Starting phenix.real_space_refine on Sat Jul 4 00:40:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mfg_23816/07_2026/7mfg_23816.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mfg_23816/07_2026/7mfg_23816.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7mfg_23816/07_2026/7mfg_23816.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mfg_23816/07_2026/7mfg_23816.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mfg_23816/07_2026/7mfg_23816.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mfg_23816/07_2026/7mfg_23816.map" model { file = "/net/cci-nas-00/data/ceres_data/7mfg_23816/07_2026/7mfg_23816.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mfg_23816/07_2026/7mfg_23816.cif" } resolution = 3.87 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= 0.003 sd= 0.020 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 87 5.16 5 C 10674 2.51 5 N 2865 2.21 5 O 3387 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17013 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2528 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 20, 'TRANS': 301} Chain: "B" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1274 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 1, 'TRANS': 155} Chain: "H" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 914 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "L" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 818 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "C" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2528 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 20, 'TRANS': 301} Chain: "D" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1274 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 1, 'TRANS': 155} Chain: "E" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 914 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "F" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 818 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "G" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2528 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 20, 'TRANS': 301} Chain: "I" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1274 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 1, 'TRANS': 155} Chain: "J" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 914 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "K" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 818 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "G" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 3.33, per 1000 atoms: 0.20 Number of scatterers: 17013 At special positions: 0 Unit cell: (138.449, 137.376, 145.962, 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 87 16.00 O 3387 8.00 N 2865 7.00 C 10674 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.03 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS I 47 " 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 B 47 " - pdb=" SG CYS C 30 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS D 137 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS D 47 " - pdb=" SG CYS G 30 " distance=2.03 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 14 " - pdb=" SG CYS I 137 " distance=2.03 Simple disulfide: pdb=" SG CYS G 52 " - pdb=" SG CYS G 277 " distance=2.03 Simple disulfide: pdb=" SG CYS G 64 " - pdb=" SG CYS G 76 " distance=2.03 Simple disulfide: pdb=" SG CYS G 97 " - pdb=" SG CYS G 139 " distance=2.03 Simple disulfide: pdb=" SG CYS G 281 " - pdb=" SG CYS G 305 " distance=2.03 Simple disulfide: pdb=" SG CYS I 144 " - pdb=" SG CYS I 148 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " NAG-ASN " NAG A 401 " - " ASN A 21 " " NAG A 402 " - " ASN A 63 " " NAG A 403 " - " ASN A 129 " " NAG A 404 " - " ASN A 94 " " NAG A 405 " - " ASN A 33 " " NAG A 406 " - " ASN A 289 " " NAG A 407 " - " ASN A 163 " " NAG C 401 " - " ASN C 21 " " NAG C 402 " - " ASN C 63 " " NAG C 403 " - " ASN C 129 " " NAG C 404 " - " ASN C 94 " " NAG C 405 " - " ASN C 33 " " NAG C 406 " - " ASN C 289 " " NAG C 407 " - " ASN C 163 " " NAG G 401 " - " ASN G 21 " " NAG G 402 " - " ASN G 63 " " NAG G 403 " - " ASN G 129 " " NAG G 404 " - " ASN G 94 " " NAG G 405 " - " ASN G 33 " " NAG G 406 " - " ASN G 289 " " NAG G 407 " - " ASN G 163 " " NAG M 1 " - " ASN B 154 " " NAG N 1 " - " ASN D 154 " " NAG O 1 " - " ASN I 154 " Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 859.1 milliseconds 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3858 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 51 sheets defined 20.7% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 77 through 81A removed outlier: 4.300A pdb=" N SER A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS A 81A" --> pdb=" O LEU A 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 77 through 81A' Processing helix chain 'A' and resid 104 through 114 removed outlier: 3.595A pdb=" N GLU A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER A 114 " --> pdb=" O GLU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 127 removed outlier: 4.069A pdb=" N TRP A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'B' and resid 37 through 59 removed outlier: 3.632A pdb=" N CYS B 47 " --> pdb=" O ASN B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 73 No H-bonds generated for 'chain 'B' and resid 71 through 73' Processing helix chain 'B' and resid 74 through 126 removed outlier: 3.558A pdb=" N ASP B 112 " --> pdb=" O LEU B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 154 Processing helix chain 'B' and resid 158 through 162 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 77 through 81A removed outlier: 4.311A pdb=" N SER C 81 " --> pdb=" O GLU C 77 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS C 81A" --> pdb=" O LEU C 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 77 through 81A' Processing helix chain 'C' and resid 104 through 114 removed outlier: 3.609A pdb=" N GLU C 110 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER C 114 " --> pdb=" O GLU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 127 removed outlier: 4.047A pdb=" N TRP C 127 " --> pdb=" O LYS C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 160 No H-bonds generated for 'chain 'C' and resid 158 through 160' Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'D' and resid 37 through 59 removed outlier: 3.623A pdb=" N CYS D 47 " --> pdb=" O ASN D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 73 No H-bonds generated for 'chain 'D' and resid 71 through 73' Processing helix chain 'D' and resid 74 through 126 removed outlier: 3.534A pdb=" N ASP D 112 " --> pdb=" O LEU D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 154 Processing helix chain 'D' and resid 158 through 162 Processing helix chain 'E' and resid 73 through 75 No H-bonds generated for 'chain 'E' and resid 73 through 75' Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'G' and resid 65 through 72 Processing helix chain 'G' and resid 77 through 81A