 224 " 0.040 2.00e-02 2.50e+03 pdb=" NH1 ARG C 224 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG C 224 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 224 " 0.915 9.50e-02 1.11e+02 4.11e-01 1.11e+02 pdb=" NE ARG D 224 " -0.074 2.00e-02 2.50e+03 pdb=" CZ ARG D 224 " 0.040 2.00e-02 2.50e+03 pdb=" NH1 ARG D 224 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG D 224 " 0.004 2.00e-02 2.50e+03 ... (remaining 3063 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 616 2.70 - 3.25: 16253 3.25 - 3.80: 27620 3.80 - 4.35: 36951 4.35 - 4.90: 63033 Nonbonded interactions: 144473 Sorted by model distance: nonbonded pdb=" NE2 GLN D 282 " pdb=" O GLY D 286 " model vdw 2.150 3.120 nonbonded pdb=" NE2 GLN A 282 " pdb=" O GLY A 286 " model vdw 2.150 3.120 nonbonded pdb=" NE2 GLN C 282 " pdb=" O GLY C 286 " model vdw 2.151 3.120 nonbonded pdb=" O PHE I 29 " pdb=" NH2 ARG I 71 " model vdw 2.186 3.120 nonbonded pdb=" O PHE G 29 " pdb=" NH2 ARG G 71 " model vdw 2.187 3.120 ... (remaining 144468 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'L' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } 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: 8.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.840 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 17571 Z= 0.223 Angle : 0.842 14.695 23865 Z= 0.440 Chirality : 0.050 0.314 2616 Planarity : 0.015 0.411 3054 Dihedral : 14.482 89.163 6561 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 1.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.96 % Allowed : 11.74 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.16), residues: 2145 helix: 0.50 (0.26), residues: 354 sheet: -0.90 (0.24), residues: 417 loop : -1.26 (0.15), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.051 0.003 ARG A 224 TYR 0.050 0.003 TYR I 100J PHE 0.027 0.002 PHE A 213 TRP 0.009 0.001 TRP G 47 HIS 0.007 0.002 HIS B 25 Details of bonding type rmsd covalent geometry : bond 0.00519 (17529) covalent geometry : angle 0.82135 (23766) SS BOND : bond 0.00599 ( 27) SS BOND : angle 1.68631 ( 54) hydrogen bonds : bond 0.16583 ( 621) hydrogen bonds : angle 7.19088 ( 1683) link_BETA1-4 : bond 0.00116 ( 3) link_BETA1-4 : angle 0.94940 ( 9) link_NAG-ASN : bond 0.00869 ( 12) link_NAG-ASN : angle 4.50922 ( 36) *********************** 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 428 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 410 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8529 (mttt) cc_final: 0.7782 (mptt) REVERT: A 220 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.8572 (mtt90) REVERT: A 229 ARG cc_start: 0.8331 (mmt-90) cc_final: 0.8044 (mpt180) REVERT: A 304 LYS cc_start: 0.8318 (mmtt) cc_final: 0.7978 (mtpt) REVERT: B 47 LYS cc_start: 0.8094 (mttp) cc_final: 0.7521 (mptt) REVERT: H 25 SER cc_start: 0.7694 (t) cc_final: 0.7300 (p) REVERT: L 87 TYR cc_start: 0.8018 (m-80) cc_final: 0.7621 (m-80) REVERT: C 32 LYS cc_start: 0.8563 (mttt) cc_final: 0.7878 (mmtm) REVERT: C 220 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.8392 (mtt90) REVERT: E 47 LYS cc_start: 0.7993 (mttp) cc_final: 0.7442 (mptt) REVERT: G 25 SER cc_start: 0.7612 (t) cc_final: 0.7180 (p) REVERT: J 87 TYR cc_start: 0.8058 (m-80) cc_final: 0.7532 (m-80) REVERT: D 32 LYS cc_start: 0.8510 (mttt) cc_final: 0.7778 (mmtm) REVERT: D 43 LEU cc_start: 0.8861 (tp) cc_final: 0.8566 (tp) REVERT: D 220 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8219 (mtt90) REVERT: D 304 LYS cc_start: 0.8305 (mmtt) cc_final: 0.8007 (mtpt) REVERT: F 47 LYS cc_start: 0.8043 (mttp) cc_final: 0.7501 (mptt) REVERT: I 25 SER cc_start: 0.7571 (t) cc_final: 0.7164 (p) outliers start: 18 outliers final: 3 residues processed: 428 average time/residue: 0.1517 time to fit residues: 93.4633 Evaluate side-chains 335 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 329 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 278 ASN Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 278 ASN Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain D residue 278 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 0.0770 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 9.9990 chunk 77 optimal weight: 0.0970 chunk 122 optimal weight: 1.