Starting phenix.real_space_refine on Thu Feb 5 14:31:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n5y_49043/02_2026/9n5y_49043.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n5y_49043/02_2026/9n5y_49043.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9n5y_49043/02_2026/9n5y_49043.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n5y_49043/02_2026/9n5y_49043.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n5y_49043/02_2026/9n5y_49043.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n5y_49043/02_2026/9n5y_49043.map" } resolution = 4.1 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= 0.010 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 72 5.16 5 C 11108 2.51 5 N 3007 2.21 5 O 3456 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17643 Number of models: 1 Model: "" Number of chains: 19 Chain: "L" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 855 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "I" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1020 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "A" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2529 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 19, 'TRANS': 304} Chain: "O" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 855 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "P" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1020 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "C" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2523 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 19, 'TRANS': 303} Chain: "M" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 855 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "J" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1020 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "E" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2529 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 19, 'TRANS': 304} Chain: "B" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1411 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 1, 'TRANS': 173} Chain: "D" Number of atoms: 1380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1380 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 1, 'TRANS': 169} Chain: "F" Number of atoms: 1380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1380 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 1, 'TRANS': 169} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" 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: "D" 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 Time building chain proxies: 4.21, per 1000 atoms: 0.24 Number of scatterers: 17643 At special positions: 0 Unit cell: (139.292, 127.804, 150.78, 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 72 16.00 O 3456 8.00 N 3007 7.00 C 11108 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 96 " distance=2.04 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS D 137 " distance=2.01 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.02 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS F 137 " distance=2.03 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 277 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.03 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.04 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A 601 " - " ASN A 94 " " NAG A 602 " - " ASN A 278 " " NAG A 603 " - " ASN A 21 " " NAG B 301 " - " ASN B 154 " " NAG B 302 " - " ASN B 146 " " NAG C 601 " - " ASN C 94 " " NAG C 602 " - " ASN C 278 " " NAG C 603 " - " ASN C 21 " " NAG C 604 " - " ASN C 289 " " NAG C 605 " - " ASN C 33 " " NAG D 301 " - " ASN D 154 " " NAG D 302 " - " ASN D 146 " " NAG E 601 " - " ASN E 94 " " NAG E 602 " - " ASN E 278 " " NAG E 603 " - " ASN E 21 " " NAG G 1 " - " ASN A 289 " " NAG H 1 " - " ASN E 289 " Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 741.3 milliseconds 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4056 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 47 sheets defined 18.9% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'L' and resid 83 through 87 removed outlier: 3.924A pdb=" N VAL L 87 " --> pdb=" O ALA L 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.544A pdb=" N THR I 91 " --> pdb=" O THR I 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 71 Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 187 through 193 Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'P' and resid 87 through 91 removed outlier: 4.075A pdb=" N THR P 91 " --> pdb=" O THR P 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 77 Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.649A pdb=" N VAL M 87 " --> pdb=" O ALA M 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.270A pdb=" N GLY E 55A" --> pdb=" O LYS E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 73 through 77 removed outlier: 3.806A pdb=" N GLU E 77 " --> pdb=" O PRO E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 112 Processing helix chain 'E' and resid 187 through 195 Processing helix chain 'B' and resid 38 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 127 Processing helix chain 'B' and resid 147 through 154 Processing helix chain 'B' and resid 158 through 174 removed outlier: 4.277A pdb=" N TYR B 162 " --> pdb=" O ASP B 158 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N GLU B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE B 173 " --> pdb=" O ASN B 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 57 Processing helix chain 'D' and resid 74 through 125 Processing helix chain 'D' and resid 145 through 153 removed outlier: 3.975A pdb=" N MET D 149 " --> pdb=" O ASP D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 170 removed outlier: 4.001A pdb=" N TYR D 162 " --> pdb=" O ASP D 158 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLU D 164 " --> pdb=" O PRO D 160 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N GLU D 165 " --> pdb=" O LYS D 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 58 removed outlier: 3.515A pdb=" N THR F 41 " --> pdb=" O ASP F 37 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS F 58 " --> pdb=" O SER F 54 " (cutoff:3.500A) 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 127 Processing helix chain 'F' and resid 145 through 155 Processing helix chain 'F' and resid 162 through 171 removed outlier: 3.989A pdb=" N GLU F 171 " --> pdb=" O LYS F 167 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AA2, first strand: chain 'L' and resid 11 through 12 removed outlier: 7.032A pdb=" N LEU L 11 " --> pdb=" O GLU L 109 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU L 37 " --> pdb=" O TYR L 53 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N TYR L 53 " --> pdb=" O LEU L 37 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TRP L 39 " --> pdb=" O LEU L 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 11 through 12 removed outlier: 7.032A pdb=" N LEU L 11 " --> pdb=" O GLU L 109 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN L 94 " --> pdb=" O THR L 101 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR L 101 " --> pdb=" O GLN L 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.503A pdb=" N SER I 25 " --> pdb=" O GLN I 3 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER I 21 " --> pdb=" O SER I 7 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.335A pdb=" N GLY I 10 " --> pdb=" O THR I 126 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 32 through 34 removed outlier: 4.102A pdb=" N GLY B 23 " --> pdb=" O GLY A 16 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY A 16 " --> pdb=" O GLY B 23 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA8, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA9, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.949A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ILE A 87 " --> pdb=" O ILE A 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 115 through 119 removed outlier: 4.658A pdb=" N SER A 116A" --> pdb=" O GLU A 261 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU A 261 " --> pdb=" O SER A 116A" (cutoff:3.500A) removed outlier: 7.073A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE A 258 