removed outlier: 4.302A pdb=" N SER G 81 " --> pdb=" O GLU G 77 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS G 81A" --> pdb=" O LEU G 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 77 through 81A' Processing helix chain 'G' and resid 104 through 114 removed outlier: 3.609A pdb=" N GLU G 110 " --> pdb=" O GLU G 106 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER G 114 " --> pdb=" O GLU G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 127 removed outlier: 4.072A pdb=" N TRP G 127 " --> pdb=" O LYS G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 158 through 160 No H-bonds generated for 'chain 'G' and resid 158 through 160' Processing helix chain 'G' and resid 187 through 196 Processing helix chain 'I' and resid 37 through 59 removed outlier: 3.615A pdb=" N CYS I 47 " --> pdb=" O ASN I 43 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 73 No H-bonds generated for 'chain 'I' and resid 71 through 73' Processing helix chain 'I' and resid 74 through 126 removed outlier: 3.550A pdb=" N ASP I 112 " --> pdb=" O LEU I 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 154 Processing helix chain 'I' and resid 158 through 162 Processing helix chain 'J' and resid 73 through 75 No H-bonds generated for 'chain 'J' and resid 73 through 75' Processing helix chain 'J' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'B' and resid 35 through 36 removed outlier: 3.590A pdb=" N ALA B 35 " --> pdb=" O TYR B 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 removed outlier: 4.155A pdb=" N ASP A 24 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.535A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ILE A 87 " --> pdb=" O ILE A 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 115 through 118 removed outlier: 4.011A pdb=" N SER A 116A" --> pdb=" O SER A 261 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA A 259 " --> pdb=" O GLU A 116C" (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA8, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AA9, first strand: chain 'A' and resid 164 through 169 removed outlier: 3.516A pdb=" N VAL A 202 " --> pdb=" O PHE A 213 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL A 204 " --> pdb=" O ARG A 211 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR A 209 " --> pdb=" O SER A 206 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 282 through 283 Processing sheet with id=AB2, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.697A pdb=" N GLU H 10 " --> pdb=" O LEU H 108 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR H 110 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL H 37 " --> pdb=" O TYR H 91 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA H 93 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLY H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN H 58 " --> pdb=" O GLY H 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.697A pdb=" N GLU H 10 " --> pdb=" O LEU H 108 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR H 110 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AB6, first strand: chain 'L' and resid 11 through 12 removed outlier: 6.321A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'L' and resid 19 through 22 Processing sheet with id=AB8, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.235A pdb=" N TRP L 35 " --> pdb=" O ILE L 47 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 35 through 36 removed outlier: 3.601A pdb=" N ALA D 35 " --> pdb=" O TYR D 24 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 24 through 26 removed outlier: 4.157A pdb=" N ASP C 24 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AC3, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AC4, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.521A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ILE C 87 " --> pdb=" O ILE C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 115 through 118 removed outlier: 3.993A pdb=" N SER C 116A" --> pdb=" O SER C 261 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA C 259 " --> pdb=" O GLU C 116C" (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AC7, first strand: chain 'C' and resid 151 through 153 Processing sheet with id=AC8, first strand: chain 'C' and resid 164 through 169 removed outlier: 3.524A pdb=" N VAL C 204 " --> pdb=" O ARG C 211 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR C 209 " --> pdb=" O SER C 206 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 282 through 283 Processing sheet with id=AD1, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AD2, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.691A pdb=" N GLU E 10 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR E 110 " --> pdb=" O GLU E 10 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL E 37 " --> pdb=" O TYR E 91 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA E 93 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLY E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN E 58 " --> pdb=" O GLY E 50 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.691A pdb=" N GLU E 10 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR E 110 " --> pdb=" O GLU E 10 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS E 102 " --> pdb=" O ARG E 94 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 4 through 5 Processing sheet with id=AD5, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.318A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'F' and resid 19 through 22 Processing sheet with id=AD7, first strand: chain 'F' and resid 53 through 54 removed outlier: 6.232A pdb=" N TRP F 35 " --> pdb=" O ILE F 47 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 35 through 36 removed outlier: 3.612A pdb=" N ALA I 35 " --> pdb=" O TYR I 24 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 24 through 26 removed outlier: 4.173A pdb=" N ASP G 24 " --> pdb=" O VAL G 36 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 39 through 41 Processing sheet with id=AE2, first strand: chain 'G' and resid 43 through 44 Processing sheet with id=AE3, first strand: chain 'G' and resid 59 through 60 removed outlier: 6.531A pdb=" N LEU G 59 " --> pdb=" O VAL G 88 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ILE G 87 " --> pdb=" O ILE G 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'G' and resid 115 through 118 removed outlier: 4.003A pdb=" N SER G 116A" --> pdb=" O SER G 261 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA G 259 " --> pdb=" O GLU G 116C" (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL G 176 " --> pdb=" O LEU G 237 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 130 through 131 Processing sheet with id=AE6, first strand: chain 'G' and resid 151 through 153 Processing sheet with id=AE7, first strand: chain 'G' and resid 164 through 169 removed outlier: 3.868A pdb=" N TYR G 209 " --> pdb=" O SER G 206 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 282 through 283 Processing