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 HIS A 298 HIS B 28 ASN C 47 HIS C 298 HIS E 28 ASN ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 HIS D 298 HIS F 28 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.197435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.162426 restraints weight = 22348.647| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 2.13 r_work: 0.3770 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17571 Z= 0.153 Angle : 0.605 9.867 23865 Z= 0.324 Chirality : 0.045 0.350 2616 Planarity : 0.004 0.053 3054 Dihedral : 6.375 56.097 2682 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.68 % Allowed : 14.58 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.16), residues: 2145 helix: 1.08 (0.27), residues: 366 sheet: -0.57 (0.27), residues: 363 loop : -1.28 (0.14), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 76 TYR 0.036 0.002 TYR I 100I PHE 0.019 0.002 PHE H 67 TRP 0.011 0.001 TRP I 36 HIS 0.005 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00344 (17529) covalent geometry : angle 0.58259 (23766) SS BOND : bond 0.00839 ( 27) SS BOND : angle 1.68578 ( 54) hydrogen bonds : bond 0.04457 ( 621) hydrogen bonds : angle 5.71737 ( 1683) link_BETA1-4 : bond 0.00192 ( 3) link_BETA1-4 : angle 1.34493 ( 9) link_NAG-ASN : bond 0.00688 ( 12) link_NAG-ASN : angle 3.75350 ( 36) *********************** 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 388 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 338 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8695 (mttt) cc_final: 0.7961 (mptt) REVERT: A 123 ILE cc_start: 0.8080 (tt) cc_final: 0.7850 (tt) REVERT: A 220 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8169 (mtt90) REVERT: A 229 ARG cc_start: 0.8157 (mmt-90) cc_final: 0.7897 (mpt180) REVERT: A 304 LYS cc_start: 0.8397 (mmtt) cc_final: 0.7978 (mtpt) REVERT: B 69 GLU cc_start: 0.7627 (pt0) cc_final: 0.7268 (pt0) REVERT: H 25 SER cc_start: 0.7876 (t) cc_final: 0.7387 (p) REVERT: H 78 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8110 (pt) REVERT: L 87 TYR cc_start: 0.7990 (m-80) cc_final: 0.7526 (m-80) REVERT: C 14 CYS cc_start: 0.6609 (m) cc_final: 0.6318 (m) REVERT: C 32 LYS cc_start: 0.8638 (mttt) cc_final: 0.8006 (mptt) REVERT: C 220 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.8138 (mtt90) REVERT: G 25 SER cc_start: 0.7717 (t) cc_final: 0.7228 (p) REVERT: G 78 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7990 (pt) REVERT: J 87 TYR cc_start: 0.8067 (m-80) cc_final: 0.7444 (m-80) REVERT: D 32 LYS cc_start: 0.8625 (mttt) cc_final: 0.8024 (mmtm) REVERT: D 43 LEU cc_start: 0.8937 (tp) cc_final: 0.8641 (tp) REVERT: D 220 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8117 (mtt90) REVERT: D 304 LYS cc_start: 0.8425 (mmtt) cc_final: 0.8130 (mtpt) REVERT: F 69 GLU cc_start: 0.7592 (pt0) cc_final: 0.7324 (pt0) REVERT: I 25 SER cc_start: 0.7727 (t) cc_final: 0.7265 (p) REVERT: I 78 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7955 (pt) REVERT: K 34 ASN cc_start: 0.8064 (OUTLIER) cc_final: 0.7455 (m110) outliers start: 50 outliers final: 30 residues processed: 369 average time/residue: 0.1464 time to fit residues: 78.4629 Evaluate side-chains 353 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 316 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 278 ASN Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain J residue 34 ASN Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain K residue 85 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 62 optimal weight: 2.9990 chunk 192 optimal weight: 0.6980 chunk 182 optimal weight: 4.9990 chunk 203 optimal weight: 4.9990 chunk 123 optimal weight: 7.9990 chunk 204 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS C 130 HIS ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 HIS F 28 ASN ** I 35 ASN ** 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 = 0.4170 r_free = 0.4170 target = 0.186330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.150402 restraints weight = 22589.511| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.20 r_work: 0.3653 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3525 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17571 Z= 0.188 Angle : 0.609 10.033 23865 Z= 0.323 Chirality : 0.046 0.342 2616 Planarity : 0.004 0.034 3054 Dihedral : 6.227 56.774 2678 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.80 % Allowed : 15.81 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.17), residues: 2145 helix: 1.16 (0.27), residues: 366 sheet: -0.71 (0.27), residues: 369 loop : -1.35 (0.14), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 76 TYR 0.028 0.002 TYR I 100I PHE 0.012 0.002 PHE K 98 TRP 0.021 0.002 TRP K 35 HIS 0.007 0.002 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00429 (17529) covalent geometry : angle 0.58555 (23766) SS BOND : bond 0.00738 ( 27) SS BOND : angle 1.79125 ( 54) hydrogen bonds : bond 0.04332 ( 621) hydrogen bonds : angle 5.42485 ( 1683) link_BETA1-4 : bond 0.00300 ( 3) link_BETA1-4 : angle 1.63135 ( 9) link_NAG-ASN : bond 0.00800 ( 12) link_NAG-ASN : angle 3.73275 ( 36) *********************** 