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 115 through 119 removed outlier: 4.658A pdb=" N SER A 116A" --> pdb=" O GLU A 261 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU A 261 " --> pdb=" O SER A 116A" (cutoff:3.500A) removed outlier: 7.073A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE A 258 " --> pdb=" O LEU A 177 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB5, first strand: chain 'A' and resid 282 through 283 Processing sheet with id=AB6, first strand: chain 'A' and resid 294 through 295 Processing sheet with id=AB7, first strand: chain 'O' and resid 4 through 5 Processing sheet with id=AB8, first strand: chain 'O' and resid 11 through 13 removed outlier: 3.615A pdb=" N GLU O 109 " --> pdb=" O LEU O 11 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU O 42 " --> pdb=" O VAL O 89 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N TRP O 39 " --> pdb=" O LEU O 51 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'O' and resid 66 through 71 removed outlier: 4.069A pdb=" N SER O 67 " --> pdb=" O THR O 78 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR O 78 " --> pdb=" O SER O 67 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER O 71 " --> pdb=" O ASP O 74 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASP O 74 " --> pdb=" O SER O 71 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'P' and resid 3 through 7 removed outlier: 3.609A pdb=" N SER P 21 " --> pdb=" O SER P 7 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'P' and resid 10 through 12 removed outlier: 5.908A pdb=" N GLY P 10 " --> pdb=" O THR P 126 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR P 123 " --> pdb=" O TYR P 94 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN P 39 " --> pdb=" O LEU P 93 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP P 99 " --> pdb=" O GLY P 33 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLY P 33 " --> pdb=" O ASP P 99 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N MET P 34 " --> pdb=" O VAL P 50 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N VAL P 50 " --> pdb=" O MET P 34 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N TRP P 36 " --> pdb=" O VAL P 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'P' and resid 10 through 12 removed outlier: 5.908A pdb=" N GLY P 10 " --> pdb=" O THR P 126 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR P 123 " --> pdb=" O TYR P 94 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N HIS P 118 " --> pdb=" O LYS P 98 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N SER P 100 " --> pdb=" O PHE P 116 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N PHE P 116 " --> pdb=" O SER P 100 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 12 through 14 removed outlier: 6.852A pdb=" N CYS D 137 " --> pdb=" O ILE D 133 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE D 133 " --> pdb=" O CYS D 137 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AC6, first strand: chain 'C' and resid 39 through 41 removed outlier: 3.506A pdb=" N VAL C 40 " --> pdb=" O LEU C 316 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 51 through 54 removed outlier: 6.372A pdb=" N LEU C 51 " --> pdb=" O HIS C 275 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N CYS C 277 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR C 279 " --> pdb=" O LYS C 53 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.750A pdb=" N VAL C 88 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE C 87 " --> pdb=" O ILE C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'C' and resid 151 through 153 removed outlier: 3.659A pdb=" N GLY C 181 " --> pdb=" O VAL C 252 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 229 through 230 Processing sheet with id=AD2, first strand: chain 'C' and resid 164 through 169 removed outlier: 3.802A pdb=" N VAL C 204 " --> pdb=" O LYS C 211 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 286 through 287 Processing sheet with id=AD4, first strand: chain 'M' and resid 4 through 6 Processing sheet with id=AD5, first strand: chain 'M' and resid 11 through 12 removed outlier: 6.561A pdb=" N TRP M 39 " --> pdb=" O LEU M 51 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.657A pdb=" N SER J 21 " --> pdb=" O SER J 7 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.740A pdb=" N ALA J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.669A pdb=" N CYS J 96 " --> pdb=" O TRP J 119 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N TRP J 119 " --> pdb=" O CYS J 96 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LYS J 98 " --> pdb=" O ASP J 117 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 31 through 36 removed outlier: 3.782A pdb=" N GLY F 31 " --> pdb=" O ASN F 28 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS F 26 " --> pdb=" O GLY F 33 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR E 12 " --> pdb=" O GLN F 27 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N CYS F 137 " --> pdb=" O ILE F 133 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE F 133 " --> pdb=" O CYS F 137 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 25 through 26 Processing sheet with id=AE2, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AE3, first strand: chain 'E' and resid 43 through 44 removed outlier: 3.785A pdb=" N GLU E 44 " --> pdb=" O PHE E 294 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 59 through 60 removed outlier: 7.186A pdb=" N LEU E 59 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ILE E 87 " --> pdb=" O ILE E 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'E' and resid 136 through 141 removed outlier: 4.016A pdb=" N CYS E 139 " --> pdb=" O SER E 146 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 151 through 152 Processing sheet with id=AE7, first strand: chain 'E' and resid 164 through 165 removed outlier: 4.203A pdb=" N VAL E 204 " --> pdb=" O LYS E 211 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS E 211 " --> pdb=" O VAL E 204 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 168 through 169 Processing sheet with id=AE9, first strand: chain 'E' and resid 231 through 237 removed outlier: 4.032A pdb=" N THR E 235 " --> pdb=" O VAL E 178 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 302 through 303 removed outlier: 3.762A pdb=" N THR F 64 " --> pdb=" O GLY E 303 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 23 through 27 removed outlier: 3.572A pdb=" N ALA D 35 " --> pdb=" O TYR D 24 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS D 26 " --> pdb=" O GLY D 33 " (cutoff:3.500A) 598 hydrogen bonds defined for protein. 1572 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: 2.19 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5687 1.34 - 1.46: 4416 1.46 - 1.58: 7858 1.58 - 1.71: 0 1.71 - 1.83: 96 Bond restraints: 18057 Sorted by residual: bond pdb=" CG1 ILE E 268 " pdb=" CD1 ILE E 268 " ideal model delta sigma weight residual 1.513 1.447 0.066 3.90e-02 6.57e+02 2.88e+00 bond pdb=" CB GLU M 85 " pdb=" CG GLU M 85 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.93e+00 bond pdb=" CA TYR E 98 " pdb=" C TYR E 98 " ideal model delta sigma weight residual 1.531 1.521 0.010 7.40e-03 1.83e+04 1.84e+00 bond pdb=" C ILE E 267 " pdb=" N ILE E 268 " ideal model delta sigma weight residual 1.329 1.313 0.017 1.38e-02 5.25e+03 1.47e+00 bond pdb=" SD MET F 59 " pdb=" CE MET F 59 " ideal model delta sigma weight residual 1.791 1.761 0.030 2.50e-02 1.60e+03 1.45e+00 ... (remaining 18052 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 23877 2.07 - 4.14: 504 4.14 - 6.20: 79 6.20 - 8.27: 16 8.27 - 10.34: 3 Bond angle restraints: 24479 Sorted by residual: angle pdb=" C ASN B 146 " pdb=" N THR B 147 " pdb=" CA THR B 147 " ideal model delta sigma weight residual 121.54 130.68 -9.14 1.91e+00 2.74e-01 2.29e+01 angle pdb=" N THR C 318 " pdb=" CA THR C 318 " pdb=" C THR C 318 " ideal model delta sigma weight residual 114.56 109.46 5.10 1.27e+00 6.20e-01 1.62e+01 angle pdb=" C ASN O 32 " pdb=" N ASN O 33 " pdb=" CA ASN O 33 " ideal model delta sigma weight residual 121.54 129.10 -7.56 1.91e+00 2.74e-01 1.57e+01 angle pdb=" C ASN C 289 " pdb=" N THR C 290 " pdb=" CA THR C 290 " ideal model delta sigma weight