sheet with id=AE9, first strand: chain 'J' and resid 4 through 6 Processing sheet with id=AF1, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.696A pdb=" N GLU J 10 " --> pdb=" O LEU J 108 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR J 110 " --> pdb=" O GLU J 10 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL J 37 " --> pdb=" O TYR J 91 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA J 93 " --> pdb=" O SER J 35 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE J 34 " --> pdb=" O GLY J 50 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLY J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN J 58 " --> pdb=" O GLY J 50 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.696A pdb=" N GLU J 10 " --> pdb=" O LEU J 108 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR J 110 " --> pdb=" O GLU J 10 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS J 102 " --> pdb=" O ARG J 94 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 4 through 5 Processing sheet with id=AF4, first strand: chain 'K' and resid 11 through 12 removed outlier: 6.303A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'K' and resid 19 through 22 Processing sheet with id=AF6, first strand: chain 'K' and resid 53 through 54 removed outlier: 6.218A pdb=" N TRP K 35 " --> pdb=" O ILE K 47 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) 569 hydrogen bonds defined for protein. 1497 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: 2.87 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5496 1.34 - 1.46: 4317 1.46 - 1.58: 7476 1.58 - 1.70: 0 1.70 - 1.81: 120 Bond restraints: 17409 Sorted by residual: bond pdb=" N GLU K 1 " pdb=" CA GLU K 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 bond pdb=" N ASP C 11 " pdb=" CA ASP C 11 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.04e+00 bond pdb=" N GLN E 1 " pdb=" CA GLN E 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.00e+00 bond pdb=" N GLU L 1 " pdb=" CA GLU L 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 bond pdb=" N ASP A 11 " pdb=" CA ASP A 11 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.96e+00 ... (remaining 17404 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 23062 1.25 - 2.49: 372 2.49 - 3.74: 119 3.74 - 4.99: 27 4.99 - 6.24: 9 Bond angle restraints: 23589 Sorted by residual: angle pdb=" N TRP G 255 " pdb=" CA TRP G 255 " pdb=" C TRP G 255 " ideal model delta sigma weight residual 114.04 109.38 4.66 1.24e+00 6.50e-01 1.41e+01 angle pdb=" N ASN A 289 " pdb=" CA ASN A 289 " pdb=" CB ASN A 289 " ideal model delta sigma weight residual 113.65 109.97 3.68 1.47e+00 4.63e-01 6.27e+00 angle pdb=" N ASN G 289 " pdb=" CA ASN G 289 " pdb=" CB ASN G 289 " ideal model delta sigma weight residual 113.65 109.98 3.67 1.47e+00 4.63e-01 6.23e+00 angle pdb=" N ASN C 289 " pdb=" CA ASN C 289 " pdb=" CB ASN C 289 " ideal model delta sigma weight residual 113.65 110.00 3.65 1.47e+00 4.63e-01 6.17e+00 angle pdb=" N GLY E 52A" pdb=" CA GLY E 52A" pdb=" C GLY E 52A" ideal model delta sigma weight residual 111.78 115.94 -4.16 1.69e+00 3.50e-01 6.05e+00 ... (remaining 23584 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 9669 17.87 - 35.74: 319 35.74 - 53.61: 63 53.61 - 71.47: 8 71.47 - 89.34: 6 Dihedral angle restraints: 10065 sinusoidal: 3987 harmonic: 6078 Sorted by residual: dihedral pdb=" CB GLU A 238 " pdb=" CG GLU A 238 " pdb=" CD GLU A 238 " pdb=" OE1 GLU A 238 " ideal model delta sinusoidal sigma weight residual 0.00 86.09 -86.09 1 3.00e+01 1.11e-03 9.94e+00 dihedral pdb=" CB MET H 53 " pdb=" CG MET H 53 " pdb=" SD MET H 53 " pdb=" CE MET H 53 " ideal model delta sinusoidal sigma weight residual 60.00 118.79 -58.79 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CB MET E 53 " pdb=" CG MET E 53 " pdb=" SD MET E 53 " pdb=" CE MET E 53 " ideal model delta sinusoidal sigma weight residual 60.00 118.02 -58.02 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 10062 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2255 0.054 - 0.108: 246 0.108 - 0.162: 97 0.162 - 0.217: 0 0.217 - 0.271: 3 Chirality restraints: 2601 Sorted by residual: chirality pdb=" C5 BMA O 3 " pdb=" C4 BMA O 3 " pdb=" C6 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C5 BMA M 3 " pdb=" C4 BMA M 3 " pdb=" C6 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" C5 BMA N 3 " pdb=" C4 BMA N 3 " pdb=" C6 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 2598 not shown) Planarity restraints: 3042 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 323 " -0.028 5.00e-02 4.00e+02 4.18e-02 2.79e+00 pdb=" N PRO A 324 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 324 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 324 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 323 " 0.026 5.00e-02 4.00e+02 3.95e-02 2.49e+00 pdb=" N PRO C 324 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO C 324 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 324 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 323 " 0.025 5.00e-02 4.00e+02 3.81e-02 2.33e+00 pdb=" N PRO G 324 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO G 324 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO G 324 " 0.021 5.00e-02 4.00e+02 ... (remaining 3039 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 209 2.57 - 3.16: 14681 3.16 - 3.74: 24334 3.74 - 4.32: 33966 4.32 - 4.90: 58455 Nonbonded interactions: 131645 Sorted by model distance: nonbonded pdb=" OG SER L 7 " pdb=" OG SER L 22 " model vdw 1.993 3.040 nonbonded pdb=" OG SER F 7 " pdb=" OG SER F 22 " model vdw 1.999 3.040 nonbonded pdb=" OG SER K 7 " pdb=" OG SER K 22 " model vdw 2.018 3.040 nonbonded pdb=" O CYS A 305 " pdb=" OG1 THR B 61 " model vdw 2.085 3.040 nonbonded pdb=" O CYS C 305 " pdb=" OG1 THR D 61 " model vdw 2.085 3.040 ... (remaining 131640 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'H' selection = chain 'E' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'F' selection = chain 'K' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.260 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 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 : 0.003 0.033 17466 Z= 0.138 Angle : 0.477 6.236 23733 Z= 0.237 Chirality : 0.042 0.271 2601 Planarity : 0.003 0.042 3018 Dihedral : 9.454 89.344 6126 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.22 % Allowed : 2.25 % Favored : 97.53 % 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: 0.42 (0.19), residues: 2097 helix: 3.16 (0.28), residues: 327 sheet: 0.60 (0.27), residues: 411 loop : -0.57 (0.17), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 54 TYR 0.005 0.001 TYR A 101 PHE 0.007 0.001 PHE C 213 TRP 0.006 0.001 TRP H 47 HIS 0.002 0.000 HIS J 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 (17409) covalent geometry : angle 0.47053 / 0.24 (23589) SS BOND : bond 0.00161 / 0.11 ( 27) SS BOND : angle 0.77497 / 0.48 ( 54) hydrogen bonds : bond 0.28146 / 19.56 ( 554) hydrogen bonds : angle 8.90004 / 6.45 ( 