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 422 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 351 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8732 (mttt) cc_final: 0.7984 (mmtm) REVERT: A 55 ARG cc_start: 0.5692 (mtm-85) cc_final: 0.5317 (mtt90) REVERT: A 123 ILE cc_start: 0.8179 (tt) cc_final: 0.7974 (tt) REVERT: A 220 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.8157 (mtt90) REVERT: A 229 ARG cc_start: 0.8257 (mmt-90) cc_final: 0.8010 (mpt180) REVERT: B 69 GLU cc_start: 0.7854 (pt0) cc_final: 0.7583 (pt0) REVERT: H 25 SER cc_start: 0.7715 (t) cc_final: 0.7464 (p) REVERT: H 78 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8086 (pt) REVERT: L 87 TYR cc_start: 0.7982 (m-80) cc_final: 0.7653 (m-80) REVERT: C 32 LYS cc_start: 0.8718 (mttt) cc_final: 0.7979 (mptt) REVERT: C 55 ARG cc_start: 0.5941 (mtm-85) cc_final: 0.5585 (mtt90) REVERT: C 220 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8166 (mtt90) REVERT: E 128 ASN cc_start: 0.6887 (t0) cc_final: 0.5913 (p0) REVERT: G 25 SER cc_start: 0.7668 (t) cc_final: 0.7405 (p) REVERT: G 78 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8123 (pt) REVERT: J 87 TYR cc_start: 0.8090 (m-80) cc_final: 0.7465 (m-80) REVERT: D 32 LYS cc_start: 0.8636 (mttt) cc_final: 0.7981 (mptt) REVERT: D 220 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.8102 (mtt90) REVERT: F 128 ASN cc_start: 0.6827 (t0) cc_final: 0.5905 (p0) REVERT: I 25 SER cc_start: 0.7690 (t) cc_final: 0.7409 (p) REVERT: I 78 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8008 (pt) REVERT: K 34 ASN cc_start: 0.8051 (m110) cc_final: 0.7478 (m110) outliers start: 71 outliers final: 41 residues processed: 397 average time/residue: 0.1362 time to fit residues: 80.7238 Evaluate side-chains 368 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 321 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain K residue 85 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 172 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 97 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 205 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 2 optimal weight: 0.3980 chunk 206 optimal weight: 9.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 GLN ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.181731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.147019 restraints weight = 22604.400| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.24 r_work: 0.3604 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3476 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 17571 Z= 0.258 Angle : 0.665 10.466 23865 Z= 0.351 Chirality : 0.047 0.331 2616 Planarity : 0.004 0.041 3054 Dihedral : 6.559 59.422 2676 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.45 % Allowed : 16.67 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.16), residues: 2145 helix: 0.96 (0.27), residues: 366 sheet: -0.65 (0.27), residues: 363 loop : -1.45 (0.14), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 99 TYR 0.035 0.002 TYR H 100I PHE 0.039 0.003 PHE C 147 TRP 0.011 0.002 TRP C 69 HIS 0.009 0.002 HIS C 184 Details of bonding type rmsd covalent geometry : bond 0.00600 (17529) covalent geometry : angle 0.64316 (23766) SS BOND : bond 0.01007 ( 27) SS BOND : angle 1.97179 ( 54) hydrogen bonds : bond 0.04505 ( 621) hydrogen bonds : angle 5.51508 ( 1683) link_BETA1-4 : bond 0.00422 ( 3) link_BETA1-4 : angle 1.38322 ( 9) link_NAG-ASN : bond 0.00907 ( 12) link_NAG-ASN : angle 3.73642 ( 36) *********************** 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 403 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 320 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 HIS cc_start: 0.8246 (OUTLIER) cc_final: 0.7474 (p-80) REVERT: A 32 LYS cc_start: 0.8777 (mttt) cc_final: 0.7947 (mptt) REVERT: A 220 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.8119 (mtt90) REVERT: A 229 ARG cc_start: 0.8310 (mmt-90) cc_final: 0.8048 (mpt180) REVERT: B 69 GLU cc_start: 0.7880 (pt0) cc_final: 0.7633 (pt0) REVERT: B 128 ASN cc_start: 0.7090 (t0) cc_final: 0.6047 (p0) REVERT: H 25 SER cc_start: 0.7886 (t) cc_final: 0.7559 (p) REVERT: H 36 TRP cc_start: 0.8035 (m100) cc_final: 0.7636 (m100) REVERT: H 78 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8149 (pt) REVERT: C 14 CYS cc_start: 0.6632 (m) cc_final: 0.6336 (m) REVERT: C 18 HIS cc_start: 0.8420 (OUTLIER) cc_final: 0.7749 (p-80) REVERT: C 32 LYS cc_start: 0.8806 (mttt) cc_final: 0.7998 (mptt) REVERT: C 220 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8143 (mtt90) REVERT: E 126 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7653 (mt) REVERT: E 128 ASN cc_start: 0.6920 (t0) cc_final: 0.5902 (p0) REVERT: G 25 SER cc_start: 0.7864 (t) cc_final: 0.7572 (p) REVERT: G 36 TRP cc_start: 0.8273 (m100) cc_final: 0.8023 (m100) REVERT: G 78 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8202 (pt) REVERT: J 87 TYR cc_start: 0.8086 (m-80) cc_final: 0.7463 (m-80) REVERT: D 32 LYS cc_start: 0.8716 (mttt) cc_final: 0.7950 (mptt) REVERT: D 220 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.8206 (mtt90) REVERT: F 126 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7626 (mt) REVERT: F 128 ASN cc_start: 0.6932 (t0) cc_final: 0.5925 (p0) REVERT: I 25 SER cc_start: 0.7847 (t) cc_final: 0.7566 (p) REVERT: I 78 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.7983 (pt) outliers start: 83 outliers final: 55 residues processed: 372 average time/residue: 0.1425 time to fit residues: 78.3568 Evaluate side-chains 369 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 304 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 278 ASN Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain J residue 34 ASN Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 278 ASN Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain K residue 85 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 176 optimal weight: 0.9980 chunk 145 optimal weight: 0.8980 chunk 140 optimal weight: 6.9990 chunk 203 optimal weight: 0.9980 chunk 152 optimal weight: 0.1980 chunk 170 optimal weight: 0.8980 chunk 97 optimal weight: 9.9990 chunk 61 optimal weight: 20.0000 chunk 106 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 chunk 208 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.184838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.149102 restraints weight = 22343.822| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.16 r_work: 0.3645 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17571 Z= 0.147 Angle : 0.579 9.907 23865 Z= 0.306 Chirality : 0.044 0.370 2616 Planarity : 0.004 0.037 3054 Dihedral : 6.076 56.075 2676 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 4.02 % Allowed : 18.22 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.17), residues: 2145 helix: 1.20 (0.28), residues: 366 sheet: -0.42 (0.27), residues: 363 loop : -1.41 (0.14), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 99 TYR 0.031 0.002 TYR H 100I PHE 0.041 0.002 PHE I 29 TRP 0.017 0.001 TRP I 36 HIS 0.004 0.001 HIS C 184 Details of bonding type rmsd covalent geometry : bond 0.00328 (17529) covalent geometry : angle 0.55568 (23766) SS BOND : bond 0.00564 ( 27) SS BOND : angle 1.81206 ( 54) hydrogen bonds : bond 0.04126 ( 621) hydrogen bonds : angle 5.32179 ( 1683) link_BETA1-4 : bond 0.00095 ( 3) link_BETA1-4 : angle 1.21453 ( 9) link_NAG-ASN : bond 0.00994 ( 12) link_NAG-ASN : angle 3.58599 ( 36) *********************** 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 424 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 349 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8745 (mttt) cc_final: 0.7966 (mptt) REVERT: H 78 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8088 (pt) REVERT: L 87 TYR cc_start: 0.7937 (m-80) cc_final: 0.7574 (m-80) REVERT: C 14 CYS cc_start: 0.6475 (m) cc_final: 0.6154 (m) REVERT: C 32 LYS cc_start: 0.8724 (mttt) cc_final: 0.7978 (mptt) REVERT: C 190 ASP cc_start: 0.7859 (m-30) cc_final: 0.7658 (m-30) REVERT: C 220 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.8042 (mtt90) REVERT: E 128 ASN cc_start: 0.6819 (t0) cc_final: 0.5834 (p0) REVERT: G 25 SER cc_start: 0.7843 (t) cc_final: 0.7558 (p) REVERT: G 78 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8204 (pt) REVERT: J 87 TYR cc_start: 0.8068 (m-80) cc_final: 0.7433 (m-80) REVERT: D 32 LYS cc_start: 0.8670 (mttt) cc_final: 0.7956 (mptt) REVERT: D 220 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.8049 (mtt90) REVERT: D 229 ARG cc_start: 0.8206 (mmt-90) cc_final: 0.7933 (mpt180) REVERT: F 126 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7561 (mt) REVERT: F 128 ASN cc_start: 0.6841 (t0) cc_final: 0.5833 (p0) REVERT: F 132 GLU cc_start: 0.7797 (tt0) cc_final: 0.7452 (tt0) REVERT: I 25 SER cc_start: 0.7854 (t) cc_final: 0.7593 (p) REVERT: I 78 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7950 (pt) outliers start: 75 outliers final: 46 residues processed: 392 average time/residue: 0.1395 time to fit residues: 81.4079 Evaluate side-chains 379 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 327 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 278 ASN Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 34 ASN Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 278 ASN Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain K residue 85 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 