Starting phenix.real_space_refine on Thu Sep 18 13:48:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mfg_23816/09_2025/7mfg_23816.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mfg_23816/09_2025/7mfg_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 { model { file = "/net/cci-nas-00/data/ceres_data/7mfg_23816/09_2025/7mfg_23816.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mfg_23816/09_2025/7mfg_23816.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mfg_23816/09_2025/7mfg_23816.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mfg_23816/09_2025/7mfg_23816.map" } 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-2.0-5805/lib/python3.9/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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 21 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 dihedrals: 21 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 dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 3.26, per 1000 atoms: 0.19 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: 1.09 Conformation dependent library (CDL) restraints added in 909.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.66 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: 3.21 Time building geometry restraints manager: 1.43 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 - 21.71: 10272 21.71 - 43.41: 307 43.41 - 65.12: 72 65.12 - 86.83: 23 86.83 - 108.54: 15 Dihedral angle restraints: 10689 sinusoidal: 4611 harmonic: 6078 Sorted by residual: dihedral pdb=" O4 BMA N 3 " pdb=" C4 BMA N 3 " pdb=" C5 BMA N 3 " pdb=" O5 BMA N 3 " ideal model delta sinusoidal sigma weight residual -71.29 -179.83 108.54 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" O4 BMA O 3 " pdb=" C4 BMA O 3 " pdb=" C5 BMA O 3 " pdb=" O5 BMA O 3 " ideal model delta sinusoidal sigma weight residual -71.29 -179.81 108.52 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" O4 BMA M 3 " pdb=" C4 BMA M 3 " pdb=" C5 BMA M 3 " pdb=" O5 BMA M 3 " ideal model delta sinusoidal sigma weight residual -71.29 -179.80 108.51 1 3.00e+01 1.11e-03 1.41e+01 ... (remaining 10686 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: 0.03 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: 2.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.400 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 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 : 11.844 108.537 6750 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 aren 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 covalent geometry : bond 0.00276 (17409) covalent geometry : angle 0.47053 (23589) SS BOND : bond 0.00161 ( 27) SS BOND : angle 0.77497 ( 54) hydrogen bonds : bond 0.28146 ( 554) hydrogen bonds : angle 8.90004 ( 1497) link_BETA1-4 : bond 0.00494 ( 6) link_BETA1-4 : angle 1.66706 ( 18) link_NAG-ASN : bond 0.00164 ( 24) link_NAG-ASN : angle 1.14189 ( 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 : 0.587 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: 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: 0.6443 (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: 0.9424 (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: 0.8511 (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: 0.1517 time to fit residues: 48.1746 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 : 0.417 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.2982 r_free = 0.2982 target = 0.037496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.029196 restraints weight = 120834.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.030234 restraints weight = 63120.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.030931 restraints weight = 41943.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.031424 restraints weight = 32005.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.031747 restraints weight = 26378.807| |-----------------------------------------------------------------------------| r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 17466 Z= 0.273 Angle : 0.692 9.933 23733 Z= 0.353 Chirality : 0.045 0.186 2601 Planarity : 0.005 0.067 3018 Dihedral : 8.928 59.949 2926 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 1.70 % Allowed : 5.33 % Favored : 92.97 % 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 aren not related in a simple way. whole: -0.10 (0.18), residues: 2097 helix: 2.24 (0.27), residues: 330 sheet: 0.33 (0.26), residues: 414 loop : -0.82 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 106 TYR 0.010 0.002 TYR G 161 PHE 0.020 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 covalent geometry : bond 0.00602 (17409) covalent geometry : angle 0.67953 (23589) SS BOND : bond 0.00274 ( 27) SS BOND : angle 0.94453 ( 54) hydrogen bonds : bond 0.05065 ( 554) hydrogen bonds : angle 6.45070 ( 1497) link_BETA1-4 : bond 0.00286 ( 6) link_BETA1-4 : angle 2.86442 ( 18) link_NAG-ASN : bond 0.00236 ( 24) link_NAG-ASN : angle 1.90714 ( 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 168 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 time to evaluate : 0.500 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: 0.9158 (mmm) cc_final: 0.8929 (mmm) REVERT: B 77 MET cc_start: 0.8481 (mmt) cc_final: 0.7827 (mmt) REVERT: B 85 ASP cc_start: 0.9111 (m-30) cc_final: 0.8689 (m-30) REVERT: B 98 LEU cc_start: 0.9660 (tp) cc_final: 0.9402 (tt) REVERT: B 149 MET cc_start: 0.8959 (mmt) cc_final: 0.8704 (mmt) REVERT: H 80 MET cc_start: 0.7505 (tpp) cc_final: 0.7180 (tpp) REVERT: L 48 MET cc_start: 0.8617 (tpp) cc_final: 0.8188 (mmm) REVERT: D 59 MET cc_start: 0.9196 (mmm) cc_final: 0.8956 (mmm) REVERT: D 85 ASP cc_start: 0.9194 (m-30) cc_final: 0.8915 (m-30) REVERT: D 149 MET cc_start: 0.8984 (mmt) cc_final: 0.8612 (mmt) REVERT: E 48 MET cc_start: 0.9182 (mmm) cc_final: 0.8851 (mmm) REVERT: E 80 MET cc_start: 0.7533 (tpp) cc_final: 0.7075 (tpp) REVERT: F 48 MET cc_start: 0.8550 (tpp) cc_final: 0.8197 (mmm) REVERT: G 275 ASP cc_start: 0.8239 (t0) cc_final: 0.7980 (t0) REVERT: I 77 MET cc_start: 0.8349 (mmt) cc_final: 0.7466 (mmt) REVERT: I 85 ASP cc_start: 0.9186 (m-30) cc_final: 0.8805 (m-30) REVERT: I 103 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7848 (tm-30) REVERT: I 149 MET cc_start: 0.9065 (mmt) cc_final: 0.8731 (mmt) REVERT: J 80 MET cc_start: 0.7379 (tpp) cc_final: 0.7116 (tpp) REVERT: K 48 MET cc_start: 0.8473 (tpp) cc_final: 0.7881 (mmm) REVERT: K 67 PHE cc_start: 0.8690 (p90) cc_final: 0.8322 (p90) REVERT: K 100 GLN cc_start: 0.7368 (pp30) cc_final: 0.7152 (pp30) outliers start: 31 outliers final: 16 residues processed: 159 average time/residue: 0.1447 time to fit residues: 33.8303 Evaluate side-chains 132 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.602 ------------------------------------------------------------------------------- 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 G residue 71 LEU 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: 1.9990 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: 0.9990 chunk 35 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 117 optimal weight: 10.0000 chunk 175 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.2993 r_free = 0.2993 target = 0.037732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.029454 restraints weight = 120623.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.030496 restraints weight = 63373.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.031212 restraints weight = 42192.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.031693 restraints weight = 32021.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.032020 restraints weight = 26467.267| |-----------------------------------------------------------------------------| r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17466 Z= 0.146 Angle : 0.577 7.154 23733 Z= 0.293 Chirality : 0.043 0.162 2601 Planarity : 0.004 0.054 3018 Dihedral : 7.501 59.922 2926 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.32 % Allowed : 7.80 % Favored : 90.88 % 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 aren not related in a simple way. whole: 0.01 (0.18), residues: 2097 helix: 2.29 (0.27), residues: 333 sheet: 0.53 (0.27), residues: 405 loop : -0.78 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 106 TYR 0.009 0.001 TYR D 94 PHE 0.024 0.001 PHE H 63 TRP 0.008 0.001 TRP K 35 HIS 0.003 0.001 HIS D 25 Details of bonding type rmsd covalent geometry : bond 0.00324 (17409) covalent geometry : angle 0.56831 (23589) SS BOND : bond 0.00229 ( 27) SS BOND : angle 0.76602 ( 54) hydrogen bonds : bond 0.04480 ( 554) hydrogen bonds : angle 5.91113 ( 1497) link_BETA1-4 : bond 0.00608 ( 6) link_BETA1-4 : angle 2.29918 ( 18) link_NAG-ASN : bond 0.00132 ( 24) link_NAG-ASN : angle 1.52256 ( 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 148 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.633 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: B 85 ASP cc_start: 0.9075 (m-30) cc_final: 0.8753 (m-30) REVERT: H 46 GLU cc_start: 0.7357 (mp0) cc_final: 0.7060 (mp0) REVERT: H 80 MET cc_start: 0.7486 (tpp) cc_final: 0.7160 (tpp) REVERT: L 48 MET cc_start: 0.8491 (tpp) cc_final: 0.8076 (mmm) REVERT: D 59 MET cc_start: 0.9169 (mmm) cc_final: 0.8943 (mmm) REVERT: D 85 ASP cc_start: 