Starting phenix.real_space_refine on Thu Feb 5 05:22:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9irs_60818/02_2026/9irs_60818.cif Found real_map, /net/cci-nas-00/data/ceres_data/9irs_60818/02_2026/9irs_60818.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9irs_60818/02_2026/9irs_60818.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9irs_60818/02_2026/9irs_60818.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9irs_60818/02_2026/9irs_60818.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9irs_60818/02_2026/9irs_60818.map" } resolution = 3.18 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= -0.001 sd= 0.049 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 92 5.16 5 C 9475 2.51 5 N 2472 2.21 5 O 2940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14979 Number of models: 1 Model: "" Number of chains: 14 Chain: "a" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 264 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "b" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 26} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain: "f" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 949 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "g" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 890 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain: "m" Number of atoms: 1924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1924 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 233} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "n" Number of atoms: 2246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2246 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 271} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "e" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 978 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "H" Number of atoms: 1675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1675 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 206} Chain: "L" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1639 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 202} Chain: "S" Number of atoms: 1675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1675 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 206} Chain: "T" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1639 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 202} Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.23, per 1000 atoms: 0.22 Number of scatterers: 14979 At special positions: 0 Unit cell: (111.22, 186.93, 156.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 92 16.00 O 2940 8.00 N 2472 7.00 C 9475 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS a 32 " - pdb=" SG CYS b 32 " distance=2.03 Simple disulfide: pdb=" SG CYS d 37 " - pdb=" SG CYS d 73 " distance=2.03 Simple disulfide: pdb=" SG CYS d 93 " - pdb=" SG CYS d 96 " distance=2.04 Simple disulfide: pdb=" SG CYS f 49 " - pdb=" SG CYS f 98 " distance=2.03 Simple disulfide: pdb=" SG CYS f 119 " - pdb=" SG CYS f 122 " distance=2.03 Simple disulfide: pdb=" SG CYS g 46 " - pdb=" SG CYS g 87 " distance=2.03 Simple disulfide: pdb=" SG CYS g 104 " - pdb=" SG CYS g 107 " distance=2.04 Simple disulfide: pdb=" SG CYS m 45 " - pdb=" SG CYS m 111 " distance=2.04 Simple disulfide: pdb=" SG CYS m 155 " - pdb=" SG CYS m 205 " distance=2.03 Simple disulfide: pdb=" SG CYS m 227 " - pdb=" SG CYS n 264 " distance=2.03 Simple disulfide: pdb=" SG CYS n 42 " - pdb=" SG CYS n 110 " distance=2.03 Simple disulfide: pdb=" SG CYS n 164 " - pdb=" SG CYS n 229 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 134 " - pdb=" SG CYS L 213 " distance=2.03 Simple disulfide: pdb=" SG CYS H 146 " - pdb=" SG CYS H 201 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS L 133 " - pdb=" SG CYS L 193 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 134 " - pdb=" SG CYS T 213 " distance=2.03 Simple disulfide: pdb=" SG CYS S 146 " - pdb=" SG CYS S 201 " distance=2.03 Simple disulfide: pdb=" SG CYS T 23 " - pdb=" SG CYS T 87 " distance=2.03 Simple disulfide: pdb=" SG CYS T 133 " - pdb=" SG CYS T 193 " 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 Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 401.1 milliseconds 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3584 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 41 sheets defined 17.6% alpha, 36.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'a' and resid 29 through 54 removed outlier: 3.814A pdb=" N TYR a 33 " --> pdb=" O PRO a 29 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU a 35 " --> pdb=" O LEU a 31 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU a 39 " --> pdb=" O LEU a 35 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU a 49 " --> pdb=" O ILE a 45 " (cutoff:3.500A) Processing helix chain 'b' and resid 28 through 54 removed outlier: 3.567A pdb=" N TYR b 33 " --> pdb=" O PRO b 29 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU b 35 " --> pdb=" O LEU b 31 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP b 36 " --> pdb=" O CYS b 32 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU b 39 " --> pdb=" O LEU b 35 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 66 No H-bonds generated for 'chain 'd' and resid 64 through 66' Processing helix chain 'd' and resid 100 through 127 removed outlier: 3.633A pdb=" N ALA d 105 " --> pdb=" O PRO d 101 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE d 123 " --> pdb=" O ALA d 119 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N CYS d 124 " --> pdb=" O LEU d 120 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N PHE d 125 " --> pdb=" O GLY d 121 " (cutoff:3.500A) Processing helix chain 'f' and resid 128 through 156 removed outlier: 3.691A pdb=" N GLY f 143 " --> pdb=" O CYS f 139 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU f 144 " --> pdb=" O ILE f 140 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU f 145 " --> pdb=" O THR f 141 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU f 146 " --> pdb=" O GLY f 142 " (cutoff:3.500A) Processing helix chain 'g' and resid 78 through 80 No H-bonds generated for 'chain 'g' and resid 78 through 80' Processing helix chain 'g' and resid 111 through 138 removed outlier: 3.505A pdb=" N ILE g 126 " --> pdb=" O GLU g 122 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL g 133 " --> pdb=" O LEU g 129 " (cutoff:3.500A) Processing helix chain 'm' and resid 204 through 209 removed outlier: 4.728A pdb=" N PHE m 209 " --> pdb=" O CYS m 205 " (cutoff:3.500A) Processing helix chain 'm' and resid 231 through 235 removed outlier: 3.514A pdb=" N SER m 235 " --> pdb=" O VAL m 232 " (cutoff:3.500A) Processing helix chain 'm' and resid 239 through 273 removed outlier: 3.638A pdb=" N PHE m 244 " --> pdb=" O THR m 240 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU m 257 " --> pdb=" O ARG m 253 " (cutoff:3.500A) Processing helix chain 'n' and resid 101 through 105 removed outlier: 4.102A pdb=" N THR n 105 " --> pdb=" O PRO n 102 " (cutoff:3.500A) Processing helix chain 'n' and resid 135 through 139 removed outlier: 3.736A pdb=" N ASN n 138 " --> pdb=" O ASP n 135 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL n 139 " --> pdb=" O LEU n 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 135 through 139' Processing helix chain 'n' and resid 150 through 157 removed outlier: 3.632A pdb=" N ILE n 154 " --> pdb=" O SER n 150 " (cutoff:3.500A) Processing helix chain 'n' and resid 217 through 221 Processing helix chain 'n' and resid 267 through 308 removed outlier: 3.729A pdb=" N GLN n 272 " --> pdb=" O SER n 268 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN n 273 " --> pdb=" O GLU n 269 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY n 274 " --> pdb=" O SER n 270 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE n 280 " --> pdb=" O LEU n 276 " (cutoff:3.500A) Processing helix chain 'e' and resid 104 through 108 removed outlier: 3.774A pdb=" N ALA e 108 " --> pdb=" O PRO e 105 " (cutoff:3.500A) Processing helix chain 'e' and resid 126 through 154 removed outlier: 3.891A pdb=" N VAL e 130 " --> pdb=" O ASP e 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.564A pdb=" N ARG H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.520A pdb=" N LYS H 65 " --> pdb=" O GLN H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.104A pdb=" N SER H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 82 removed outlier: 3.961A pdb=" N ASP L 81 " --> pdb=" O GLU L 78 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA L 82 " --> pdb=" O ALA L 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 82' Processing helix chain 'L' and resid 120 through 127 Processing helix chain 'L' and resid 182 through 186 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.755A pdb=" N SER S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'T' and resid 120 through 127 Processing helix chain 'T' and resid 182 through 186 removed outlier: 3.628A pdb=" N GLU T 186 " --> pdb=" O LYS T 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 182 through 186' Processing sheet with id=AA1, first strand: chain 'd' and resid 26 through 27 removed outlier: 5.697A pdb=" N VAL d 33 " --> pdb=" O LEU d 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'd' and resid 42 through 46 removed outlier: 6.561A pdb=" N ILE d 70 " --> pdb=" O VAL d 44 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLY d 46 " --> pdb=" O ARG d 68 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ARG d 68 " --> pdb=" O GLY d 46 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY d 69 " --> pdb=" O VAL d 88 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N CYS d 73 " --> pdb=" O SER d 84 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER d 84 " --> pdb=" O CYS d 73 " (cutoff:3.500A) removed outlier: 9.191A pdb=" N TYR e 111 " --> pdb=" O GLU d 83 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N THR d 85 " --> pdb=" O TYR e 111 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N TYR e 113 " --> pdb=" O THR d 85 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLN d 87 " --> pdb=" O TYR e 113 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N ARG e 115 " --> pdb=" O GLN d 87 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N HIS d 89 " --> pdb=" O ARG e 115 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N TRP e 59 " --> pdb=" O ILE e 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'd' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'f' and resid 37 through 40 removed outlier: 3.555A pdb=" N LEU f 47 " --> pdb=" O LEU f 82 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'f' and resid 64 through 66 removed outlier: 3.609A pdb=" N ILE f 66 " --> pdb=" O TRP f 59 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TRP f 59 " --> pdb=" O ILE f 66 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY f 94 " --> pdb=" O LEU f 114 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN g 98 " --> pdb=" O TYR f 111 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY g 83 " --> pdb=" O VAL g 99 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ILE g 53 " --> pdb=" O PHE g 64 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N PHE g 64 " --> pdb=" O ILE g 53 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N TRP g 55 " --> pdb=" O ILE g 62 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'f' and resid 122 through 124 Processing sheet with id=AA7, first strand: chain 'g' and resid 31 through 34 removed outlier: 5.927A pdb=" N VAL g 42 " --> pdb=" O LEU g 74 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'm' and resid 33 through 36 removed outlier: 6.217A pdb=" N LEU m 33 " --> pdb=" O LEU m 129 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N SER m 131 " --> pdb=" O LEU m 33 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL m 35 " --> pdb=" O SER m 131 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET m 70 " --> pdb=" O TRP m 57 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ARG m 59 " --> pdb=" O