1497) link_BETA1-4 : bond 0.00494 / 0.28 ( 6) link_BETA1-4 : angle 1.66706 / 1.01 ( 18) link_NAG-ASN : bond 0.00164 / 0.11 ( 24) link_NAG-ASN : angle 1.14189 / 0.71 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 217 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.8885 (mtp) cc_final: 0.8412 (ttp) REVERT: B 59 MET cc_start: 0.9235 (mmm) cc_final: 0.9028 (mmm) REVERT: B 85 ASP cc_start: 0.9177 (m-30) cc_final: 0.8837 (m-30) REVERT: B 112 ASP cc_start: 0.9353 (m-30) cc_final: 0.9141 (m-30) REVERT: B 149 MET cc_start: 0.8814 (mmt) cc_final: 0.8406 (mmt) REVERT: H 45 LEU cc_start: 0.8422 (mp) cc_final: 0.8181 (mt) REVERT: H 80 MET cc_start: 0.7829 (tpp) cc_final: 0.6444 (tpp) REVERT: L 48 MET cc_start: 0.8587 (tpp) cc_final: 0.7984 (mmm) REVERT: C 316 MET cc_start: 0.8832 (mtp) cc_final: 0.8515 (ttp) REVERT: D 85 ASP cc_start: 0.9226 (m-30) cc_final: 0.8865 (m-30) REVERT: D 112 ASP cc_start: 0.9423 (m-30) cc_final: 0.9223 (m-30) REVERT: D 149 MET cc_start: 0.8832 (mmt) cc_final: 0.8258 (mmt) REVERT: E 80 MET cc_start: 0.7841 (tpp) cc_final: 0.6634 (tpp) REVERT: F 48 MET cc_start: 0.8539 (tpp) cc_final: 0.7947 (mmm) REVERT: G 275 ASP cc_start: 0.7894 (t0) cc_final: 0.7670 (t0) REVERT: G 316 MET cc_start: 0.8893 (mtp) cc_final: 0.8644 (ttp) REVERT: I 38 GLN cc_start: 0.9123 (mt0) cc_final: 0.8908 (mm-40) REVERT: I 59 MET cc_start: 0.9206 (mmm) cc_final: 0.8709 (mmm) REVERT: I 85 ASP cc_start: 0.9232 (m-30) cc_final: 0.8920 (m-30) REVERT: I 112 ASP cc_start: 0.9333 (m-30) cc_final: 0.9116 (m-30) REVERT: I 149 MET cc_start: 0.8860 (mmt) cc_final: 0.8296 (mmt) REVERT: J 80 MET cc_start: 0.7915 (tpp) cc_final: 0.6528 (tpp) REVERT: K 48 MET cc_start: 0.8512 (tpp) cc_final: 0.7894 (mmm) REVERT: K 67 PHE cc_start: 0.8551 (p90) cc_final: 0.8198 (p90) outliers start: 4 outliers final: 4 residues processed: 221 average time/residue: 0.1223 time to fit residues: 39.2538 Evaluate side-chains 125 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 121 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain I residue 148 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 8.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 ASN A 322 ASN H 3 GLN H 64 GLN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 ASN E 3 GLN E 64 GLN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 190 ASN J 64 GLN ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.037528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.029196 restraints weight = 120975.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.030239 restraints weight = 63410.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.030948 restraints weight = 42124.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.031438 restraints weight = 32018.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.031764 restraints weight = 26434.961| |-----------------------------------------------------------------------------| r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 17466 Z= 0.274 Angle : 0.681 9.828 23733 Z= 0.350 Chirality : 0.045 0.198 2601 Planarity : 0.005 0.066 3018 Dihedral : 4.317 39.902 2302 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.59 % Allowed : 5.38 % Favored : 93.03 % 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: -0.08 (0.18), residues: 2097 helix: 2.27 (0.27), residues: 330 sheet: 0.36 (0.26), residues: 414 loop : -0.81 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 24 TYR 0.010 0.002 TYR G 161 PHE 0.022 0.002 PHE E 63 TRP 0.014 0.002 TRP H 103 HIS 0.006 0.001 HIS D 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00604 / 0.27 (17409) covalent geometry : angle 0.67187 / 0.35 (23589) SS BOND : bond 0.00286 / 0.17 ( 27) SS BOND : angle 0.94196 / 0.60 ( 54) hydrogen bonds : bond 0.05093 / 3.56 ( 554) hydrogen bonds : angle 6.46191 / 4.66 ( 1497) link_BETA1-4 : bond 0.00202 / 0.11 ( 6) link_BETA1-4 : angle 2.18900 / 1.43 ( 18) link_NAG-ASN : bond 0.00240 / 0.17 ( 24) link_NAG-ASN : angle 1.80451 / 1.16 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 MET cc_start: 0.9153 (mmm) cc_final: 0.8923 (mmm) REVERT: B 77 MET cc_start: 0.8482 (mmt) cc_final: 0.7789 (mmt) REVERT: B 85 ASP cc_start: 0.9113 (m-30) cc_final: 0.8698 (m-30) REVERT: B 149 MET cc_start: 0.8961 (mmt) cc_final: 0.8705 (mmt) REVERT: H 80 MET cc_start: 0.7504 (tpp) cc_final: 0.7179 (tpp) REVERT: L 48 MET cc_start: 0.8613 (tpp) cc_final: 0.8186 (mmm) REVERT: L 49 TYR cc_start: 0.9386 (p90) cc_final: 0.9125 (p90) REVERT: C 274 MET cc_start: 0.8760 (tpp) cc_final: 0.8368 (mmm) REVERT: D 59 MET cc_start: 0.9195 (mmm) cc_final: 0.8953 (mmm) REVERT: D 85 ASP cc_start: 0.9195 (m-30) cc_final: 0.8920 (m-30) REVERT: D 149 MET cc_start: 0.8986 (mmt) cc_final: 0.8614 (mmt) REVERT: E 48 MET cc_start: 0.9181 (mmm) cc_final: 0.8852 (mmm) REVERT: E 80 MET cc_start: 0.7533 (tpp) cc_final: 0.7078 (tpp) REVERT: F 48 MET cc_start: 0.8563 (tpp) cc_final: 0.8183 (mmm) REVERT: F 77 ARG cc_start: 0.8579 (mtp-110) cc_final: 0.8328 (mtp-110) REVERT: G 275 ASP cc_start: 0.8238 (t0) cc_final: 0.8000 (t0) REVERT: I 77 MET cc_start: 0.8350 (mmt) cc_final: 0.7998 (tpp) REVERT: I 85 ASP cc_start: 0.9187 (m-30) cc_final: 0.8806 (m-30) REVERT: I 103 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7883 (tm-30) REVERT: I 149 MET cc_start: 0.9065 (mmt) cc_final: 0.8730 (mmt) REVERT: J 80 MET cc_start: 0.7377 (tpp) cc_final: 0.7090 (tpp) REVERT: K 48 MET cc_start: 0.8466 (tpp) cc_final: 0.7879 (mmm) REVERT: K 67 PHE cc_start: 0.8678 (p90) cc_final: 0.8347 (p90) REVERT: K 100 GLN cc_start: 0.7364 (pp30) cc_final: 0.7114 (pp30) outliers start: 29 outliers final: 15 residues processed: 155 average time/residue: 0.1284 time to fit residues: 29.4547 Evaluate side-chains 131 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain D residue 144 CYS Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 144 CYS Chi-restraints excluded: chain I residue 148 CYS Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 100 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 97 optimal weight: 0.3980 chunk 189 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 170 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 117 optimal weight: 10.0000 chunk 175 optimal weight: 9.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 ASN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 ASN C 322 ASN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 ASN ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.038183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.029931 restraints weight = 119456.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.030990 restraints weight = 62311.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.031709 restraints weight = 41249.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.032203 restraints weight = 31216.