residual 121.54 128.28 -6.74 1.91e+00 2.74e-01 1.24e+01 angle pdb=" CB MET O 4 " pdb=" CG MET O 4 " pdb=" SD MET O 4 " ideal model delta sigma weight residual 112.70 123.04 -10.34 3.00e+00 1.11e-01 1.19e+01 ... (remaining 24474 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.86: 10286 22.86 - 45.72: 602 45.72 - 68.57: 63 68.57 - 91.43: 29 91.43 - 114.29: 1 Dihedral angle restraints: 10981 sinusoidal: 4615 harmonic: 6366 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 92 " pdb=" CB CYS L 92 " ideal model delta sinusoidal sigma weight residual 93.00 175.89 -82.89 1 1.00e+01 1.00e-02 8.41e+01 dihedral pdb=" CB CYS O 23 " pdb=" SG CYS O 23 " pdb=" SG CYS O 92 " pdb=" CB CYS O 92 " ideal model delta sinusoidal sigma weight residual 93.00 172.87 -79.87 1 1.00e+01 1.00e-02 7.91e+01 dihedral pdb=" CB CYS A 52 " pdb=" SG CYS A 52 " pdb=" SG CYS A 277 " pdb=" CB CYS A 277 " ideal model delta sinusoidal sigma weight residual -86.00 -11.23 -74.77 1 1.00e+01 1.00e-02 7.08e+01 ... (remaining 10978 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2363 0.075 - 0.150: 292 0.150 - 0.225: 23 0.225 - 0.300: 5 0.300 - 0.375: 2 Chirality restraints: 2685 Sorted by residual: chirality pdb=" C1 NAG B 302 " pdb=" ND2 ASN B 146 " pdb=" C2 NAG B 302 " pdb=" O5 NAG B 302 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CB ILE E 219 " pdb=" CA ILE E 219 " pdb=" CG1 ILE E 219 " pdb=" CG2 ILE E 219 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CB ILE E 269 " pdb=" CA ILE E 269 " pdb=" CG1 ILE E 269 " pdb=" CG2 ILE E 269 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 2682 not shown) Planarity restraints: 3155 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP M 54 " 0.023 2.00e-02 2.50e+03 1.97e-02 9.68e+00 pdb=" CG TRP M 54 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP M 54 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP M 54 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP M 54 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP M 54 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP M 54 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 54 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 54 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP M 54 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP I 47 " 0.011 2.00e-02 2.50e+03 1.67e-02 6.97e+00 pdb=" CG TRP I 47 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP I 47 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP I 47 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP I 47 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP I 47 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP I 47 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 47 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 47 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP I 47 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 94 " 0.012 2.00e-02 2.50e+03 1.81e-02 6.55e+00 pdb=" CG TYR B 94 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR B 94 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR B 94 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR B 94 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR B 94 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 94 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR B 94 " -0.004 2.00e-02 2.50e+03 ... (remaining 3152 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.93: 7306 2.93 - 3.42: 17485 3.42 - 3.91: 29430 3.91 - 4.41: 32198 4.41 - 4.90: 54501 Nonbonded interactions: 140920 Sorted by model distance: nonbonded pdb=" O5 NAG H 1 " pdb=" O6 NAG H 1 " model vdw 2.432 2.432 nonbonded pdb=" O GLU D 150 " pdb=" CB ASN D 154 " model vdw 2.432 3.440 nonbonded pdb=" OD1 ASN B 146 " pdb=" C1 NAG B 302 " model vdw 2.510 2.776 nonbonded pdb=" O5 NAG D 302 " pdb=" O6 NAG D 302 " model vdw 2.519 2.432 nonbonded pdb=" O ASP E 225 " pdb=" OD1 ASP E 225 " model vdw 2.530 3.040 ... (remaining 140915 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 324 or resid 601 through 603)) selection = (chain 'C' and (resid 10 through 324 or resid 602 through 604)) selection = (chain 'E' and (resid 10 through 324 or resid 601 through 603)) } ncs_group { reference = (chain 'B' and resid 1 through 171) selection = (chain 'D' and resid 1 through 171) selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'P' } ncs_group { reference = chain 'L' selection = chain 'M' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.360 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: 0.040 Set scattering table: 0.030 Process input model: 14.910 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 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 : 0.004 0.066 18100 Z= 0.170 Angle : 0.761 10.341 24584 Z= 0.391 Chirality : 0.051 0.375 2685 Planarity : 0.005 0.050 3138 Dihedral : 13.643 114.292 6853 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.96 (0.17), residues: 2184 helix: 0.82 (0.27), residues: 352 sheet: -0.68 (0.24), residues: 496 loop : -1.03 (0.16), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 18 TYR 0.042 0.002 TYR B 94 PHE 0.033 0.002 PHE E 147 TRP 0.054 0.002 TRP M 54 HIS 0.011 0.001 HIS P 118 Details of bonding type rmsd covalent geometry : bond 0.00390 (18057) covalent geometry : angle 0.74357 (24479) SS BOND : bond 0.00534 ( 24) SS BOND : angle 1.62571 ( 48) hydrogen bonds : bond 0.21197 ( 579) hydrogen bonds : angle 9.02228 ( 1572) link_BETA1-4 : bond 0.00440 ( 2) link_BETA1-4 : angle 3.99679 ( 6) link_NAG-ASN : bond 0.00516 ( 17) link_NAG-ASN : angle 3.09887 ( 51) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 414 time to evaluate : 0.539 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: L 18 ARG cc_start: 0.8019 (mmm-85) cc_final: 0.7646 (mmm-85) REVERT: L 49 LYS cc_start: 0.8750 (mmtp) cc_final: 0.8503 (mmmm) REVERT: L 79 ILE cc_start: 0.7002 (mt) cc_final: 0.6317 (mt) REVERT: L 83 GLN cc_start: 0.8924 (mm110) cc_final: 0.8650 (mm110) REVERT: I 89 GLU cc_start: 0.8402 (tp30) cc_final: 0.8127 (tp30) REVERT: A 50 LYS cc_start: 0.8476 (mmtm) cc_final: 0.7919 (ptmt) REVERT: A 133 ASN cc_start: 0.9060 (m-40) cc_final: 0.8830 (m-40) REVERT: A 147 PHE cc_start: 0.8039 (t80) cc_final: 0.7347 (t80) REVERT: A 153 TRP cc_start: 0.8681 (t-100) cc_final: 0.8470 (t-100) REVERT: A 168 TYR cc_start: 0.8600 (t80) cc_final: 0.7938 (t80) REVERT: A 227 GLU cc_start: 0.8760 (tp30) cc_final: 0.8513 (tp30) REVERT: A 230 MET cc_start: 0.8653 (ttm) cc_final: 0.7960 (ttm) REVERT: A 295 GLN cc_start: 0.8735 (pp30) cc_final: 0.7935 (pp30) REVERT: A 322 ASN cc_start: 0.8830 (t0) cc_final: 0.8626 (t0) REVERT: O 62 VAL cc_start: 0.8309 (t) cc_final: 0.8049 (t) REVERT: O 93 GLN cc_start: 0.8212 (pp30) cc_final: 0.7613 (pm20) REVERT: C 53 LYS cc_start: 0.7951 (mttt) cc_final: 0.7660 (mtpp) REVERT: C 116 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7430 (tm-30) REVERT: C 180 TRP cc_start: 0.8173 (p90) cc_final: 0.7765 (p90) REVERT: C 184 HIS cc_start: 0.6844 (m-70) cc_final: 0.6345 (m-70) REVERT: C 230 MET cc_start: 0.7954 (ttp) cc_final: 0.7363 (tmm) REVERT: M 93 GLN cc_start: 0.8041 (tm-30) cc_final: 0.7637 (tm-30) REVERT: E 37 THR cc_start: 0.9532 (p) cc_final: 0.9082 (t) REVERT: E 105 TYR cc_start: 0.7298 (t80) cc_final: 0.6977 (t80) REVERT: E 203 PHE cc_start: 0.8395 (t80) cc_final: 0.7931 (t80) REVERT: E 263 ASN cc_start: 0.8540 (p0) cc_final: 0.8185 (p0) REVERT: E 298 HIS cc_start: 0.8392 (t-90) cc_final: 0.7683 (t70) REVERT: E 310 LYS cc_start: 0.8671 (ttpt) cc_final: 0.8221 (pttt) REVERT: B 6 ILE cc_start: 0.9233 (mm) cc_final: 0.8834 (mm) REVERT: B 100 VAL cc_start: 0.8641 (t) cc_final: 0.8433 (t) REVERT: B 104 ASN cc_start: 0.9188 (m-40) cc_final: 0.8558 (m110) REVERT: B 127 LYS cc_start: 0.8376 (pttt) cc_final: 0.8093 (pttt) REVERT: D 6 ILE cc_start: 0.8289 (pt) cc_final: 0.7985 (pt) REVERT: D 50 ASN cc_start: 0.8878 (t0) cc_final: 0.8102 (t0) REVERT: D 53 ASN cc_start: 0.9034 (m110) cc_final: 0.8811 (m110) REVERT: D 78 GLU cc_start: 0.8786 (tt0) cc_final: 0.7948 (tm-30) REVERT: D 154 ASN cc_start: 0.7158 (t0) cc_final: 0.6891 (t0) REVERT: D 158 ASP cc_start: 0.8711 (t0) cc_final: 0.8377 (t0) REVERT: D 170 ARG cc_start: 0.8131 (mtm110) cc_final: 0.7738 (mtm110) REVERT: F 14 TRP cc_start: 0.8026 (m100) cc_final: 0.7713 (m100) REVERT: F 90 ASP cc_start: 0.8308 (m-30) cc_final: 0.7728 (m-30) REVERT: F 156 THR cc_start: 0.8447 (p) cc_final: 0.8092 (t) REVERT: F 158 ASP cc_start: 0.8988 (t0) cc_final: 0.8614 (t0) outliers start: 0 outliers final: 0 residues processed: 414 average time/residue: 0.1182 time to fit residues: 76.5289 Evaluate side-chains 355 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 355 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 5.9990 chunk 212 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 80 ASN ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 ASN P 74 ASN M 35 ASN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 ASN D 125 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.092671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.078565 restraints weight = 38841.