0.9195 (m-30) cc_final: 0.8918 (m-30) REVERT: D 149 MET cc_start: 0.9013 (mmt) cc_final: 0.8657 (mmt) REVERT: F 48 MET cc_start: 0.8467 (tpp) cc_final: 0.8092 (mmm) REVERT: I 59 MET cc_start: 0.9174 (mmm) cc_final: 0.8871 (mmm) REVERT: I 85 ASP cc_start: 0.9201 (m-30) cc_final: 0.8855 (m-30) REVERT: J 3 GLN cc_start: 0.9085 (tp-100) cc_final: 0.8506 (tm-30) REVERT: K 48 MET cc_start: 0.8415 (tpp) cc_final: 0.7814 (mmm) REVERT: K 67 PHE cc_start: 0.8683 (p90) cc_final: 0.8205 (p90) outliers start: 24 outliers final: 18 residues processed: 145 average time/residue: 0.1456 time to fit residues: 30.9962 Evaluate side-chains 133 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 112 ASP 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 102 LEU 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 305 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 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: 4.9990 chunk 28 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 205 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 203 optimal weight: 9.9990 chunk 143 optimal weight: 0.8980 chunk 2 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.2967 r_free = 0.2967 target = 0.037014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.028733 restraints weight = 122214.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.029761 restraints weight = 63916.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.030466 restraints weight = 42499.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.030951 restraints weight = 32275.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.031257 restraints weight = 26647.585| |-----------------------------------------------------------------------------| r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17466 Z= 0.196 Angle : 0.589 8.249 23733 Z= 0.299 Chirality : 0.043 0.163 2601 Planarity : 0.004 0.056 3018 Dihedral : 6.708 58.593 2925 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.92 % Allowed : 8.95 % Favored : 89.13 % 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 aren not related in a simple way. whole: -0.11 (0.18), residues: 2097 helix: 2.16 (0.27), residues: 339 sheet: 0.36 (0.26), residues: 411 loop : -0.84 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 77 TYR 0.010 0.001 TYR E 59 PHE 0.023 0.001 PHE H 63 TRP 0.010 0.001 TRP L 35 HIS 0.003 0.001 HIS B 25 Details of bonding type rmsd covalent geometry : bond 0.00437 (17409) covalent geometry : angle 0.57904 (23589) SS BOND : bond 0.00270 ( 27) SS BOND : angle 0.91053 ( 54) hydrogen bonds : bond 0.04007 ( 554) hydrogen bonds : angle 5.71208 ( 1497) link_BETA1-4 : bond 0.00401 ( 6) link_BETA1-4 : angle 2.13826 ( 18) link_NAG-ASN : bond 0.00130 ( 24) link_NAG-ASN : angle 1.70641 ( 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 156 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 121 time to evaluate : 0.559 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: A 217 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8899 (mp) REVERT: B 103 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8785 (mm-30) REVERT: L 48 MET cc_start: 0.8612 (tpp) cc_final: 0.8223 (mmm) REVERT: C 217 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8850 (mp) REVERT: D 149 MET cc_start: 0.9049 (mmt) cc_final: 0.8667 (mmt) REVERT: F 18 ARG cc_start: 0.8796 (mmm-85) cc_final: 0.8509 (tpp80) REVERT: F 48 MET cc_start: 0.8540 (tpp) cc_final: 0.8167 (mmm) REVERT: I 59 MET cc_start: 0.9243 (mmm) cc_final: 0.8941 (mmm) REVERT: I 85 ASP cc_start: 0.9203 (m-30) cc_final: 0.8854 (m-30) REVERT: I 149 MET cc_start: 0.9221 (mmt) cc_final: 0.8774 (mmm) REVERT: K 48 MET cc_start: 0.8514 (tpp) cc_final: 0.7943 (mmm) REVERT: K 67 PHE cc_start: 0.8780 (p90) cc_final: 0.8282 (p90) outliers start: 35 outliers final: 28 residues processed: 151 average time/residue: 0.1396 time to fit residues: 31.4307 Evaluate side-chains 148 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 0.469 ------------------------------------------------------------------------------- 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 67 VAL Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 5 THR 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 19 ASP 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 177 LEU Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 305 CYS Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 144 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 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: 0.8980 chunk 151 optimal weight: 0.7980 chunk 85 optimal weight: 10.0000 chunk 40 optimal weight: 0.9980 chunk 106 optimal weight: 7.9990 chunk 90 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 166 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.2993 r_free = 0.2993 target = 0.037631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.029381 restraints weight = 120985.