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.032535 restraints weight = 25649.159| |-----------------------------------------------------------------------------| r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17466 Z= 0.117 Angle : 0.560 7.544 23733 Z= 0.284 Chirality : 0.042 0.160 2601 Planarity : 0.004 0.052 3018 Dihedral : 4.060 38.069 2302 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.04 % Allowed : 7.74 % Favored : 91.21 % 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: 0.08 (0.18), residues: 2097 helix: 2.35 (0.27), residues: 339 sheet: 0.55 (0.26), residues: 411 loop : -0.74 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 18 TYR 0.008 0.001 TYR D 94 PHE 0.014 0.001 PHE I 110 TRP 0.007 0.001 TRP G 180 HIS 0.003 0.001 HIS H 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (17409) covalent geometry : angle 0.55359 / 0.28 (23589) SS BOND : bond 0.00220 / 0.14 ( 27) SS BOND : angle 0.74002 / 0.49 ( 54) hydrogen bonds : bond 0.04409 / 3.10 ( 554) hydrogen bonds : angle 5.82803 / 4.21 ( 1497) link_BETA1-4 : bond 0.00523 / 0.30 ( 6) link_BETA1-4 : angle 1.66475 / 1.01 ( 18) link_NAG-ASN : bond 0.00197 / 0.13 ( 24) link_NAG-ASN : angle 1.33027 / 0.83 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 85 ASP cc_start: 0.9073 (m-30) cc_final: 0.8747 (m-30) REVERT: H 46 GLU cc_start: 0.7292 (mp0) cc_final: 0.6960 (mp0) REVERT: H 80 MET cc_start: 0.7474 (tpp) cc_final: 0.7150 (tpp) REVERT: L 48 MET cc_start: 0.8458 (tpp) cc_final: 0.8054 (mmm) REVERT: L 49 TYR cc_start: 0.9377 (p90) cc_final: 0.9142 (p90) REVERT: C 274 MET cc_start: 0.8729 (tpp) cc_final: 0.8203 (mmm) REVERT: D 59 MET cc_start: 0.9129 (mmm) cc_final: 0.8919 (mmm) REVERT: D 85 ASP cc_start: 0.9174 (m-30) cc_final: 0.8892 (m-30) REVERT: D 149 MET cc_start: 0.9033 (mmt) cc_final: 0.8691 (mmt) REVERT: F 48 MET cc_start: 0.8420 (tpp) cc_final: 0.8085 (mmm) REVERT: I 59 MET cc_start: 0.9129 (mmm) cc_final: 0.8869 (mmm) REVERT: I 85 ASP cc_start: 0.9194 (m-30) cc_final: 0.8851 (m-30) REVERT: J 3 GLN cc_start: 0.9080 (tp-100) cc_final: 0.8492 (tm-30) REVERT: K 48 MET cc_start: 0.8361 (tpp) cc_final: 0.7774 (mmm) REVERT: K 67 PHE cc_start: 0.8624 (p90) cc_final: 0.8215 (p90) outliers start: 19 outliers final: 12 residues processed: 143 average time/residue: 0.1375 time to fit residues: 28.7227 Evaluate side-chains 131 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain D residue 144 CYS Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 305 CYS Chi-restraints excluded: chain I residue 148 CYS Chi-restraints excluded: chain J residue 100 PHE Chi-restraints excluded: chain K residue 5 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 67 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 132 optimal weight: 8.9990 chunk 95 optimal weight: 0.0770 chunk 13 optimal weight: 0.5980 chunk 205 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 203 optimal weight: 10.0000 chunk 143 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 overall best weight: 1.5344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 322 ASN ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.037934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.029744 restraints weight = 119603.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.030797 restraints weight = 62425.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.031520 restraints weight = 41187.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.032002 restraints weight = 31009.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.032324 restraints weight = 25497.340| |-----------------------------------------------------------------------------| r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17466 Z= 0.124 Angle : 0.549 7.627 23733 Z= 0.278 Chirality : 0.042 0.156 2601 Planarity : 0.004 0.054 3018 Dihedral : 3.908 25.286 2299 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.70 % Allowed : 8.29 % Favored : 90.01 % 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: 0.04 (0.18), residues: 2097 helix: 2.29 (0.27), residues: 339 sheet: 0.53 (0.26), residues: 411 loop : -0.76 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 18 TYR 0.008 0.001 TYR H 59 PHE 0.027 0.001 PHE H 63 TRP 0.008 0.001 TRP L 35 HIS 0.002 0.001 HIS H 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (17409) covalent geometry : angle 0.54273 / 0.28 (23589) SS BOND : bond 0.00215 / 0.14 ( 27) SS BOND : angle 0.72834 / 0.49 ( 54) hydrogen bonds : bond 0.03925 / 2.76 ( 554) hydrogen bonds : angle 5.56628 / 4.02 ( 1497) link_BETA1-4 : bond 0.00473 / 0.26 ( 6) link_BETA1-4 : angle 1.69720 / 1.03 ( 18) link_NAG-ASN : bond 0.00127 / 0.09 ( 24) link_NAG-ASN : angle 1.36629 / 0.86 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8858 (mp) REVERT: B 77 MET cc_start: 0.7935 (mmt) cc_final: 0.7290 (mmt) REVERT: L 48 MET cc_start: 0.8551 (tpp) cc_final: 0.8143 (mmm) REVERT: L 49 TYR cc_start: 0.9392 (p90) cc_final: 0.9121 (p90) REVERT: C 217 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8848 (mp) REVERT: C 274 MET cc_start: 0.8753 (tpp) cc_final: 0.8248 (mmm) REVERT: D 149 MET cc_start: 0.9025 (mmt) cc_final: 0.8658 (mmt) REVERT: E 98 TYR cc_start: 0.9092 (p90) cc_final: 0.8669 (p90) REVERT: F 18 ARG cc_start: 0.8780 (mmm-85) cc_final: 0.8502 (mmm-85) REVERT: F 48 MET cc_start: 0.8320 (tpp) cc_final: 0.7996 (mmm) REVERT: I 59 MET cc_start: 0.9174 (mmm) cc_final: 0.8875 (mmm) REVERT: I 85 ASP cc_start: 0.9191 (m-30) cc_final: 0.8837 (m-30) REVERT: I 149 MET cc_start: 0.9191 (mmt) cc_final: 0.8743 (mmm) REVERT: J 3 GLN cc_start: 0.9087 (tp-100) cc_final: 0.8479 (tm-30) REVERT: K 48 MET cc_start: 0.8423 (tpp) cc_final: 0.7903 (mmm) REVERT: K 67 PHE cc_start: 0.8685 (p90) cc_final: 0.8287 (p90) outliers start: 31 outliers final: 23 residues processed: 158 average time/residue: 0.1233 time to fit residues: 28.8534 Evaluate side-chains 146 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain D residue 144 CYS Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 305 CYS Chi-restraints excluded: chain I residue 144 CYS Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 100 PHE Chi-restraints excluded: chain K residue 5 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 89 optimal weight: 0.2980 chunk 151 optimal weight: 0.0370 chunk 85 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 106 optimal weight: 6.9990 chunk 90 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 132 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 166 optimal weight: 1.9990 overall best weight: 1.0662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.038068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.029837 restraints weight = 119718.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.030883 restraints weight = 62829.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.031595 restraints weight = 41675.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.032091 restraints weight = 31602.