76 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 47 optimal weight: 0.0970 chunk 105 optimal weight: 6.9990 chunk 205 optimal weight: 7.9990 chunk 63 optimal weight: 9.9990 chunk 207 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 133 optimal weight: 10.0000 chunk 164 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.179973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.144997 restraints weight = 22485.376| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.16 r_work: 0.3592 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 17571 Z= 0.296 Angle : 0.697 10.575 23865 Z= 0.367 Chirality : 0.047 0.347 2616 Planarity : 0.004 0.043 3054 Dihedral : 6.374 59.176 2672 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 4.93 % Allowed : 18.01 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.17), residues: 2145 helix: 0.87 (0.27), residues: 366 sheet: -0.48 (0.27), residues: 363 loop : -1.55 (0.14), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 99 TYR 0.030 0.002 TYR H 100I PHE 0.041 0.003 PHE H 29 TRP 0.012 0.002 TRP C 69 HIS 0.011 0.002 HIS C 184 Details of bonding type rmsd covalent geometry : bond 0.00688 (17529) covalent geometry : angle 0.67390 (23766) SS BOND : bond 0.01003 ( 27) SS BOND : angle 2.25936 ( 54) hydrogen bonds : bond 0.04560 ( 621) hydrogen bonds : angle 5.54330 ( 1683) link_BETA1-4 : bond 0.00240 ( 3) link_BETA1-4 : angle 1.29743 ( 9) link_NAG-ASN : bond 0.00985 ( 12) link_NAG-ASN : angle 3.72191 ( 36) *********************** 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 396 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 304 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8786 (mttt) cc_final: 0.8014 (mptt) REVERT: A 83 SER cc_start: 0.7883 (p) cc_final: 0.7642 (m) REVERT: A 129 ASN cc_start: 0.8001 (OUTLIER) cc_final: 0.7692 (m-40) REVERT: A 220 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.8051 (mtt90) REVERT: B 128 ASN cc_start: 0.7177 (t0) cc_final: 0.6113 (p0) REVERT: H 78 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8149 (pt) REVERT: C 14 CYS cc_start: 0.6445 (m) cc_final: 0.6116 (m) REVERT: C 18 HIS cc_start: 0.8386 (OUTLIER) cc_final: 0.7695 (p-80) REVERT: C 32 LYS cc_start: 0.8838 (mttt) cc_final: 0.8020 (mptt) REVERT: C 220 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8102 (mtt90) REVERT: E 128 ASN cc_start: 0.6985 (t0) cc_final: 0.5946 (p0) REVERT: G 25 SER cc_start: 0.8022 (t) cc_final: 0.7805 (m) REVERT: G 78 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8310 (pt) REVERT: J 87 TYR cc_start: 0.8111 (m-80) cc_final: 0.7570 (m-80) REVERT: D 32 LYS cc_start: 0.8737 (mttt) cc_final: 0.7980 (mptt) REVERT: D 220 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.8139 (mtt90) REVERT: F 128 ASN cc_start: 0.6953 (t0) cc_final: 0.5899 (p0) REVERT: I 25 SER cc_start: 0.8007 (t) cc_final: 0.7805 (m) REVERT: I 78 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8068 (pt) outliers start: 92 outliers final: 66 residues processed: 359 average time/residue: 0.1401 time to fit residues: 74.7941 Evaluate side-chains 373 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 299 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 278 ASN Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 91 TYR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 34 ASN Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 278 ASN Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain K residue 85 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 93 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 140 optimal weight: 6.9990 chunk 58 optimal weight: 0.2980 chunk 88 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 200 optimal weight: 8.9990 chunk 162 optimal weight: 0.5980 chunk 209 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 56 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.184626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.149020 restraints weight = 22330.034| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.16 r_work: 0.3649 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17571 Z= 0.138 Angle : 0.593 9.861 23865 Z= 0.311 Chirality : 0.044 0.376 2616 Planarity : 0.004 0.037 3054 Dihedral : 5.869 54.775 2672 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.86 % Allowed : 19.24 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.17), residues: 2145 helix: 1.17 (0.28), residues: 366 sheet: -0.25 (0.28), residues: 363 loop : -1.48 (0.15), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 99 TYR 0.027 0.002 TYR H 100I PHE 0.045 0.002 PHE I 29 TRP 0.022 0.001 TRP H 36 HIS 0.004 0.001 HIS E 142 Details of bonding type rmsd covalent geometry : bond 0.00306 (17529) covalent geometry : angle 0.57133 (23766) SS BOND : bond 0.00535 ( 27) SS BOND : angle 1.85486 ( 54) hydrogen bonds : bond 0.04112 ( 621) hydrogen bonds : angle 5.29089 ( 1683) link_BETA1-4 : bond 0.00472 ( 3) link_BETA1-4 : angle 1.30340 ( 9) link_NAG-ASN : bond 0.00936 ( 12) link_NAG-ASN : angle 3.51480 ( 36) *********************** 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 400 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 328 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8752 (mttt) cc_final: 0.7985 (mptt) REVERT: A 83 SER cc_start: 0.7839 (p) cc_final: 0.7601 (m) REVERT: H 78 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8146 (pt) REVERT: C 32 LYS cc_start: 0.8790 (mttt) cc_final: 0.7964 (mmtm) REVERT: C 190 ASP cc_start: 0.7882 (m-30) cc_final: 0.7651 (m-30) REVERT: E 116 LYS cc_start: 0.8128 (mttt) cc_final: 0.7776 (tptp) REVERT: E 128 ASN cc_start: 0.6847 (t0) cc_final: 0.5827 (p0) REVERT: G 25 SER cc_start: 0.8046 (t) cc_final: 0.7754 (p) REVERT: J 87 TYR cc_start: 0.8053 (m-80) cc_final: 0.7375 (m-80) REVERT: D 32 LYS cc_start: 0.8636 (mttt) cc_final: 0.7893 (mptt) REVERT: D 43 LEU cc_start: 0.9121 (tp) cc_final: 0.8895 (tp) REVERT: D 220 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8006 (mtt90) REVERT: F 128 ASN cc_start: 0.6886 (t0) cc_final: 0.5819 (p0) REVERT: I 25 SER cc_start: 0.7947 (t) cc_final: 0.7741 (m) REVERT: I 78 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8034 (pt) outliers start: 72 outliers final: 55 residues processed: 369 average time/residue: 0.1380 time to fit residues: 75.5786 Evaluate side-chains 375 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 317 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 278 ASN Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 34 ASN Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain D residue 278 ASN Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 91 TYR Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain K residue 85 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 142 optimal weight: 0.6980 chunk 2 optimal weight: 0.0020 chunk 6 optimal weight: 0.5980 chunk 129 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 184 optimal weight: 0.9990 chunk 32 optimal weight: 0.0170 overall best weight: 0.3826 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 56 ASN K 56 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.187703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.152441 restraints weight = 22369.249| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 2.17 r_work: 0.3683 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3555 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17571 Z= 0.116 Angle : 0.558 9.685 23865 Z= 0.294 Chirality : 0.044 0.377 2616 Planarity : 0.004 0.041 3054 Dihedral : 5.302 48.900 2668 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.11 % Allowed : 19.61 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.17), residues: 2145 helix: 1.24 (0.28), residues: 372 sheet: 0.13 (0.28), residues: 351 loop : -1.36 (0.15), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 99 TYR 0.023 0.001 TYR H 100I PHE 0.040 0.002 PHE I 29 TRP 0.025 0.002 TRP H 36 HIS 0.004 0.001 HIS E 142 Details of bonding type rmsd covalent geometry : bond 0.00250 (17529) covalent geometry : angle 0.53726 (23766) SS BOND : bond 0.00466 ( 27) SS BOND : angle 1.53998 ( 54) hydrogen bonds : bond 0.03831 ( 621) hydrogen bonds : angle 5.11122 ( 1683) link_BETA1-4 : bond 0.00288 ( 3) link_BETA1-4 : angle 1.54552 ( 9) link_NAG-ASN : bond 0.00887 ( 12) link_NAG-ASN : angle 3.46230 ( 36) *********************** 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 411 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 353 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8745 (mttt) cc_final: 0.7992 (mptt) REVERT: A 55 ARG cc_start: 0.6216 (mtm-85) cc_final: 0.5923 (mtm180) REVERT: A 83 SER cc_start: 0.7688 (p) cc_final: 0.7444 (m) REVERT: A 110 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7152 (tt0) REVERT: A 129 ASN cc_start: 0.7953 (OUTLIER) cc_final: 0.7612 (m-40) REVERT: B 123 ARG cc_start: 0.7046 (ptp-170) cc_final: 0.6774 (ptp-170) REVERT: H 78 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8081 (pt) REVERT: H 100 SER cc_start: 0.7954 (p) cc_final: 0.7541 (t) REVERT: L 87 TYR cc_start: 0.7789 (m-80) cc_final: 0.7210 (m-80) REVERT: C 32 LYS cc_start: 0.8687 (mttt) cc_final: 0.7918 (mmtm) REVERT: C 190 ASP cc_start: 0.7721 (m-30) cc_final: 0.7502 (m-30) REVERT: G 25 SER cc_start: 0.8068 (t) cc_final: 0.7755 (p) REVERT: G 100 SER cc_start: 0.8055 (p) cc_final: 0.7630 (t) REVERT: D 32 LYS cc_start: 0.8621 (mttt) cc_final: 