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.030435 restraints weight = 62983.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.031151 restraints weight = 41648.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.031649 restraints weight = 31546.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.031963 restraints weight = 25865.300| |-----------------------------------------------------------------------------| r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17466 Z= 0.102 Angle : 0.544 8.005 23733 Z= 0.274 Chirality : 0.042 0.155 2601 Planarity : 0.004 0.055 3018 Dihedral : 6.144 58.025 2923 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.65 % Allowed : 10.27 % Favored : 88.08 % 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 aren not related in a simple way. whole: -0.01 (0.18), residues: 2097 helix: 2.32 (0.27), residues: 339 sheet: 0.43 (0.26), residues: 411 loop : -0.80 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 77 TYR 0.008 0.001 TYR D 94 PHE 0.018 0.001 PHE H 63 TRP 0.008 0.001 TRP G 180 HIS 0.002 0.001 HIS H 101 Details of bonding type rmsd covalent geometry : bond 0.00222 (17409) covalent geometry : angle 0.53623 (23589) SS BOND : bond 0.00209 ( 27) SS BOND : angle 0.73057 ( 54) hydrogen bonds : bond 0.03746 ( 554) hydrogen bonds : angle 5.40244 ( 1497) link_BETA1-4 : bond 0.00637 ( 6) link_BETA1-4 : angle 1.88021 ( 18) link_NAG-ASN : bond 0.00196 ( 24) link_NAG-ASN : angle 1.43808 ( 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 159 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 129 time to evaluate : 0.562 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: 0.9109 (OUTLIER) cc_final: 0.8869 (mp) REVERT: B 103 GLU cc_start: 0.9135 (mm-30) cc_final: 0.8817 (mm-30) REVERT: L 48 MET cc_start: 0.8473 (tpp) cc_final: 0.8090 (mmm) REVERT: C 217 ILE cc_start: 0.9079 (OUTLIER) cc_final: 0.8860 (mp) REVERT: D 149 MET cc_start: 0.9072 (mmt) cc_final: 0.8686 (mmt) REVERT: F 48 MET cc_start: 0.8365 (tpp) cc_final: 0.8013 (mmm) REVERT: I 59 MET cc_start: 0.9228 (mmm) cc_final: 0.8937 (mmm) REVERT: I 85 ASP cc_start: 0.9188 (m-30) cc_final: 0.8823 (m-30) REVERT: I 149 MET cc_start: 0.9200 (mmt) cc_final: 0.8721 (mmm) REVERT: J 3 GLN cc_start: 0.9146 (tp-100) cc_final: 0.8543 (tm-30) REVERT: K 48 MET cc_start: 0.8396 (tpp) cc_final: 0.7850 (mmm) REVERT: K 67 PHE cc_start: 0.8736 (p90) cc_final: 0.8253 (p90) outliers start: 30 outliers final: 21 residues processed: 157 average time/residue: 0.1199 time to fit residues: 28.3251 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 : 0.634 ------------------------------------------------------------------------------- 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 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 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 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: 4.9990 chunk 204 optimal weight: 9.9990 chunk 141 optimal weight: 9.9990 chunk 187 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 170 optimal weight: 10.0000 chunk 161 optimal weight: 0.8980 chunk 117 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.036451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.028262 restraints weight = 122827.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.029277 restraints weight = 64613.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.029972 restraints weight = 43051.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.030450 restraints weight = 32709.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.030776 restraints weight = 26966.068| |-----------------------------------------------------------------------------| r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 17466 Z= 0.231 Angle : 0.601 8.494 23733 Z= 0.304 Chirality : 0.042 0.160 2601 Planarity : 0.004 0.056 3018 Dihedral : 6.274 54.528 2922 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.20 % Allowed : 11.15 % 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 aren not related in a simple way. whole: -0.13 (0.18), residues: 2097 helix: 2.27 (0.27), residues: 339 sheet: 0.30 (0.26), residues: 408 loop : -0.87 (0.16), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 77 TYR 0.012 0.001 TYR H 59 PHE 0.018 0.002 PHE H 63 TRP 0.010 0.001 TRP H 103 HIS 0.003 0.001 HIS E 101 Details of bonding type rmsd