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.032427 restraints weight = 25965.142| |-----------------------------------------------------------------------------| r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17466 Z= 0.103 Angle : 0.543 8.252 23733 Z= 0.271 Chirality : 0.042 0.158 2601 Planarity : 0.004 0.054 3018 Dihedral : 3.799 25.119 2298 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.54 % Allowed : 10.16 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.18), residues: 2097 helix: 2.41 (0.27), residues: 339 sheet: 0.56 (0.26), residues: 411 loop : -0.73 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 77 TYR 0.008 0.001 TYR B 94 PHE 0.027 0.001 PHE E 63 TRP 0.006 0.001 TRP G 180 HIS 0.002 0.000 HIS H 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (17409) covalent geometry : angle 0.53753 / 0.27 (23589) SS BOND : bond 0.00207 / 0.13 ( 27) SS BOND : angle 0.69996 / 0.47 ( 54) hydrogen bonds : bond 0.03672 / 2.58 ( 554) hydrogen bonds : angle 5.32572 / 3.85 ( 1497) link_BETA1-4 : bond 0.00530 / 0.29 ( 6) link_BETA1-4 : angle 1.63586 / 0.98 ( 18) link_NAG-ASN : bond 0.00180 / 0.13 ( 24) link_NAG-ASN : angle 1.28261 / 0.81 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 ILE cc_start: 0.9115 (OUTLIER) cc_final: 0.8897 (mp) REVERT: C 274 MET cc_start: 0.8748 (tpp) cc_final: 0.8267 (mmm) REVERT: D 149 MET cc_start: 0.9057 (mmt) cc_final: 0.8673 (mmt) REVERT: F 18 ARG cc_start: 0.8776 (mmm-85) cc_final: 0.8364 (tpp80) REVERT: I 59 MET cc_start: 0.9161 (mmm) cc_final: 0.8904 (mmm) REVERT: I 85 ASP cc_start: 0.9171 (m-30) cc_final: 0.8811 (m-30) REVERT: I 149 MET cc_start: 0.9190 (mmt) cc_final: 0.8710 (mmm) REVERT: J 3 GLN cc_start: 0.9110 (tp-100) cc_final: 0.8523 (tm-30) REVERT: K 67 PHE cc_start: 0.8674 (p90) cc_final: 0.8280 (p90) outliers start: 28 outliers final: 22 residues processed: 155 average time/residue: 0.1183 time to fit residues: 27.5176 Evaluate side-chains 140 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain D residue 144 CYS Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 305 CYS Chi-restraints excluded: chain I residue 144 CYS Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 100 PHE Chi-restraints excluded: chain K residue 5 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 94 optimal weight: 10.0000 chunk 204 optimal weight: 9.9990 chunk 141 optimal weight: 10.0000 chunk 187 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 170 optimal weight: 5.9990 chunk 161 optimal weight: 0.4980 chunk 117 optimal weight: 8.9990 chunk 96 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 ASN ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.036794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.028689 restraints weight = 122061.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.029690 restraints weight = 64766.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.030379 restraints weight = 43349.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.030854 restraints weight = 33018.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.031174 restraints weight = 27210.172| |-----------------------------------------------------------------------------| r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 17466 Z= 0.218 Angle : 0.592 8.825 23733 Z= 0.301 Chirality : 0.042 0.163 2601 Planarity : 0.004 0.055 3018 Dihedral : 4.080 26.525 2298 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.31 % Allowed : 11.04 % Favored : 86.66 % 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: -0.04 (0.18), residues: 2097 helix: 2.38 (0.27), residues: 339 sheet: 0.40 (0.26), residues: 411 loop : -0.83 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 83 TYR 0.027 0.001 TYR L 49 PHE 0.018 0.001 PHE H 63 TRP 0.010 0.001 TRP H 103 HIS 0.003 0.001 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.22 (17409) covalent geometry : angle 0.58372 / 0.30 (23589) SS BOND : bond 0.00282 / 0.18 ( 27) SS BOND : angle 0.87101 / 0.57 ( 54) hydrogen bonds : bond 0.03767 / 2.64 ( 554) hydrogen bonds : angle 5.41506 / 3.92 ( 1497) link_BETA1-4 : bond 0.00320 / 0.18 ( 6) link_BETA1-4 : angle 1.54999 / 0.95 ( 18) link_NAG-ASN : bond 0.00223 / 0.15 ( 24) link_NAG-ASN : angle 1.65247 / 1.07 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 115 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 ILE cc_start: 0.9140 (OUTLIER) cc_final: 0.8914 (mp) REVERT: L 48 MET cc_start: 0.8546 (tpp) cc_final: 0.8223 (mmm) REVERT: L 49 TYR cc_start: 0.9453 (p90) cc_final: 0.9208 (p90) REVERT: C 274 MET cc_start: 0.8823 (tpp) cc_final: 0.8336 (mmm) REVERT: D 149 MET cc_start: 0.9059 (mmt) cc_final: 0.8682 (mmt) REVERT: F 48 MET cc_start: 0.8521 (tpp) cc_final: 0.8173 (mmm) REVERT: I 59 MET cc_start: 0.9280 (mmm) cc_final: 0.8977 (mmm) REVERT: I 85 ASP cc_start: 0.9200 (m-30) cc_final: 0.8861 (m-30) REVERT: I 149 MET cc_start: 0.9200 (mmt) cc_final: 0.8718 (mmm) REVERT: K 48 MET cc_start: 0.8502 (tpp) cc_final: 0.7923 (mmm) outliers start: 42 outliers final: 34 residues processed: 152 average time/residue: 0.1235 time to fit residues: 28.0739 Evaluate side-chains 146 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 111 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 144 CYS Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain E residue 62 LYS Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 305 CYS Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain I residue 144 CYS Chi-restraints excluded: chain I residue 148 CYS Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 100 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 195 optimal weight: 9.9990 chunk 60 optimal weight: 20.0000 chunk 64 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 203 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.037061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.028910 restraints weight = 122143.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.029930 restraints weight = 64531.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.030636 restraints weight = 43054.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.031099 restraints weight = 32624.