0.7943 (mptt) REVERT: D 43 LEU cc_start: 0.9080 (tp) cc_final: 0.8775 (tp) REVERT: D 83 SER cc_start: 0.7617 (p) cc_final: 0.7396 (m) REVERT: F 76 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.8175 (mtm180) REVERT: F 116 LYS cc_start: 0.8092 (ptpt) cc_final: 0.7601 (ptpt) REVERT: I 25 SER cc_start: 0.7958 (t) cc_final: 0.7703 (p) REVERT: I 78 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.7974 (pt) outliers start: 58 outliers final: 43 residues processed: 387 average time/residue: 0.1390 time to fit residues: 79.9853 Evaluate side-chains 375 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 327 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 148 TYR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 278 ASN Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 34 ASN Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain K residue 85 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 145 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 15 optimal weight: 0.0370 chunk 87 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 137 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 chunk 196 optimal weight: 9.9990 chunk 14 optimal weight: 0.7980 overall best weight: 1.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.183915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.147946 restraints weight = 22401.509| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 2.17 r_work: 0.3636 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3509 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 17571 Z= 0.195 Angle : 0.628 10.403 23865 Z= 0.329 Chirality : 0.045 0.373 2616 Planarity : 0.004 0.040 3054 Dihedral : 5.439 52.220 2664 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.02 % Allowed : 19.02 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.17), residues: 2145 helix: 1.26 (0.28), residues: 366 sheet: -0.23 (0.28), residues: 369 loop : -1.44 (0.15), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 99 TYR 0.032 0.002 TYR A 148 PHE 0.034 0.002 PHE I 29 TRP 0.023 0.002 TRP G 36 HIS 0.007 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00451 (17529) covalent geometry : angle 0.60799 (23766) SS BOND : bond 0.00699 ( 27) SS BOND : angle 1.71510 ( 54) hydrogen bonds : bond 0.04129 ( 621) hydrogen bonds : angle 5.23094 ( 1683) link_BETA1-4 : bond 0.00167 ( 3) link_BETA1-4 : angle 1.04078 ( 9) link_NAG-ASN : bond 0.00959 ( 12) link_NAG-ASN : angle 3.59344 ( 36) *********************** 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 390 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 315 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8775 (mttt) cc_final: 0.7975 (mptt) REVERT: A 83 SER cc_start: 0.7843 (p) cc_final: 0.7568 (m) REVERT: A 110 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7350 (tt0) REVERT: H 78 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8088 (pt) REVERT: H 82 MET cc_start: 0.7998 (mtp) cc_final: 0.7778 (mtp) REVERT: H 100 SER cc_start: 0.7980 (p) cc_final: 0.7582 (t) REVERT: C 32 LYS cc_start: 0.8806 (mttt) cc_final: 0.7988 (mptt) REVERT: C 190 ASP cc_start: 0.7849 (m-30) cc_final: 0.7607 (m-30) REVERT: C 220 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.8169 (mtt90) REVERT: E 128 ASN cc_start: 0.6897 (t0) cc_final: 0.5852 (p0) REVERT: G 25 SER cc_start: 0.8130 (t) cc_final: 0.7823 (p) REVERT: J 87 TYR cc_start: 0.8053 (m-80) cc_final: 0.7384 (m-80) REVERT: D 32 LYS cc_start: 0.8727 (mttt) cc_final: 0.7995 (mptt) REVERT: D 83 SER cc_start: 0.7688 (p) cc_final: 0.7439 (m) REVERT: F 76 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8146 (mtm180) REVERT: I 25 SER cc_start: 0.7980 (t) cc_final: 0.7761 (m) REVERT: I 78 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8024 (pt) outliers start: 75 outliers final: 55 residues processed: 362 average time/residue: 0.1377 time to fit residues: 74.8013 Evaluate side-chains 365 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 305 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 148 TYR Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 278 ASN Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 91 TYR Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 34 ASN Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain D residue 278 ASN Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 91 TYR Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain K residue 85 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 148 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 207 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 91 optimal weight: 0.0050 chunk 20 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 135 