covalent geometry : bond 0.00512 (17409) covalent geometry : angle 0.59030 (23589) SS BOND : bond 0.00286 ( 27) SS BOND : angle 0.88476 ( 54) hydrogen bonds : bond 0.03817 ( 554) hydrogen bonds : angle 5.48551 ( 1497) link_BETA1-4 : bond 0.00288 ( 6) link_BETA1-4 : angle 1.89822 ( 18) link_NAG-ASN : bond 0.00226 ( 24) link_NAG-ASN : angle 1.81001 ( 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 156 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 116 time to evaluate : 0.692 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: 0.9109 (OUTLIER) cc_final: 0.8900 (mp) REVERT: L 48 MET cc_start: 0.8579 (tpp) cc_final: 0.8215 (mmm) REVERT: C 217 ILE cc_start: 0.9117 (OUTLIER) cc_final: 0.8888 (mp) REVERT: D 149 MET cc_start: 0.9101 (mmt) cc_final: 0.8735 (mmt) REVERT: F 18 ARG cc_start: 0.9044 (tpp80) cc_final: 0.8802 (mmm-85) REVERT: F 48 MET cc_start: 0.8533 (tpp) cc_final: 0.8173 (mmm) REVERT: G 274 MET cc_start: 0.9237 (OUTLIER) cc_final: 0.8460 (mpp) REVERT: I 59 MET cc_start: 0.9286 (mmm) cc_final: 0.8966 (mmm) REVERT: I 149 MET cc_start: 0.9200 (mmt) cc_final: 0.8715 (mmm) REVERT: K 48 MET cc_start: 0.8495 (tpp) cc_final: 0.8228 (tpp) outliers start: 40 outliers final: 29 residues processed: 149 average time/residue: 0.1533 time to fit residues: 34.2661 Evaluate side-chains 148 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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 217 ILE Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain D residue 19 ASP 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 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 148 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 195 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 chunk 64 optimal weight: 0.1980 chunk 86 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 2 optimal weight: 0.1980 chunk 203 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.2988 r_free = 0.2988 target = 0.037428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.029259 restraints weight = 120708.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.030300 restraints weight = 63563.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.031011 restraints weight = 42212.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.031494 restraints weight = 31954.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.031806 restraints weight = 26300.503| |-----------------------------------------------------------------------------| r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17466 Z= 0.098 Angle : 0.559 8.778 23733 Z= 0.277 Chirality : 0.042 0.156 2601 Planarity : 0.004 0.055 3018 Dihedral : 5.731 51.729 2922 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.65 % Allowed : 12.14 % 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 aren not related in a simple way. whole: -0.00 (0.18), residues: 2097 helix: 2.49 (0.27), residues: 339 sheet: 0.55 (0.27), residues: 405 loop : -0.88 (0.16), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 77 TYR 0.009 0.001 TYR D 94 PHE 0.014 0.001 PHE I 110 TRP 0.012 0.001 TRP A 180 HIS 0.003 0.000 HIS H 101 Details of bonding type rmsd covalent geometry : bond 0.00215 (17409) covalent geometry : angle 0.55214 (23589) SS BOND : bond 0.00208 ( 27) SS BOND : angle 0.66404 ( 54) hydrogen bonds : bond 0.03576 ( 554) hydrogen bonds : angle 5.20250 ( 1497) link_BETA1-4 : bond 0.00623 ( 6) link_BETA1-4 : angle 1.74662 ( 18) link_NAG-ASN : bond 0.00248 ( 24) link_NAG-ASN : angle 1.43148 ( 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 151 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 0.717 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: A 217 ILE cc_start: 0.9117 (OUTLIER) cc_final: 0.8883 (mp) REVERT: C 217 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8870 (mp) REVERT: D 126 LEU cc_start: 0.9096 (tp) cc_final: 0.8828 (mt) REVERT: D 149 MET cc_start: 0.9140 (mmt) cc_final: 0.8778 (mmt) REVERT: F 18 ARG cc_start: 0.9039 (tpp80) cc_final: 0.8774 (mmm-85) REVERT: G 274 MET cc_start: 0.9276 (OUTLIER) cc_final: 0.8590 (mpp) REVERT: I 59 MET cc_start: 0.9270 (mmm) cc_final: 0.8999 (mmm) REVERT: I 85 ASP cc_start: 0.9188 (m-30) cc_final: 0.8831 (m-30) REVERT: I 149 MET cc_start: 0.9191 (mmt) cc_final: 0.8673 (mmm) REVERT: J 48 MET cc_start: 0.8972 (mmm) cc_final: 0.8090 (mmm) REVERT: K 48 MET cc_start: 0.8289 (tpp) cc_final: 0.8050 (tpp) outliers start: 30 outliers final: 21 residues processed: 146 average time/residue: 0.1437 time to fit residues: 31.3195 Evaluate side-chains 138 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.712 ------------------------------------------------------------------------------- 