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.031432 restraints weight = 26995.092| |-----------------------------------------------------------------------------| r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17466 Z= 0.135 Angle : 0.557 8.640 23733 Z= 0.279 Chirality : 0.041 0.163 2601 Planarity : 0.004 0.055 3018 Dihedral : 3.967 25.280 2298 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.09 % Allowed : 11.70 % Favored : 86.22 % 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: 0.00 (0.18), residues: 2097 helix: 2.56 (0.27), residues: 339 sheet: 0.53 (0.27), residues: 405 loop : -0.89 (0.16), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 77 TYR 0.025 0.001 TYR L 49 PHE 0.019 0.001 PHE H 63 TRP 0.007 0.001 TRP L 35 HIS 0.002 0.001 HIS H 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (17409) covalent geometry : angle 0.54977 / 0.28 (23589) SS BOND : bond 0.00229 / 0.15 ( 27) SS BOND : angle 0.76366 / 0.50 ( 54) hydrogen bonds : bond 0.03609 / 2.53 ( 554) hydrogen bonds : angle 5.25925 / 3.80 ( 1497) link_BETA1-4 : bond 0.00450 / 0.25 ( 6) link_BETA1-4 : angle 1.50875 / 0.90 ( 18) link_NAG-ASN : bond 0.00128 / 0.09 ( 24) link_NAG-ASN : angle 1.46520 / 0.94 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 115 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8895 (mp) REVERT: H 80 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7261 (tpp) REVERT: L 48 MET cc_start: 0.8465 (tpp) cc_final: 0.8098 (mmm) REVERT: L 49 TYR cc_start: 0.9466 (p90) cc_final: 0.9223 (p90) REVERT: C 274 MET cc_start: 0.8733 (tpp) cc_final: 0.8278 (mmm) REVERT: D 149 MET cc_start: 0.9102 (mmt) cc_final: 0.8714 (mmt) REVERT: F 48 MET cc_start: 0.8397 (tpp) cc_final: 0.8196 (tpp) REVERT: G 274 MET cc_start: 0.9313 (OUTLIER) cc_final: 0.8525 (mpp) REVERT: I 59 MET cc_start: 0.9294 (mmm) cc_final: 0.8994 (mmm) REVERT: I 85 ASP cc_start: 0.9194 (m-30) cc_final: 0.8842 (m-30) REVERT: I 149 MET cc_start: 0.9147 (mmt) cc_final: 0.8636 (mmm) REVERT: K 48 MET cc_start: 0.8441 (tpp) cc_final: 0.8190 (tpp) outliers start: 38 outliers final: 29 residues processed: 149 average time/residue: 0.1133 time to fit residues: 26.0968 Evaluate side-chains 144 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 144 CYS Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 274 MET Chi-restraints excluded: chain G residue 305 CYS Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain I residue 144 CYS Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 100 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 162 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 180 optimal weight: 6.9990 chunk 159 optimal weight: 0.9980 chunk 188 optimal weight: 10.0000 chunk 106 optimal weight: 20.0000 chunk 154 optimal weight: 9.9990 chunk 173 optimal weight: 10.0000 chunk 186 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 125 GLN J 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.035654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.027249 restraints weight = 125069.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.028289 restraints weight = 64282.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.028999 restraints weight = 42282.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.029484 restraints weight = 31843.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.029812 restraints weight = 26142.211| |-----------------------------------------------------------------------------| r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 17466 Z= 0.280 Angle : 0.648 7.668 23733 Z= 0.330 Chirality : 0.043 0.176 2601 Planarity : 0.005 0.056 3018 Dihedral : 4.416 31.304 2298 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.25 % Allowed : 11.70 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.31 (0.18), residues: 2097 helix: 2.20 (0.27), residues: 339 sheet: 0.16 (0.26), residues: 414 loop : -1.01 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG K 24 TYR 0.025 0.002 TYR L 49 PHE 0.018 0.002 PHE G 118 TRP 0.012 0.002 TRP H 103 HIS 0.004 0.001 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.28 (17409) covalent geometry : angle 0.63786 / 0.33 (23589) SS BOND : bond 0.00327 / 0.22 ( 27) SS BOND : angle 1.03591 / 0.67 ( 54) hydrogen bonds : bond 0.03843 / 2.70 ( 554) hydrogen bonds : angle 5.47143 / 3.96 ( 1497) link_BETA1-4 : bond 0.00234 / 0.13 ( 6) link_BETA1-4 : angle 1.49728 / 0.90 ( 18) link_NAG-ASN : bond 0.00318 / 0.21 ( 24) link_NAG-ASN : angle 1.89981 / 1.24 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 115 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 ILE cc_start: 0.9129 (OUTLIER) cc_final: 0.8856 (mp) REVERT: B 85 ASP cc_start: 0.9306 (m-30) cc_final: 0.8981 (m-30) REVERT: H 80 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.7231 (tpp) REVERT: L 31 SER cc_start: 0.9238 (m) cc_final: 0.9017 (p) REVERT: C 274 MET cc_start: 0.8767 (tpp) cc_final: 0.8326 (mmm) REVERT: D 149 MET cc_start: 0.9026 (mmt) cc_final: 0.8673 (mmm) REVERT: F 18 ARG cc_start: 0.9098 (tpp80) cc_final: 0.8800 (mmm-85) REVERT: F 48 MET cc_start: 0.8660 (tpp) cc_final: 0.8425 (tpp) REVERT: G 274 MET cc_start: 0.9230 (OUTLIER) cc_final: 0.8519 (mpp) REVERT: G 275 ASP cc_start: 0.8040 (t0) cc_final: 0.7667 (t0) REVERT: I 17 MET cc_start: 0.8548 (tmm) cc_final: 0.8243 (tmm) REVERT: I 59 MET cc_start: 0.9417 (mmm) cc_final: 0.9107 (mmm) REVERT: I 85 ASP cc_start: 0.9263 (m-30) cc_final: 0.8942 (m-30) REVERT: I 149 MET cc_start: 0.9082 (mmt) cc_final: 0.8569 (mmm) REVERT: J 12 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8399 (mmtm) REVERT: K 48 MET cc_start: 0.8595 (tpp) cc_final: 0.8331 (tpp) outliers start: 41 outliers final: 31 residues processed: 149 average time/residue: 0.1249 time to fit residues: 28.3699 Evaluate side-chains 147 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 112 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 274 MET Chi-restraints excluded: chain G residue 305 CYS Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 148 CYS Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 100 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 125 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 37 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 137 optimal weight: 0.0070 chunk 78 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 60 optimal weight: 20.0000 chunk 45 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 overall best weight: 1.9804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.036493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.028385 restraints weight = 123541.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.029414 restraints weight = 64680.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.030113 restraints weight = 42854.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.030588 restraints weight = 32432.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.030917 restraints weight = 26701.440| |-----------------------------------------------------------------------------| r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17466 Z= 0.143 Angle : 0.583 8.438 23733 Z= 0.292 Chirality : 0.042 0.167 2601 Planarity : 0.004 0.057 3018 Dihedral : 4.195 29.727 2298 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.98 % Allowed : 11.92 % Favored : 86.11 % 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: -0.16 (0.18), residues: 2097 helix: 2.44 (0.27), residues: 339 sheet: 0.48 (0.27), residues: 399 loop : -1.02 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 83 TYR 0.027 0.001 TYR L 49 PHE 0.014 0.001 PHE C 213 TRP 0.009 0.001 TRP J 36 HIS 0.002 0.001 HIS A 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (17409) covalent geometry : angle 0.57538 / 0.29 (23589) SS BOND : bond 0.00227 / 0.15 ( 27) SS BOND : angle 0.87110 / 0.57 ( 54) hydrogen bonds : bond 0.03623 / 2.55 ( 554) hydrogen bonds : angle 5.24698 / 3.80 ( 1497) link_BETA1-4 : bond 0.00385 / 0.24 ( 6) link_BETA1-4 : angle 1.42595 / 0.84 ( 18) link_NAG-ASN : bond 0.00123 / 0.08 ( 24) link_NAG-ASN : angle 1.60209 / 1.03 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 119 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 MET cc_start: 0.8850 (tmm) cc_final: 0.8504 (tmm) REVERT: H 80 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.7178 (tpp) REVERT: L 31 SER cc_start: 0.9162 (m) cc_final: 0.8932 (p) REVERT: L 48 MET cc_start: 0.8642 (tpp) cc_final: 0.8112 (tpp) REVERT: D 149 MET cc_start: 0.9167 (mmt) cc_final: 0.8828 (mmm) REVERT: F 18 ARG cc_start: 0.9051 (tpp80) cc_final: 0.8402 (mmm-85) REVERT: G 274 MET cc_start: 0.9263 (OUTLIER) cc_final: 0.8503 (mpp) REVERT: G 275 ASP cc_start: 0.8078 (t0) cc_final: 0.7787 (t0) REVERT: I 17 MET cc_start: 0.8848 (tmm) cc_final: 0.8604 (tmm) REVERT: I 59 MET cc_start: 0.9274 (mmm) cc_final: 0.8998 (mmm) REVERT: I 85 ASP cc_start: 0.9216 (m-30) cc_final: 0.8902 (m-30) REVERT: I 149 MET cc_start: 0.9208 (mmt) cc_final: 0.8695 (mmm) REVERT: J 12 LYS cc_start: 0.9181 (OUTLIER) cc_final: 0.8604 (mmtm) REVERT: K 48 MET cc_start: 0.8492 (tpp) cc_final: 0.8243 (tpp) outliers start: 36 outliers final: 27 residues processed: 151 average time/residue: 0.1188 time to fit residues: 27.5831 Evaluate side-chains 143 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 274 MET Chi-restraints excluded: chain G residue 305 CYS Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 100 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 149 optimal weight: 0.6980 chunk 4 optimal weight: 0.1980 chunk 87 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 176 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 140 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 200 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.036129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.028053 restraints weight = 123874.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.029062 restraints weight = 65145.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.029748 restraints weight = 43321.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.030218 restraints weight = 32935.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.030540 restraints weight = 27133.525| |-----------------------------------------------------------------------------| r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17466 Z= 0.198 Angle : 0.619 12.609 23733 Z= 0.311 Chirality : 0.042 0.170 2601 Planarity : 0.004 0.058 3018 Dihedral : 4.277 31.041 2298 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 1.81 % Allowed : 12.14 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.24 (0.18), residues: 2097 helix: 2.40 (0.27), residues: 339 sheet: 0.35 (0.27), residues: 411 loop : -1.06 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 77 TYR 0.027 0.001 TYR L 49 PHE 0.031 0.002 PHE E 63 TRP 0.011 0.001 TRP J 36 HIS 0.003 0.001 HIS E 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.20 (17409) covalent geometry : angle 0.60991 / 0.31 (23589) SS BOND : bond 0.00253 / 0.16 ( 27) SS BOND : angle 1.25764 / 0.96 ( 54) hydrogen bonds : bond 0.03627 / 2.54 ( 554) hydrogen bonds : angle 5.28697 / 3.83 ( 1497) link_BETA1-4 : bond 0.00322 / 0.19 ( 6) link_BETA1-4 : angle 1.46461 / 0.86 ( 18) link_NAG-ASN : bond 0.00168 / 0.11 ( 24) link_NAG-ASN : angle 1.67992 / 1.09 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 115 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 MET cc_start: 0.8908 (tmm) cc_final: 0.8574 (tmm) REVERT: B 149 MET cc_start: 0.9237 (mmp) cc_final: 0.8947 (mmp) REVERT: H 80 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.7177 (tpp) REVERT: L 31 SER cc_start: 0.9198 (m) cc_final: 0.8940 (p) REVERT: L 48 MET cc_start: 0.8640 (tpp) cc_final: 0.8440 (tpp) REVERT: D 149 MET cc_start: 0.9159 (mmt) cc_final: 0.8823 (mmm) REVERT: E 85 GLU cc_start: 0.8572 (pm20) cc_final: 0.7605 (tm-30) REVERT: F 48 MET cc_start: 0.8561 (tpp) cc_final: 0.8050 (mmm) REVERT: G 274 MET cc_start: 0.9237 (OUTLIER) cc_final: 0.8405 (mpp) REVERT: G 275 ASP cc_start: 0.8051 (t0) cc_final: 0.7751 (t0) REVERT: I 17 MET cc_start: 0.8865 (tmm) cc_final: 0.8610 (tmm) REVERT: I 59 MET cc_start: 0.9290 (mmm) cc_final: 0.9012 (mmm) REVERT: I 85 ASP cc_start: 0.9203 (m-30) cc_final: 0.8848 (m-30) REVERT: I 149 MET cc_start: 0.9159 (mmt) cc_final: 0.8626 (mmm) REVERT: J 12 LYS cc_start: 0.9218 (OUTLIER) cc_final: 0.8599 (mmtm) REVERT: K 18 ARG cc_start: 0.9105 (tpp80) cc_final: 0.8864 (tpp80) REVERT: K 48 MET cc_start: 0.8508 (tpp) cc_final: 0.8259 (tpp) outliers start: 33 outliers final: 28 residues processed: 144 average time/residue: 0.1183 time to fit residues: 25.7196 Evaluate side-chains 143 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 112 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 274 MET Chi-restraints excluded: chain G residue 305 CYS Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 100 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 102 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 134 optimal weight: 8.9990 chunk 188 optimal weight: 6.9990 chunk 180 optimal weight: 0.9980 chunk 148 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 99 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 151 optimal weight: 3.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.035555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.027213 restraints weight = 125237.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.028243 restraints weight = 64274.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.028950 restraints weight = 42270.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.029436 restraints weight = 31778.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.029743 restraints weight = 26073.917| |-----------------------------------------------------------------------------| r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 17466 Z= 0.245 Angle : 0.657 11.657 23733 Z= 0.330 Chirality : 0.043 0.186 2601 Planarity : 0.005 0.064 3018 Dihedral : 4.453 30.219 2298 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 1.81 % Allowed : 12.14 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.36 (0.18), residues: 2097 helix: 2.34 (0.28), residues: 339 sheet: 0.19 (0.26), residues: 414 loop : -1.13 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG F 77 TYR 0.027 0.001 TYR L 49 PHE 0.031 0.002 PHE E 63 TRP 0.010 0.001 TRP H 103 HIS 0.003 0.001 HIS E 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.24 (17409) covalent geometry : angle 0.64725 / 0.33 (23589) SS BOND : bond 0.00494 / 0.36 ( 27) SS BOND : angle 1.39115 / 0.98 ( 54) hydrogen bonds : bond 0.03687 / 2.59 ( 554) hydrogen bonds : angle 5.36394 / 3.88 ( 1497) link_BETA1-4 : bond 0.00229 / 0.12 ( 6) link_BETA1-4 : angle 1.46640 / 0.86 ( 18) link_NAG-ASN : bond 0.00215 / 0.15 ( 24) link_NAG-ASN : angle 1.78244 / 1.16 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2193.19 seconds wall clock time: 39 minutes 6.32 seconds (2346.32 seconds total)