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.080866 restraints weight = 22932.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.082466 restraints weight = 15513.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.083542 restraints weight = 11551.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.084283 restraints weight = 9301.311| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 18100 Z= 0.258 Angle : 0.700 8.499 24584 Z= 0.361 Chirality : 0.048 0.255 2685 Planarity : 0.005 0.044 3138 Dihedral : 7.524 120.833 2793 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.10 % Allowed : 4.72 % Favored : 95.18 % 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: -0.94 (0.18), residues: 2184 helix: 0.80 (0.27), residues: 374 sheet: -0.65 (0.23), residues: 520 loop : -1.04 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 18 TYR 0.019 0.002 TYR B 110 PHE 0.018 0.002 PHE B 9 TRP 0.036 0.002 TRP I 47 HIS 0.006 0.001 HIS E 184 Details of bonding type rmsd covalent geometry : bond 0.00592 (18057) covalent geometry : angle 0.68118 (24479) SS BOND : bond 0.00539 ( 24) SS BOND : angle 1.66029 ( 48) hydrogen bonds : bond 0.04891 ( 579) hydrogen bonds : angle 6.55855 ( 1572) link_BETA1-4 : bond 0.00177 ( 2) link_BETA1-4 : angle 3.75966 ( 6) link_NAG-ASN : bond 0.00584 ( 17) link_NAG-ASN : angle 3.05403 ( 51) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 389 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 49 LYS cc_start: 0.8303 (mmtp) cc_final: 0.8034 (mmmm) REVERT: L 59 GLU cc_start: 0.8521 (tp30) cc_final: 0.8077 (tp30) REVERT: L 79 ILE cc_start: 0.8084 (mt) cc_final: 0.7656 (mt) REVERT: L 83 GLN cc_start: 0.8848 (mm110) cc_final: 0.8518 (mm110) REVERT: L 89 VAL cc_start: 0.8725 (t) cc_final: 0.8516 (t) REVERT: L 98 THR cc_start: 0.8268 (p) cc_final: 0.7954 (p) REVERT: I 89 GLU cc_start: 0.7730 (tp30) cc_final: 0.7483 (tp30) REVERT: A 133 ASN cc_start: 0.8566 (m-40) cc_final: 0.8295 (m-40) REVERT: A 322 ASN cc_start: 0.8757 (t0) cc_final: 0.8365 (t0) REVERT: O 86 ASP cc_start: 0.7289 (m-30) cc_final: 0.7004 (m-30) REVERT: O 93 GLN cc_start: 0.8041 (pp30) cc_final: 0.7751 (pp30) REVERT: C 69 TRP cc_start: 0.8439 (t-100) cc_final: 0.8187 (t-100) REVERT: C 116 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7965 (tm-30) REVERT: C 184 HIS cc_start: 0.7293 (m-70) cc_final: 0.6947 (m-70) REVERT: M 7 SER cc_start: 0.8733 (m) cc_final: 0.8487 (t) REVERT: M 42 GLU cc_start: 0.8559 (pm20) cc_final: 0.8339 (pm20) REVERT: M 93 GLN cc_start: 0.8453 (tm-30) cc_final: 0.8134 (tm-30) REVERT: J 54 ASP cc_start: 0.8842 (p0) cc_final: 0.8487 (p0) REVERT: J 107 TYR cc_start: 0.8899 (m-10) cc_final: 0.8691 (m-80) REVERT: E 37 THR cc_start: 0.9605 (p) cc_final: 0.9288 (t) REVERT: E 263 ASN cc_start: 0.8630 (p0) cc_final: 0.7950 (p0) REVERT: B 59 MET cc_start: 0.8828 (ttt) cc_final: 0.8627 (ttt) REVERT: B 104 ASN cc_start: 0.9246 (m-40) cc_final: 0.8782 (m110) REVERT: B 105 GLU cc_start: 0.7833 (tp30) cc_final: 0.7586 (tp30) REVERT: D 50 ASN cc_start: 0.8894 (t0) cc_final: 0.8162 (t0) REVERT: F 90 ASP cc_start: 0.8054 (m-30) cc_final: 0.7676 (m-30) REVERT: F 156 THR cc_start: 0.8633 (p) cc_final: 0.8141 (t) outliers start: 2 outliers final: 1 residues processed: 390 average time/residue: 0.1148 time to fit residues: 70.6797 Evaluate side-chains 323 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 322 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 45 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 13 optimal weight: 0.0970 chunk 84 optimal weight: 0.4980 chunk 18 optimal weight: 0.5980 chunk 124 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 142 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 74 ASN ** P 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN J 74 ASN E 47 HIS E 191 GLN D 95 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.097759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.083714 restraints weight = 38042.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.086137 restraints weight = 22199.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.087794 restraints weight = 14818.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.088973 restraints weight = 10917.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.089692 restraints weight = 8661.029| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18100 Z= 0.126 Angle : 0.611 7.348 24584 Z= 0.313 Chirality : 0.046 0.259 2685 Planarity : 0.004 0.052 3138 Dihedral : 7.082 116.499 2793 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % 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: -0.70 (0.18), residues: 2184 helix: 1.24 (0.27), residues: 365 sheet: -0.55 (0.23), residues: 521 loop : -0.92 (0.17), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 262 TYR 0.019 0.001 TYR M 53 PHE 0.017 0.001 PHE P 108 TRP 0.036 0.002 TRP I 47 HIS 0.015 0.001 HIS P 118 Details of bonding type rmsd covalent geometry : bond 0.00282 (18057) covalent geometry : angle 0.59412 (24479) SS BOND : bond 0.00334 ( 24) SS BOND : angle 1.56812 ( 48) hydrogen bonds : bond 0.04321 ( 579) hydrogen bonds : angle 6.06412 ( 1572) link_BETA1-4 : bond 0.00361 ( 2) link_BETA1-4 : angle 3.31430 ( 6) link_NAG-ASN : bond 0.00363 ( 17) link_NAG-ASN : angle 2.61671 ( 51) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 435 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 59 GLU cc_start: 0.8620 (tp30) cc_final: 0.8383 (tp30) REVERT: L 79 ILE cc_start: 0.7885 (mt) cc_final: 0.7602 (mt) REVERT: L 83 GLN cc_start: 0.8758 (mm110) cc_final: 0.8501 (mm110) REVERT: L 98 THR cc_start: 0.8061 (p) cc_final: 0.7762 (p) REVERT: I 34 MET cc_start: 0.8680 (mmm) cc_final: 0.8167 (mmt) REVERT: I 89 GLU cc_start: 0.7783 (tp30) cc_final: 0.7570 (tp30) REVERT: I 109 ASP cc_start: 0.7193 (t70) cc_final: 0.6511 (t70) REVERT: A 50 LYS cc_start: 0.7701 (ptmt) cc_final: 0.7294 (ptmt) REVERT: A 133 ASN cc_start: 0.8549 (m-40) cc_final: 0.8300 (m-40) REVERT: A 169 ILE cc_start: 0.8715 (mm) cc_final: 0.8468 (mm) REVERT: A 230 MET cc_start: 0.8517 (ttm) cc_final: 0.7985 (ttm) REVERT: A 322 ASN cc_start: 0.8666 (t0) cc_final: 0.8425 (t0) REVERT: P 36 TRP cc_start: 0.7925 (m100) cc_final: 0.7598 (m100) REVERT: P 95 TYR cc_start: 0.8626 (m-10) cc_final: 0.8294 (m-80) REVERT: C 43 LEU cc_start: 0.8794 (tp) cc_final: 0.8402 (tp) REVERT: C 116 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7905 (tm-30) REVERT: C 180 TRP cc_start: 0.8712 (p90) cc_final: 0.8308 (p90) REVERT: M 106 THR cc_start: 0.8578 (t) cc_final: 0.8250 (m) REVERT: J 54 ASP cc_start: 0.8841 (p0) cc_final: 0.8464 (p0) REVERT: J 107 TYR cc_start: 0.8896 (m-10) cc_final: 0.8612 (m-80) REVERT: E 105 TYR cc_start: 0.7271 (t80) cc_final: 0.6892 (t80) REVERT: E 263 ASN cc_start: 0.8622 (p0) cc_final: 0.7728 (p0) REVERT: B 104 ASN cc_start: 0.9202 (m-40) cc_final: 0.8773 (m110) REVERT: D 50 ASN cc_start: 0.8733 (t0) cc_final: 0.7990 (t0) REVERT: D 170 ARG cc_start: 0.8007 (mtm110) cc_final: 0.7666 (mtm110) REVERT: F 19 ASP cc_start: 0.7855 (p0) cc_final: 0.7548 (p0) REVERT: F 90 ASP cc_start: 0.8154 (m-30) cc_final: 0.7718 (m-30) REVERT: F 156 THR cc_start: 0.8518 (p) cc_final: 0.8030 (t) REVERT: F 158 ASP cc_start: 0.8505 (t0) cc_final: 0.8280 (t0) outliers start: 0 outliers final: 0 residues processed: 435 average time/residue: 0.1198 time to fit residues: 80.6876 Evaluate side-chains 342 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 187 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 191 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 140 optimal weight: 0.1980 chunk 6 optimal weight: 10.0000 chunk 154 optimal weight: 0.5980 chunk 43 optimal weight: 6.9990 chunk 26 optimal weight: 0.4980 chunk 76 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS O 35 ASN ** O 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 74 ASN ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN B 111 HIS F 25 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.096322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.082278 restraints weight = 38394.