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 108 LEU 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 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 I residue 148 CYS Chi-restraints excluded: chain J residue 53 MET 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: 3.9990 chunk 66 optimal weight: 9.9990 chunk 180 optimal weight: 0.7980 chunk 159 optimal weight: 7.9990 chunk 188 optimal weight: 9.9990 chunk 106 optimal weight: 7.9990 chunk 154 optimal weight: 5.9990 chunk 173 optimal weight: 6.9990 chunk 186 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 282 GLN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 282 GLN J 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.035564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2564 r_free = 0.2564 target = 0.027099 restraints weight = 125984.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.028137 restraints weight = 65193.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.028843 restraints weight = 43088.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.029322 restraints weight = 32521.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.029654 restraints weight = 26850.785| |-----------------------------------------------------------------------------| r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 17466 Z= 0.316 Angle : 0.664 7.351 23733 Z= 0.337 Chirality : 0.044 0.169 2601 Planarity : 0.005 0.055 3018 Dihedral : 6.218 53.573 2922 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 2.47 % Allowed : 11.48 % Favored : 86.05 % 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 aren not related in a simple way. whole: -0.33 (0.18), residues: 2097 helix: 2.20 (0.27), residues: 339 sheet: 0.17 (0.26), residues: 414 loop : -1.04 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 117 TYR 0.029 0.002 TYR L 49 PHE 0.019 0.002 PHE G 118 TRP 0.013 0.002 TRP H 103 HIS 0.005 0.001 HIS C 38 Details of bonding type rmsd covalent geometry : bond 0.00690 (17409) covalent geometry : angle 0.65323 (23589) SS BOND : bond 0.00343 ( 27) SS BOND : angle 1.00094 ( 54) hydrogen bonds : bond 0.03868 ( 554) hydrogen bonds : angle 5.49288 ( 1497) link_BETA1-4 : bond 0.00171 ( 6) link_BETA1-4 : angle 1.92113 ( 18) link_NAG-ASN : bond 0.00376 ( 24) link_NAG-ASN : angle 2.01309 ( 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 159 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 114 time to evaluate : 0.658 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: 0.9136 (OUTLIER) cc_final: 0.8829 (mp) REVERT: A 314 LEU cc_start: 0.9623 (OUTLIER) cc_final: 0.9391 (pp) REVERT: B 85 ASP cc_start: 0.9296 (m-30) cc_final: 0.8980 (m-30) REVERT: L 31 SER cc_start: 0.9262 (m) cc_final: 0.9045 (p) REVERT: L 48 MET cc_start: 0.8733 (tpp) cc_final: 0.8174 (mmm) REVERT: C 217 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8749 (mp) REVERT: D 149 MET cc_start: 0.9058 (mmt) cc_final: 0.8701 (mmm) REVERT: F 48 MET cc_start: 0.8699 (tpp) cc_final: 0.8141 (mmm) REVERT: G 274 MET cc_start: 0.9234 (OUTLIER) cc_final: 0.8525 (mpp) REVERT: I 17 MET cc_start: 0.8607 (tmm) cc_final: 0.8327 (tmm) REVERT: I 59 MET cc_start: 0.9435 (mmm) cc_final: 0.9103 (mmm) REVERT: I 85 ASP cc_start: 0.9282 (m-30) cc_final: 0.8955 (m-30) REVERT: I 149 MET cc_start: 0.9084 (mmt) cc_final: 0.8564 (mmm) REVERT: J 12 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8438 (mmtm) REVERT: K 31 SER cc_start: 0.9217 (m) cc_final: 0.8958 (p) REVERT: K 48 MET cc_start: 0.8541 (tpp) cc_final: 0.8260 (tpp) outliers start: 45 outliers final: 32 residues processed: 149 average time/residue: 0.1387 time to fit residues: 31.4206 Evaluate side-chains 147 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 110 time to evaluate : 0.691 ------------------------------------------------------------------------------- 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 A residue 314 LEU Chi-restraints excluded: chain B residue 19 ASP 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 115 VAL 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 D residue 19 ASP Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 67 VAL 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 177 LEU 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 19 ASP Chi-restraints excluded: chain I residue 108 LEU 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 53 MET Chi-restraints excluded: chain J residue 67 VAL 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: 2.9990 chunk 92 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 137 optimal weight: 0.4980 chunk 78 optimal weight: 0.7980 chunk 167 optimal weight: 0.3980 chunk 60 optimal weight: 20.0000 chunk 45 optimal weight: 8.9990 chunk 61 optimal weight: 8.