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 111 GLN ** D 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.182642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.146787 restraints weight = 22367.745| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.16 r_work: 0.3621 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17571 Z= 0.220 Angle : 0.661 10.295 23865 Z= 0.346 Chirality : 0.047 0.394 2616 Planarity : 0.004 0.045 3054 Dihedral : 5.627 51.774 2664 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.43 % Allowed : 19.72 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.17), residues: 2145 helix: 1.23 (0.28), residues: 366 sheet: -0.31 (0.28), residues: 369 loop : -1.50 (0.15), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 99 TYR 0.031 0.002 TYR A 148 PHE 0.033 0.002 PHE I 29 TRP 0.076 0.002 TRP G 36 HIS 0.008 0.001 HIS C 184 Details of bonding type rmsd covalent geometry : bond 0.00509 (17529) covalent geometry : angle 0.63793 (23766) SS BOND : bond 0.00899 ( 27) SS BOND : angle 2.30247 ( 54) hydrogen bonds : bond 0.04246 ( 621) hydrogen bonds : angle 5.37641 ( 1683) link_BETA1-4 : bond 0.00191 ( 3) link_BETA1-4 : angle 1.09296 ( 9) link_NAG-ASN : bond 0.00964 ( 12) link_NAG-ASN : angle 3.56154 ( 36) ********************** 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 369 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 305 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8782 (mttt) cc_final: 0.8026 (mptt) REVERT: A 83 SER cc_start: 0.7877 (p) cc_final: 0.7575 (m) REVERT: A 110 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7405 (tt0) REVERT: A 129 ASN cc_start: 0.7981 (OUTLIER) cc_final: 0.6538 (t0) REVERT: H 78 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8140 (pt) REVERT: H 82 MET cc_start: 0.8006 (mtp) cc_final: 0.7790 (mtp) REVERT: L 87 TYR cc_start: 0.7901 (m-80) cc_final: 0.7545 (m-80) REVERT: C 32 LYS cc_start: 0.8840 (mttt) cc_final: 0.7966 (mptt) REVERT: C 220 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.8145 (mtt90) REVERT: E 128 ASN cc_start: 0.6926 (t0) cc_final: 0.5864 (p0) REVERT: G 25 SER cc_start: 0.8172 (t) cc_final: 0.7950 (m) REVERT: D 83 SER cc_start: 0.7697 (p) cc_final: 0.7444 (m) REVERT: F 76 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8369 (mtm180) REVERT: F 128 ASN cc_start: 0.7001 (t0) cc_final: 0.5903 (p0) REVERT: I 36 TRP cc_start: 0.8226 (m100) cc_final: 0.7778 (m100) REVERT: I 78 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8068 (pt) outliers start: 64 outliers final: 55 residues processed: 339 average time/residue: 0.1415 time to fit residues: 71.1292 Evaluate side-chains 370 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 309 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 148 TYR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 278 ASN Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 34 ASN Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain D residue 278 ASN Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 91 TYR Chi-restraints excluded: chain K residue 85 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 0.4980 chunk 8 optimal weight: 0.9980 chunk 192 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 45 optimal weight: 10.0000 chunk 149 optimal weight: 0.6980 chunk 182 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 90 GLN D 111 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.185022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.149247 restraints weight = 22457.538| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.18 r_work: 0.3653 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3527 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17571 Z= 0.154 Angle : 0.606 9.865 23865 Z= 0.319 Chirality : 0.045 0.401 2616 Planarity : 0.004 0.041 3054 Dihedral : 5.412 49.533 2664 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.32 % Allowed : 19.77 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.17), residues: 2145 helix: 1.26 (0.28), residues: 372 sheet: -0.26 (0.27), residues: 369 loop : -1.44 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 99 TYR 0.029 0.002 TYR A 148 PHE 0.034 0.002 PHE I 29 TRP 0.056 0.002 TRP K 35 HIS 0.006 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00349 (17529) covalent geometry : angle 0.58498 (23766) SS BOND : bond 0.00660 ( 27) SS BOND : angle 1.84942 ( 54) hydrogen bonds : bond 0.04017 ( 621) hydrogen bonds : angle 5.28781 ( 1683) link_BETA1-4 : bond 0.00247 ( 3) link_BETA1-4 : angle 1.08918 ( 9) link_NAG-ASN : bond 0.00943 ( 12) link_NAG-ASN : angle 3.48885 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4954.77 seconds wall clock time: 85 minutes 27.55 seconds (5127.55 seconds total)