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.084650 restraints weight = 22403.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.086206 restraints weight = 15008.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.087416 restraints weight = 11173.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.088216 restraints weight = 8882.528| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18100 Z= 0.156 Angle : 0.614 7.703 24584 Z= 0.314 Chirality : 0.046 0.247 2685 Planarity : 0.004 0.047 3138 Dihedral : 7.004 117.787 2793 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.36 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % 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: -0.67 (0.18), residues: 2184 helix: 1.28 (0.27), residues: 361 sheet: -0.54 (0.23), residues: 529 loop : -0.89 (0.17), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 87 TYR 0.027 0.001 TYR B 159 PHE 0.014 0.002 PHE A 203 TRP 0.042 0.002 TRP I 47 HIS 0.004 0.001 HIS P 35 Details of bonding type rmsd covalent geometry : bond 0.00363 (18057) covalent geometry : angle 0.59871 (24479) SS BOND : bond 0.00549 ( 24) SS BOND : angle 1.53601 ( 48) hydrogen bonds : bond 0.04026 ( 579) hydrogen bonds : angle 5.76915 ( 1572) link_BETA1-4 : bond 0.00216 ( 2) link_BETA1-4 : angle 3.41888 ( 6) link_NAG-ASN : bond 0.00324 ( 17) link_NAG-ASN : angle 2.48234 ( 51) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 398 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 59 GLU cc_start: 0.8615 (tp30) cc_final: 0.8278 (tp30) REVERT: L 83 GLN cc_start: 0.8761 (mm110) cc_final: 0.8505 (mm110) REVERT: I 53 TYR cc_start: 0.9233 (p90) cc_final: 0.8811 (p90) REVERT: I 109 ASP cc_start: 0.7255 (t70) cc_final: 0.6581 (t70) REVERT: A 50 LYS cc_start: 0.7755 (ptmt) cc_final: 0.7367 (ptmt) REVERT: A 133 ASN cc_start: 0.8543 (m-40) cc_final: 0.8294 (m-40) REVERT: A 169 ILE cc_start: 0.8776 (mm) cc_final: 0.8525 (mm) REVERT: A 230 MET cc_start: 0.8644 (ttm) cc_final: 0.8158 (ttm) REVERT: A 322 ASN cc_start: 0.8718 (t0) cc_final: 0.8365 (t0) REVERT: C 43 LEU cc_start: 0.8863 (tp) cc_final: 0.8624 (tp) REVERT: C 116 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7939 (tm-30) REVERT: C 180 TRP cc_start: 0.8804 (p90) cc_final: 0.8402 (p90) REVERT: C 301 THR cc_start: 0.8761 (p) cc_final: 0.8540 (p) REVERT: M 106 THR cc_start: 0.8611 (t) cc_final: 0.8314 (m) REVERT: J 54 ASP cc_start: 0.8855 (p0) cc_final: 0.8475 (p0) REVERT: J 107 TYR cc_start: 0.8982 (m-10) cc_final: 0.8704 (m-80) REVERT: E 203 PHE cc_start: 0.7973 (t80) cc_final: 0.7725 (t80) REVERT: E 263 ASN cc_start: 0.8687 (p0) cc_final: 0.7741 (p0) REVERT: B 104 ASN cc_start: 0.9211 (m-40) cc_final: 0.8782 (m110) REVERT: B 110 TYR cc_start: 0.9558 (t80) cc_final: 0.9284 (t80) REVERT: D 50 ASN cc_start: 0.8738 (t0) cc_final: 0.8088 (t0) REVERT: F 19 ASP cc_start: 0.7813 (p0) cc_final: 0.7545 (p0) REVERT: F 90 ASP cc_start: 0.8201 (m-30) cc_final: 0.7744 (m-30) REVERT: F 156 THR cc_start: 0.8589 (p) cc_final: 0.8114 (t) REVERT: F 158 ASP cc_start: 0.8512 (t0) cc_final: 0.8218 (t0) outliers start: 0 outliers final: 0 residues processed: 398 average time/residue: 0.1118 time to fit residues: 69.1054 Evaluate side-chains 323 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 323 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 9 optimal weight: 1.9990 chunk 85 optimal weight: 0.0870 chunk 196 optimal weight: 0.7980 chunk 191 optimal weight: 3.9990 chunk 117 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 125 optimal weight: 0.5980 chunk 133 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 ASN P 74 ASN ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN ** J 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 GLN E 196 GLN ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.096635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.082537 restraints weight = 38089.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.084911 restraints weight = 22154.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.086594 restraints weight = 14857.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.087757 restraints weight = 10915.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.088486 restraints weight = 8663.063| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18100 Z= 0.142 Angle : 0.600 7.128 24584 Z= 0.308 Chirality : 0.046 0.243 2685 Planarity : 0.004 0.044 3138 Dihedral : 6.905 116.615 2793 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.08 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % 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: -0.59 (0.18), residues: 2184 helix: 1.37 (0.27), residues: 363 sheet: -0.45 (0.23), residues: 514 loop : -0.88 (0.17), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 262 TYR 0.023 0.001 TYR J 59 PHE 0.040 0.002 PHE C 213 TRP 0.048 0.002 TRP I 47 HIS 0.006 0.001 HIS P 118 Details of bonding type rmsd covalent geometry : bond 0.00328 (18057) covalent geometry : angle 0.58569 (24479) SS BOND : bond 0.00335 ( 24) SS BOND : angle 1.35770 ( 48) hydrogen bonds : bond 0.03935 ( 579) hydrogen bonds : angle 5.58990 ( 1572) link_BETA1-4 : bond 0.00282 ( 2) link_BETA1-4 : angle 3.32369 ( 6) link_NAG-ASN : bond 0.00306 ( 17) link_NAG-ASN : angle 2.38792 ( 51) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 397 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 59 GLU cc_start: 0.8628 (tp30) cc_final: 0.8280 (tp30) REVERT: L 83 GLN cc_start: 0.8795 (mm110) cc_final: 0.8555 (mm110) REVERT: L 89 VAL cc_start: 0.8726 (t) cc_final: 0.8510 (t) REVERT: I 34 MET cc_start: 0.8603 (mmm) cc_final: 0.8161 (mmt) REVERT: I 53 TYR cc_start: 0.9212 (p90) cc_final: 0.8823 (p90) REVERT: I 109 ASP cc_start: 0.7275 (t70) cc_final: 0.6538 (t70) REVERT: A 50 LYS cc_start: 0.7838 (ptmt) cc_final: 0.7483 (ptmt) REVERT: A 112 LEU cc_start: 0.8849 (mt) cc_final: 0.8472 (tt) REVERT: A 133 ASN cc_start: 0.8594 (m-40) cc_final: 0.8354 (m-40) REVERT: A 169 ILE cc_start: 0.8789 (mm) cc_final: 0.8537 (mm) REVERT: A 230 MET cc_start: 0.8561 (ttm) cc_final: 0.8269 (ttm) REVERT: A 322 ASN cc_start: 0.8708 (t0) cc_final: 0.8360 (t0) REVERT: O 62 VAL cc_start: 0.8452 (t) cc_final: 0.8212 (t) REVERT: O 91 TYR cc_start: 0.8359 (m-80) cc_final: 0.7970 (m-80) REVERT: O 109 GLU cc_start: 0.5398 (tm-30) cc_final: 0.4508 (tt0) REVERT: C 116 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7949 (tm-30) REVERT: C 180 TRP cc_start: 0.8832 (p90) cc_final: 0.8408 (p90) REVERT: C 301 THR cc_start: 0.8767 (p) cc_final: 0.8546 (p) REVERT: M 93 GLN cc_start: 0.8235 (tm-30) cc_final: 0.7888 (tm-30) REVERT: M 106 THR cc_start: 0.8634 (t) cc_final: 0.8323 (m) REVERT: J 54 ASP cc_start: 0.8904 (p0) cc_final: 0.8514 (p0) REVERT: J 107 TYR cc_start: 0.9006 (m-10) cc_final: 0.8729 (m-10) REVERT: E 263 ASN cc_start: 0.8658 (p0) cc_final: 0.7704 (p0) REVERT: B 57 GLU cc_start: 0.8061 (tp30) cc_final: 0.7781 (tp30) REVERT: B 104 ASN cc_start: 0.9194 (m-40) cc_final: 0.8791 (m110) REVERT: B 110 TYR cc_start: 0.9534 (t80) cc_final: 0.9239 (t80) REVERT: D 50 ASN cc_start: 0.8752 (t0) cc_final: 0.8047 (t0) REVERT: F 19 ASP cc_start: 0.7656 (p0) cc_final: 0.7420 (p0) REVERT: F 90 ASP cc_start: 0.8197 (m-30) cc_final: 0.7761 (m-30) REVERT: F 156 THR cc_start: 0.8576 (p) cc_final: 0.8089 (t) REVERT: F 158 ASP cc_start: 0.8520 (t0) cc_final: 0.8201 (t0) outliers start: 0 outliers final: 0 residues processed: 397 average time/residue: 0.1103 time to fit residues: 68.8699 Evaluate side-chains 318 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 30 optimal weight: 0.9990 chunk 200 optimal weight: 5.9990 chunk 151 optimal weight: 0.9990 chunk 172 optimal weight: 0.7980 chunk 195 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 189 optimal weight: 0.9990 chunk 204 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 83 GLN ** O 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 191 GLN E 192 GLN ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 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 = 0.3326 r_free = 0.3326 target = 0.097090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.083146 restraints weight = 37663.