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.2967 r_free = 0.2967 target = 0.036858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.028755 restraints weight = 122433.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.029795 restraints weight = 63786.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.030503 restraints weight = 42166.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.030988 restraints weight = 31844.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.031298 restraints weight = 26135.905| |-----------------------------------------------------------------------------| r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 17466 Z= 0.105 Angle : 0.578 8.901 23733 Z= 0.286 Chirality : 0.042 0.161 2601 Planarity : 0.004 0.057 3018 Dihedral : 5.633 50.881 2922 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.65 % Allowed : 12.36 % Favored : 86.00 % 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 aren not related in a simple way. whole: -0.16 (0.18), residues: 2097 helix: 2.47 (0.27), residues: 339 sheet: 0.50 (0.27), residues: 405 loop : -1.04 (0.16), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 18 TYR 0.028 0.001 TYR L 49 PHE 0.015 0.001 PHE I 110 TRP 0.012 0.001 TRP A 180 HIS 0.003 0.001 HIS H 101 Details of bonding type rmsd covalent geometry : bond 0.00237 (17409) covalent geometry : angle 0.56800 (23589) SS BOND : bond 0.00227 ( 27) SS BOND : angle 1.20492 ( 54) hydrogen bonds : bond 0.03578 ( 554) hydrogen bonds : angle 5.18856 ( 1497) link_BETA1-4 : bond 0.00591 ( 6) link_BETA1-4 : angle 1.66813 ( 18) link_NAG-ASN : bond 0.00215 ( 24) link_NAG-ASN : angle 1.56589 ( 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 146 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 0.678 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 17 MET cc_start: 0.8903 (tmm) cc_final: 0.8573 (tmm) REVERT: L 31 SER cc_start: 0.9145 (m) cc_final: 0.8886 (p) REVERT: L 48 MET cc_start: 0.8572 (tpp) cc_final: 0.8110 (mmm) REVERT: L 49 TYR cc_start: 0.9504 (p90) cc_final: 0.9281 (p90) REVERT: C 217 ILE cc_start: 0.9010 (OUTLIER) cc_final: 0.8808 (mp) REVERT: C 274 MET cc_start: 0.8764 (tpp) cc_final: 0.8159 (mmm) REVERT: D 126 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8856 (mt) REVERT: D 149 MET cc_start: 0.9173 (mmt) cc_final: 0.8709 (mmm) REVERT: F 48 MET cc_start: 0.8482 (tpp) cc_final: 0.7991 (mmm) REVERT: G 274 MET cc_start: 0.9254 (OUTLIER) cc_final: 0.8613 (mpp) REVERT: I 17 MET cc_start: 0.8897 (tmm) cc_final: 0.8671 (tmm) REVERT: I 59 MET cc_start: 0.9274 (mmm) cc_final: 0.8998 (mmm) REVERT: I 85 ASP cc_start: 0.9205 (m-30) cc_final: 0.8888 (m-30) REVERT: I 149 MET cc_start: 0.9220 (mmt) cc_final: 0.8701 (mmm) REVERT: K 48 MET cc_start: 0.8352 (tpp) cc_final: 0.8109 (tpp) outliers start: 30 outliers final: 25 residues processed: 142 average time/residue: 0.1374 time to fit residues: 29.3939 Evaluate side-chains 142 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.771 ------------------------------------------------------------------------------- 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 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 D residue 126 LEU 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 I residue 148 CYS Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 53 MET 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: 3.9990 chunk 4 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 176 optimal weight: 1.9990 chunk 132 optimal weight: 0.4980 chunk 140 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 22 optimal weight: 8.9990 chunk 200 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 101 HIS ** F 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 = 0.2970 r_free = 0.2970 target = 0.036905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.028827 restraints weight = 122033.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.029861 restraints weight = 63847.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.030566 restraints weight = 42230.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.031047 restraints weight = 31865.