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.085507 restraints weight = 22089.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.087040 restraints weight = 14854.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.088235 restraints weight = 11094.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.088943 restraints weight = 8817.689| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18100 Z= 0.131 Angle : 0.595 7.115 24584 Z= 0.305 Chirality : 0.045 0.242 2685 Planarity : 0.004 0.046 3138 Dihedral : 6.781 114.987 2793 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.22 % Favored : 94.73 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % 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: -0.55 (0.18), residues: 2184 helix: 1.35 (0.27), residues: 364 sheet: -0.43 (0.23), residues: 524 loop : -0.83 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 123 TYR 0.017 0.001 TYR E 86 PHE 0.019 0.002 PHE C 213 TRP 0.048 0.002 TRP I 47 HIS 0.004 0.001 HIS P 35 Details of bonding type rmsd covalent geometry : bond 0.00301 (18057) covalent geometry : angle 0.58079 (24479) SS BOND : bond 0.00307 ( 24) SS BOND : angle 1.56007 ( 48) hydrogen bonds : bond 0.03874 ( 579) hydrogen bonds : angle 5.42605 ( 1572) link_BETA1-4 : bond 0.00285 ( 2) link_BETA1-4 : angle 3.29989 ( 6) link_NAG-ASN : bond 0.00294 ( 17) link_NAG-ASN : angle 2.27960 ( 51) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 403 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 59 GLU cc_start: 0.8577 (tp30) cc_final: 0.8324 (tp30) REVERT: L 83 GLN cc_start: 0.8736 (mm110) cc_final: 0.8502 (mm110) REVERT: I 53 TYR cc_start: 0.9245 (p90) cc_final: 0.8750 (p90) REVERT: I 109 ASP cc_start: 0.7270 (t70) cc_final: 0.6549 (t70) REVERT: A 50 LYS cc_start: 0.7865 (ptmt) cc_final: 0.7449 (ptmt) REVERT: A 112 LEU cc_start: 0.8854 (mt) cc_final: 0.8425 (tt) REVERT: A 133 ASN cc_start: 0.8588 (m-40) cc_final: 0.8346 (m-40) REVERT: A 169 ILE cc_start: 0.8817 (mm) cc_final: 0.8564 (mm) REVERT: A 230 MET cc_start: 0.8573 (ttm) cc_final: 0.8095 (ttm) REVERT: A 322 ASN cc_start: 0.8701 (t0) cc_final: 0.8412 (t0) REVERT: O 91 TYR cc_start: 0.8340 (m-80) cc_final: 0.7927 (m-80) REVERT: O 109 GLU cc_start: 0.5198 (tm-30) cc_final: 0.4337 (tt0) REVERT: C 23 THR cc_start: 0.8674 (m) cc_final: 0.8368 (t) REVERT: C 116 GLU cc_start: 0.8277 (tm-30) cc_final: 0.7946 (tm-30) REVERT: C 170 ASN cc_start: 0.8789 (t0) cc_final: 0.8566 (t0) REVERT: C 180 TRP cc_start: 0.8806 (p90) cc_final: 0.8374 (p90) REVERT: C 301 THR cc_start: 0.8726 (p) cc_final: 0.8524 (p) REVERT: M 34 LYS cc_start: 0.7966 (tptp) cc_final: 0.7719 (tptp) REVERT: M 83 GLN cc_start: 0.8405 (tm-30) cc_final: 0.8148 (tm-30) REVERT: M 93 GLN cc_start: 0.8216 (tm-30) cc_final: 0.7907 (tm-30) REVERT: M 106 THR cc_start: 0.8639 (t) cc_final: 0.8319 (m) REVERT: J 54 ASP cc_start: 0.8907 (p0) cc_final: 0.8518 (p0) REVERT: J 107 TYR cc_start: 0.8999 (m-10) cc_final: 0.8731 (m-10) REVERT: E 154 LEU cc_start: 0.9079 (mp) cc_final: 0.8759 (mp) REVERT: E 263 ASN cc_start: 0.8684 (p0) cc_final: 0.7693 (p0) REVERT: B 57 GLU cc_start: 0.8043 (tp30) cc_final: 0.7692 (tp30) REVERT: B 100 VAL cc_start: 0.8943 (t) cc_final: 0.8668 (t) REVERT: B 104 ASN cc_start: 0.9160 (m-40) cc_final: 0.8793 (m110) REVERT: B 110 TYR cc_start: 0.9477 (t80) cc_final: 0.9134 (t80) REVERT: D 50 ASN cc_start: 0.8741 (t0) cc_final: 0.8074 (t0) REVERT: F 19 ASP cc_start: 0.7620 (p0) cc_final: 0.7369 (p0) REVERT: F 90 ASP cc_start: 0.8170 (m-30) cc_final: 0.7740 (m-30) REVERT: F 156 THR cc_start: 0.8548 (p) cc_final: 0.8062 (t) REVERT: F 158 ASP cc_start: 0.8550 (t0) cc_final: 0.8241 (t0) outliers start: 0 outliers final: 0 residues processed: 403 average time/residue: 0.1035 time to fit residues: 66.2754 Evaluate side-chains 332 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 332 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 89 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 159 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 199 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 190 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 ASN ** O 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 ASN J 6 GLN E 192 GLN B 62 GLN ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.091508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.077439 restraints weight = 39218.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.079698 restraints weight = 23140.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.081343 restraints weight = 15558.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.082462 restraints weight = 11561.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.083139 restraints weight = 9239.791| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 18100 Z= 0.254 Angle : 0.685 8.619 24584 Z= 0.352 Chirality : 0.049 0.272 2685 Planarity : 0.004 0.047 3138 Dihedral : 7.265 117.411 2793 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.14 % Favored : 93.82 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % 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: -0.71 (0.18), residues: 2184 helix: 1.11 (0.27), residues: 365 sheet: -0.49 (0.23), residues: 522 loop : -0.92 (0.17), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 24 TYR 0.020 0.002 TYR I 95 PHE 0.022 0.002 PHE A 203 TRP 0.062 0.002 TRP I 47 HIS 0.005 0.001 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00584 (18057) covalent geometry : angle 0.66876 (24479) SS BOND : bond 0.01002 ( 24) SS BOND : angle 1.75112 ( 48) hydrogen bonds : bond 0.04179 ( 579) hydrogen bonds : angle 5.60212 ( 1572) link_BETA1-4 : bond 0.00339 ( 2) link_BETA1-4 : angle 3.61538 ( 6) link_NAG-ASN : bond 0.00498 ( 17) link_NAG-ASN : angle 2.64219 ( 51) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 392 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 59 GLU cc_start: 0.8652 (tp30) cc_final: 0.8438 (tp30) REVERT: L 83 GLN cc_start: 0.8823 (mm110) cc_final: 0.8486 (mm110) REVERT: I 53 TYR cc_start: 0.9294 (p90) cc_final: 0.8956 (p90) REVERT: I 101 GLN cc_start: 0.8411 (mm-40) cc_final: 0.8099 (mm-40) REVERT: I 109 ASP cc_start: 0.7379 (t70) cc_final: 0.6945 (t70) REVERT: A 20 ASN cc_start: 0.9352 (p0) cc_final: 0.9145 (p0) REVERT: A 50 LYS cc_start: 0.7917 (ptmt) cc_final: 0.7490 (ptmt) REVERT: A 133 ASN cc_start: 0.8693 (m-40) cc_final: 0.8470 (m-40) REVERT: A 230 MET cc_start: 0.8669 (ttm) cc_final: 0.8436 (ttm) REVERT: A 322 ASN cc_start: 0.8790 (t0) cc_final: 0.8377 (t0) REVERT: O 46 GLN cc_start: 0.8551 (mm-40) cc_final: 0.8061 (mm-40) REVERT: O 83 GLN cc_start: 0.8428 (mm-40) cc_final: 0.8205 (mm110) REVERT: O 86 ASP cc_start: 0.7350 (m-30) cc_final: 0.7131 (m-30) REVERT: O 91 TYR cc_start: 0.8415 (m-80) cc_final: 0.7950 (m-80) REVERT: O 109 GLU cc_start: 0.5090 (tm-30) cc_final: 0.4274 (tt0) REVERT: P 36 TRP cc_start: 0.8101 (m100) cc_final: 0.7477 (m100) REVERT: C 23 THR cc_start: 0.8773 (m) cc_final: 0.8507 (t) REVERT: C 116 GLU cc_start: 0.8361 (tm-30) cc_final: 0.7960 (tm-30) REVERT: C 180 TRP cc_start: 0.8918 (p90) cc_final: 0.8474 (p90) REVERT: C 301 THR cc_start: 0.8876 (p) cc_final: 0.8649 (p) REVERT: M 83 GLN cc_start: 0.8495 (tm-30) cc_final: 0.8152 (tm-30) REVERT: M 93 GLN cc_start: 0.8461 (tm-30) cc_final: 0.7768 (tm-30) REVERT: M 106 THR cc_start: 0.8747 (t) cc_final: 0.8332 (m) REVERT: J 54 ASP cc_start: 0.8856 (p0) cc_final: 0.8552 (p0) REVERT: J 99 ASP cc_start: 0.8954 (t0) cc_final: 0.8695 (t70) REVERT: J 107 TYR cc_start: 0.9085 (m-10) cc_final: 0.8793 (m-80) REVERT: E 263 ASN cc_start: 0.8682 (p0) cc_final: 0.7804 (p0) REVERT: B 57 GLU cc_start: 0.8175 (tp30) cc_final: 0.7768 (tp30) REVERT: B 104 ASN cc_start: 0.9198 (m-40) cc_final: 0.8843 (m110) REVERT: B 110 TYR cc_start: 0.9526 (t80) cc_final: 0.9106 (t80) REVERT: D 50 ASN cc_start: 0.8865 (t0) cc_final: 0.8292 (t0) REVERT: D 111 HIS cc_start: 0.8921 (m-70) cc_final: 0.8549 (m-70) REVERT: F 19 ASP cc_start: 0.7737 (p0) cc_final: 0.7481 (p0) REVERT: F 90 ASP cc_start: 0.8214 (m-30) cc_final: 0.7799 (m-30) REVERT: F 156 THR cc_start: 0.8664 (p) cc_final: 0.8193 (t) REVERT: F 158 ASP cc_start: 0.8647 (t0) cc_final: 0.8393 (t0) outliers start: 0 outliers final: 0 residues processed: 392 average time/residue: 0.1071 time to fit residues: 66.2433 Evaluate side-chains 323 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 323 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 2.9990 chunk 212 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 177 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 144 optimal weight: 0.9990 chunk 183 optimal weight: 5.9990 chunk 13 optimal weight: 0.0570 overall best weight: 1.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 73 ASN ** O 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 6 GLN M 35 ASN ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.094596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.080647 restraints weight = 38385.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.082982 restraints weight = 22417.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.084581 restraints weight = 15037.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.085662 restraints weight = 11157.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.086394 restraints weight = 8966.433| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 18100 Z= 0.155 Angle : 0.628 7.456 24584 Z= 0.324 Chirality : 0.046 0.238 2685 Planarity : 0.004 0.048 3138 Dihedral : 7.064 115.254 2793 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.59 % Favored : 94.37 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % 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: -0.62 (0.18), residues: 2184 helix: 1.36 (0.27), residues: 363 sheet: -0.44 (0.23), residues: 514 loop : -0.92 (0.17), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 16 TYR 0.021 0.001 TYR C 308 PHE 0.017 0.002 PHE C 213 TRP 0.059 0.002 TRP I 47 HIS 0.005 0.001 HIS C 184 Details of bonding type rmsd covalent geometry : bond 0.00364 (18057) covalent geometry : angle 0.61431 (24479) SS BOND : bond 0.00407 ( 24) SS BOND : angle 1.58444 ( 48) hydrogen bonds : bond 0.03992 ( 579) hydrogen bonds : angle 5.49328 ( 1572) link_BETA1-4 : bond 0.00260 ( 2) link_BETA1-4 : angle 3.42951 ( 6) link_NAG-ASN : bond 0.00274 ( 17) link_NAG-ASN : angle 2.33440 ( 51) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 398 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 59 GLU cc_start: 0.8583 (tp30) cc_final: 0.8362 (tp30) REVERT: L 83 GLN cc_start: 0.8753 (mm110) cc_final: 0.8467 (mm110) REVERT: I 53 TYR cc_start: 0.9285 (p90) cc_final: 0.9052 (p90) REVERT: I 101 GLN cc_start: 0.8362 (mm-40) cc_final: 0.8060 (mm-40) REVERT: I 109 ASP cc_start: 0.7288 (t70) cc_final: 0.6852 (t70) REVERT: A 50 LYS cc_start: 0.7937 (ptmt) cc_final: 0.7488 (ptmt) REVERT: A 133 ASN cc_start: 0.8636 (m-40) cc_final: 0.8418 (m-40) REVERT: A 230 MET cc_start: 0.8634 (ttm) cc_final: 0.8366 (ttm) REVERT: A 322 ASN cc_start: 0.8728 (t0) cc_final: 0.8451 (t0) REVERT: O 58 ARG cc_start: 0.7491 (ttp80) cc_final: 0.7233 (ttp80) REVERT: O 83 GLN cc_start: 0.8450 (mm-40) cc_final: 0.8186 (mm110) REVERT: O 86 ASP cc_start: 0.7277 (m-30) cc_final: 0.7066 (m-30) REVERT: O 91 TYR cc_start: 0.8340 (m-80) cc_final: 0.7892 (m-80) REVERT: O 109 GLU cc_start: 0.5062 (tm-30) cc_final: 0.4259 (tt0) REVERT: C 23 THR cc_start: 0.8724 (m) cc_final: 0.8472 (t) REVERT: C 116 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7904 (tm-30) REVERT: C 180 TRP cc_start: 0.8876 (p90) cc_final: 0.8434 (p90) REVERT: C 301 THR cc_start: 0.8869 (p) cc_final: 0.8609 (p) REVERT: M 83 GLN cc_start: 0.8440 (tm-30) cc_final: 0.8053 (tm-30) REVERT: M 106 THR cc_start: 0.8506 (t) cc_final: 0.8211 (m) REVERT: J 54 ASP cc_start: 0.8841 (p0) cc_final: 0.8535 (p0) REVERT: J 99 ASP cc_start: 0.8963 (t0) cc_final: 0.8647 (t0) REVERT: J 107 TYR cc_start: 0.9061 (m-10) cc_final: 0.8767 (m-80) REVERT: E 37 THR cc_start: 0.9592 (p) cc_final: 0.9269 (t) REVERT: E 154 LEU cc_start: 0.9024 (mp) cc_final: 0.8713 (mp) REVERT: E 263 ASN cc_start: 0.8666 (p0) cc_final: 0.7730 (p0) REVERT: B 57 GLU cc_start: 0.8142 (tp30) cc_final: 0.7736 (tp30) REVERT: B 104 ASN cc_start: 0.9157 (m-40) cc_final: 0.8801 (m110) REVERT: B 110 TYR cc_start: 0.9511 (t80) cc_final: 0.9226 (t80) REVERT: D 50 ASN cc_start: 0.8795 (t0) cc_final: 0.8176 (t0) REVERT: F 19 ASP cc_start: 0.7678 (p0) cc_final: 0.7438 (p0) REVERT: F 90 ASP cc_start: 0.8204 (m-30) cc_final: 0.7805 (m-30) REVERT: F 127 LYS cc_start: 0.8952 (mttp) cc_final: 0.8507 (mptt) REVERT: F 156 THR cc_start: 0.8630 (p) cc_final: 0.8160 (t) REVERT: F 158 ASP cc_start: 0.8593 (t0) cc_final: 0.8342 (t0) outliers start: 0 outliers final: 0 residues processed: 398 average time/residue: 0.1108 time to fit residues: 69.9025 Evaluate side-chains 331 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 51 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 209 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 57 optimal weight: 7.9990 chunk 105 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 194 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 214 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 ASN ** O 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 HIS M 35 ASN ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.095198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.081239 restraints weight = 38372.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.083576 restraints weight = 22430.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.085151 restraints weight = 15079.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.086287 restraints weight = 11222.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.087083 restraints weight = 8960.621| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18100 Z= 0.152 Angle : 0.623 7.066 24584 Z= 0.322 Chirality : 0.046 0.231 2685 Planarity : 0.004 0.049 3138 Dihedral : 6.970 114.424 2793 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.59 % Favored : 94.37 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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: -0.54 (0.18), residues: 2184 helix: 1.42 (0.27), residues: 363 sheet: -0.40 (0.23), residues: 504 loop : -0.85 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 16 TYR 0.031 0.001 TYR D 22 PHE 0.016 0.002 PHE E 203 TRP 0.061 0.002 TRP I 47 HIS 0.010 0.001 HIS D 111 Details of bonding type rmsd covalent geometry : bond 0.00353 (18057) covalent geometry : angle 0.60906 (24479) SS BOND : bond 0.00345 ( 24) SS BOND : angle 1.62213 ( 48) hydrogen bonds : bond 0.03914 ( 579) hydrogen bonds : angle 5.38393 ( 1572) link_BETA1-4 : bond 0.00341 ( 2) link_BETA1-4 : angle 3.33741 ( 6) link_NAG-ASN : bond 0.00276 ( 17) link_NAG-ASN : angle 2.29583 ( 51) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 394 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 83 GLN cc_start: 0.8727 (mm110) cc_final: 0.8467 (mm110) REVERT: I 47 TRP cc_start: 0.8478 (t60) cc_final: 0.8251 (t60) REVERT: I 101 GLN cc_start: 0.8396 (mm-40) cc_final: 0.8058 (mm-40) REVERT: I 109 ASP cc_start: 0.7331 (t70) cc_final: 0.6899 (t70) REVERT: A 50 LYS cc_start: 0.7943 (ptmt) cc_final: 0.7477 (ptmt) REVERT: A 133 ASN cc_start: 0.8657 (m-40) cc_final: 0.8449 (m-40) REVERT: A 230 MET cc_start: 0.8640 (ttm) cc_final: 0.8339 (ttm) REVERT: A 322 ASN cc_start: 0.8742 (t0) cc_final: 0.8468 (t0) REVERT: O 58 ARG cc_start: 0.7443 (ttp80) cc_final: 0.7233 (ttp80) REVERT: O 83 GLN cc_start: 0.8463 (mm-40) cc_final: 0.8193 (mm110) REVERT: O 91 TYR cc_start: 0.8326 (m-80) cc_final: 0.7920 (m-80) REVERT: O 109 GLU cc_start: 0.5061 (tm-30) cc_final: 0.4282 (tt0) REVERT: C 23 THR cc_start: 0.8728 (m) cc_final: 0.8507 (t) REVERT: C 116 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7898 (tm-30) REVERT: C 180 TRP cc_start: 0.8866 (p90) cc_final: 0.8420 (p90) REVERT: C 301 THR cc_start: 0.8729 (p) cc_final: 0.8492 (p) REVERT: M 34 LYS cc_start: 0.7920 (tptp) cc_final: 0.7589 (tptp) REVERT: M 83 GLN cc_start: 0.8440 (tm-30) cc_final: 0.8042 (tm-30) REVERT: M 106 THR cc_start: 0.8493 (t) cc_final: 0.8245 (m) REVERT: J 54 ASP cc_start: 0.8892 (p0) cc_final: 0.8559 (p0) REVERT: J 99 ASP cc_start: 0.8917 (t0) cc_final: 0.8671 (t0) REVERT: J 107 TYR cc_start: 0.9060 (m-10) cc_final: 0.8752 (m-10) REVERT: E 37 THR cc_start: 0.9593 (p) cc_final: 0.9271 (t) REVERT: E 154 LEU cc_start: 0.9017 (mp) cc_final: 0.8731 (mp) REVERT: E 203 PHE cc_start: 0.8028 (t80) cc_final: 0.7735 (t80) REVERT: E 263 ASN cc_start: 0.8659 (p0) cc_final: 0.7748 (p0) REVERT: B 57 GLU cc_start: 0.8150 (tp30) cc_final: 0.7718 (tp30) REVERT: B 104 ASN cc_start: 0.9162 (m-40) cc_final: 0.8775 (m110) REVERT: B 110 TYR cc_start: 0.9504 (t80) cc_final: 0.9220 (t80) REVERT: D 50 ASN cc_start: 0.8824 (t0) cc_final: 0.8157 (t0) REVERT: F 19 ASP cc_start: 0.7715 (p0) cc_final: 0.7369 (p0) REVERT: F 90 ASP cc_start: 0.8190 (m-30) cc_final: 0.7797 (m-30) REVERT: F 127 LYS cc_start: 0.8950 (mttp) cc_final: 0.8483 (mptt) REVERT: F 156 THR cc_start: 0.8604 (p) cc_final: 0.8144 (t) REVERT: F 158 ASP cc_start: 0.8588 (t0) cc_final: 0.8366 (t0) outliers start: 0 outliers final: 0 residues processed: 394 average time/residue: 0.1070 time to fit residues: 67.1971 Evaluate side-chains 330 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 330 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 148 optimal weight: 0.5980 chunk 1 optimal weight: 0.4980 chunk 86 optimal weight: 0.4980 chunk 187 optimal weight: 2.9990 chunk 206 optimal weight: 0.8980 chunk 188 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 197 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 ASN ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 ASN B 62 GLN ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN ** D 114 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 = 0.3321 r_free = 0.3321 target = 0.096865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.082943 restraints weight = 37941.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.085278 restraints weight = 22158.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.086993 restraints weight = 14751.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.088036 restraints weight = 10839.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.088859 restraints weight = 8695.655| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18100 Z= 0.126 Angle : 0.615 7.559 24584 Z= 0.317 Chirality : 0.046 0.243 2685 Planarity : 0.004 0.049 3138 Dihedral : 6.764 112.543 2793 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.27 % Favored : 94.69 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: -0.43 (0.18), residues: 2184 helix: 1.50 (0.27), residues: 363 sheet: -0.27 (0.23), residues: 519 loop : -0.81 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 262 TYR 0.024 0.001 TYR D 22 PHE 0.015 0.002 PHE C 213 TRP 0.054 0.002 TRP I 47 HIS 0.009 0.001 HIS D 111 Details of bonding type rmsd covalent geometry : bond 0.00293 (18057) covalent geometry : angle 0.60279 (24479) SS BOND : bond 0.00319 ( 24) SS BOND : angle 1.46089 ( 48) hydrogen bonds : bond 0.03799 ( 579) hydrogen bonds : angle 5.28973 ( 1572) link_BETA1-4 : bond 0.00308 ( 2) link_BETA1-4 : angle 3.28683 ( 6) link_NAG-ASN : bond 0.00233 ( 17) link_NAG-ASN : angle 2.13859 ( 51) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 386 time to evaluate : 0.494 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: L 83 GLN cc_start: 0.8681 (mm110) cc_final: 0.8448 (mm110) REVERT: I 101 GLN cc_start: 0.8375 (mm-40) cc_final: 0.8120 (mm-40) REVERT: I 109 ASP cc_start: 0.7290 (t70) cc_final: 0.6861 (t70) REVERT: A 50 LYS cc_start: 0.7926 (ptmt) cc_final: 0.7473 (ptmt) REVERT: A 133 ASN cc_start: 0.8648 (m-40) cc_final: 0.8447 (m-40) REVERT: A 230 MET cc_start: 0.8558 (ttm) cc_final: 0.8333 (ttm) REVERT: A 322 ASN cc_start: 0.8729 (t0) cc_final: 0.8346 (t0) REVERT: O 62 VAL cc_start: 0.8262 (t) cc_final: 0.8035 (t) REVERT: O 91 TYR cc_start: 0.8262 (m-80) cc_final: 0.7741 (m-80) REVERT: O 109 GLU cc_start: 0.4939 (tm-30) cc_final: 0.4128 (tt0) REVERT: C 23 THR cc_start: 0.8689 (m) cc_final: 0.8473 (t) REVERT: C 116 GLU cc_start: 0.8286 (tm-30) cc_final: 0.7886 (tm-30) REVERT: C 180 TRP cc_start: 0.8836 (p90) cc_final: 0.8404 (p90) REVERT: C 301 THR cc_start: 0.8679 (p) cc_final: 0.8438 (p) REVERT: M 106 THR cc_start: 0.8447 (t) cc_final: 0.8220 (m) REVERT: J 37 VAL cc_start: 0.8745 (p) cc_final: 0.8515 (m) REVERT: J 54 ASP cc_start: 0.8866 (p0) cc_final: 0.8542 (p0) REVERT: J 99 ASP cc_start: 0.8929 (t0) cc_final: 0.8686 (t0) REVERT: J 107 TYR cc_start: 0.9052 (m-10) cc_final: 0.8737 (m-10) REVERT: E 105 TYR cc_start: 0.7355 (t80) cc_final: 0.6944 (t80) REVERT: E 153 TRP cc_start: 0.8133 (m-10) cc_final: 0.7903 (m-10) REVERT: E 154 LEU cc_start: 0.8982 (mp) cc_final: 0.8740 (mp) REVERT: E 203 PHE cc_start: 0.7962 (t80) cc_final: 0.7639 (t80) REVERT: E 263 ASN cc_start: 0.8639 (p0) cc_final: 0.7704 (p0) REVERT: B 57 GLU cc_start: 0.8087 (tp30) cc_final: 0.7669 (tp30) REVERT: B 104 ASN cc_start: 0.9146 (m-40) cc_final: 0.8763 (m110) REVERT: B 110 TYR cc_start: 0.9495 (t80) cc_final: 0.9255 (t80) REVERT: B 149 MET cc_start: 0.8074 (mmp) cc_final: 0.7645 (mmp) REVERT: D 50 ASN cc_start: 0.8730 (t0) cc_final: 0.8099 (t0) REVERT: D 145 ASP cc_start: 0.7861 (p0) cc_final: 0.7486 (p0) REVERT: F 19 ASP cc_start: 0.7632 (p0) cc_final: 0.7376 (p0) REVERT: F 90 ASP cc_start: 0.8144 (m-30) cc_final: 0.7777 (m-30) REVERT: F 127 LYS cc_start: 0.8940 (mttp) cc_final: 0.8486 (mptt) REVERT: F 156 THR cc_start: 0.8504 (p) cc_final: 0.8042 (t) outliers start: 0 outliers final: 0 residues processed: 386 average time/residue: 0.1043 time to fit residues: 64.5130 Evaluate side-chains 329 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 329 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 105 optimal weight: 0.9990 chunk 145 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 210 optimal weight: 3.9990 chunk 181 optimal weight: 5.9990 chunk 189 optimal weight: 3.9990 chunk 119 optimal weight: 0.5980 chunk 125 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 ASN ** O 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 74 ASN ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 GLN B 62 GLN ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 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 = 0.3309 r_free = 0.3309 target = 0.096024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.082151 restraints weight = 38384.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.084505 restraints weight = 22443.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.086057 restraints weight = 14983.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.087235 restraints weight = 11114.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.087971 restraints weight = 8821.407| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18100 Z= 0.146 Angle : 0.622 7.351 24584 Z= 0.320 Chirality : 0.046 0.244 2685 Planarity : 0.004 0.049 3138 Dihedral : 6.765 112.892 2793 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.49 % Favored : 94.46 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % 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: -0.46 (0.18), residues: 2184 helix: 1.49 (0.27), residues: 362 sheet: -0.27 (0.23), residues: 535 loop : -0.84 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 16 TYR 0.023 0.001 TYR C 308 PHE 0.021 0.002 PHE A 203 TRP 0.052 0.002 TRP I 47 HIS 0.008 0.001 HIS D 111 Details of bonding type rmsd covalent geometry : bond 0.00342 (18057) covalent geometry : angle 0.61027 (24479) SS BOND : bond 0.00338 ( 24) SS BOND : angle 1.49016 ( 48) hydrogen bonds : bond 0.03789 ( 579) hydrogen bonds : angle 5.26264 ( 1572) link_BETA1-4 : bond 0.00249 ( 2) link_BETA1-4 : angle 3.32177 ( 6) link_NAG-ASN : bond 0.00236 ( 17) link_NAG-ASN : angle 2.15467 ( 51) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2658.49 seconds wall clock time: 47 minutes 12.53 seconds (2832.53 seconds total)