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.031372 restraints weight = 26144.684| |-----------------------------------------------------------------------------| r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.3513 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= 0.116 Angle : 0.573 13.204 23733 Z= 0.283 Chirality : 0.042 0.168 2601 Planarity : 0.004 0.055 3018 Dihedral : 5.397 51.835 2922 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.65 % Allowed : 12.74 % Favored : 85.61 % 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 aren not related in a simple way. whole: -0.09 (0.18), residues: 2097 helix: 2.61 (0.27), residues: 339 sheet: 0.56 (0.27), residues: 405 loop : -1.02 (0.16), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 24 TYR 0.028 0.001 TYR L 49 PHE 0.013 0.001 PHE D 110 TRP 0.007 0.001 TRP K 35 HIS 0.002 0.001 HIS H 101 Details of bonding type rmsd covalent geometry : bond 0.00265 (17409) covalent geometry : angle 0.56417 (23589) SS BOND : bond 0.00204 ( 27) SS BOND : angle 1.15331 ( 54) hydrogen bonds : bond 0.03451 ( 554) hydrogen bonds : angle 5.08698 ( 1497) link_BETA1-4 : bond 0.00504 ( 6) link_BETA1-4 : angle 1.75161 ( 18) link_NAG-ASN : bond 0.00149 ( 24) link_NAG-ASN : angle 1.53751 ( 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 143 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 0.716 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: B 17 MET cc_start: 0.8991 (tmm) cc_final: 0.8655 (tmm) REVERT: B 149 MET cc_start: 0.9223 (mmp) cc_final: 0.8929 (mmp) REVERT: L 31 SER cc_start: 0.9152 (m) cc_final: 0.8905 (p) REVERT: C 217 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8812 (mp) REVERT: C 274 MET cc_start: 0.8755 (tpp) cc_final: 0.8148 (mmm) REVERT: D 126 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8802 (mt) REVERT: D 149 MET cc_start: 0.9198 (mmt) cc_final: 0.8736 (mmm) REVERT: F 48 MET cc_start: 0.8517 (tpp) cc_final: 0.8020 (mmm) REVERT: G 274 MET cc_start: 0.9239 (OUTLIER) cc_final: 0.8472 (mpp) REVERT: I 17 MET cc_start: 0.8913 (tmm) cc_final: 0.8690 (tmm) REVERT: I 59 MET cc_start: 0.9249 (mmm) cc_final: 0.9007 (mmm) REVERT: I 85 ASP cc_start: 0.9186 (m-30) cc_final: 0.8822 (m-30) REVERT: I 149 MET cc_start: 0.9250 (mmt) cc_final: 0.8726 (mmm) REVERT: J 12 LYS cc_start: 0.9245 (OUTLIER) cc_final: 0.8583 (mmtm) REVERT: K 48 MET cc_start: 0.8266 (tpp) cc_final: 0.8059 (tpp) outliers start: 30 outliers final: 25 residues processed: 139 average time/residue: 0.1541 time to fit residues: 32.0187 Evaluate side-chains 138 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 0.710 ------------------------------------------------------------------------------- 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 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 D residue 108 LEU Chi-restraints excluded: chain D residue 126 LEU 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 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 53 MET 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: 9.9990 chunk 93 optimal weight: 6.9990 chunk 134 optimal weight: 5.9990 chunk 188 optimal weight: 9.9990 chunk 180 optimal weight: 5.9990 chunk 148 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.2907 r_free = 0.2907 target = 0.035417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.027108 restraints weight = 124965.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.028135 restraints weight = 64343.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.028841 restraints weight = 42345.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.029322 restraints weight = 31869.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.029648 restraints weight = 26180.204| |-----------------------------------------------------------------------------| r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 17466 Z= 0.307 Angle : 0.696 11.484 23733 Z= 0.350 Chirality : 0.044 0.178 2601 Planarity : 0.005 0.055 3018 Dihedral : 6.006 53.316 2922 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 1.76 % Allowed : 12.63 % Favored : 85.61 % 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 aren not related in a simple way. whole: -0.38 (0.18), residues: 2097 helix: 2.32 (0.27), residues: 339 sheet: 0.18 (0.26), residues: 414 loop : -1.14 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 117 TYR 0.026 0.002 TYR F 49 PHE 0.017 0.002 PHE C 118 TRP 0.013 0.002 TRP H 103 HIS 0.005 0.001 HIS E 101 Details of bonding type rmsd covalent geometry : bond 0.00677 (17409) covalent geometry : angle 0.68403 (23589) SS BOND : bond 0.00332 ( 27) SS BOND : angle 1.37790 ( 54) hydrogen bonds : bond 0.03781 ( 554) hydrogen bonds : angle 5.42615 ( 1497) link_BETA1-4 : bond 0.00179 ( 6) link_BETA1-4 : angle 1.89353 ( 18) link_NAG-ASN : bond 0.00337 ( 24) link_NAG-ASN : angle 1.96437 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2400.33 seconds wall clock time: 42 minutes 44.26 seconds (2564.26 seconds total)