LEU m 68 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N LEU m 68 " --> pdb=" O ARG m 59 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'm' and resid 33 through 36 removed outlier: 6.217A pdb=" N LEU m 33 " --> pdb=" O LEU m 129 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N SER m 131 " --> pdb=" O LEU m 33 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL m 35 " --> pdb=" O SER m 131 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'm' and resid 40 through 46 removed outlier: 3.716A pdb=" N ALA m 85 " --> pdb=" O LYS m 78 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS m 78 " --> pdb=" O ALA m 85 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL m 87 " --> pdb=" O GLY m 76 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY m 76 " --> pdb=" O VAL m 87 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'm' and resid 141 through 143 removed outlier: 3.590A pdb=" N SER m 153 " --> pdb=" O SER m 198 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER m 198 " --> pdb=" O SER m 153 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'm' and resid 180 through 184 removed outlier: 3.640A pdb=" N THR m 180 " --> pdb=" O SER m 193 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'n' and resid 23 through 26 removed outlier: 3.705A pdb=" N MET n 38 " --> pdb=" O LEU n 97 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'n' and resid 31 through 33 removed outlier: 6.497A pdb=" N LEU n 32 " --> pdb=" O THR n 133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'n' and resid 74 through 76 removed outlier: 3.524A pdb=" N TYR n 67 " --> pdb=" O ASP n 75 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N TRP n 53 " --> pdb=" O ILE n 65 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N TYR n 67 " --> pdb=" O MET n 51 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N MET n 51 " --> pdb=" O TYR n 67 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL n 107 " --> pdb=" O GLN n 56 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'n' and resid 143 through 147 removed outlier: 3.520A pdb=" N VAL n 163 " --> pdb=" O PHE n 147 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N TYR n 207 " --> pdb=" O GLY n 168 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG n 212 " --> pdb=" O SER n 190 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'n' and resid 143 through 147 removed outlier: 3.520A pdb=" N VAL n 163 " --> pdb=" O PHE n 147 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N TYR n 207 " --> pdb=" O GLY n 168 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'n' and resid 183 through 184 Processing sheet with id=AC1, first strand: chain 'e' and resid 39 through 40 Processing sheet with id=AC2, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.747A pdb=" N VAL H 18 " --> pdb=" O LEU H 83 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.506A pdb=" N TYR H 94 " --> pdb=" O THR H 113 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.506A pdb=" N TYR H 94 " --> pdb=" O THR H 113 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ARG H 98 " --> pdb=" O ASP H 107 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS H 105 " --> pdb=" O TYR H 100 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 126 through 130 removed outlier: 3.739A pdb=" N SER H 126 " --> pdb=" O LYS H 149 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY H 145 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS H 146 " --> pdb=" O SER H 185 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 126 through 130 removed outlier: 3.739A pdb=" N SER H 126 " --> pdb=" O LYS H 149 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY H 145 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N LYS H 149 " --> pdb=" O LEU H 183 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LEU H 183 " --> pdb=" O LYS H 149 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N TYR H 151 " --> pdb=" O TYR H 181 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 159 through 160 removed outlier: 3.536A pdb=" N LYS H 214 " --> pdb=" O CYS H 201 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL H 203 " --> pdb=" O VAL H 212 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL H 212 " --> pdb=" O VAL H 203 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.542A pdb=" N THR L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER L 66 " --> pdb=" O SER L 69 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.580A pdb=" N TYR L 85 " --> pdb=" O THR L 101 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N GLN L 36 " --> pdb=" O ARG L 45 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ARG L 45 " --> pdb=" O GLN L 36 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.580A pdb=" N TYR L 85 " --> pdb=" O THR L 101 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 113 through 117 removed outlier: 3.787A pdb=" N ALA L 129 " --> pdb=" O LEU L 180 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU L 178 " --> pdb=" O VAL L 131 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER L 176 " --> pdb=" O CYS L 133 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU L 135 " --> pdb=" O MET L 174 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 144 through 149 removed outlier: 3.656A pdb=" N TYR L 191 " --> pdb=" O PHE L 208 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE L 208 " --> pdb=" O TYR L 191 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'S' and resid 3 through 6 removed outlier: 3.551A pdb=" N VAL S 18 " --> pdb=" O LEU S 83 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.561A pdb=" N VAL S 37 " --> pdb=" O TYR S 95 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR S 33 " --> pdb=" O TYR S 99 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N TRP S 36 " --> pdb=" O ILE S 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.775A pdb=" N CYS S 105 " --> pdb=" O TYR S 100 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'S' and resid 126 through 130 removed outlier: 3.852A pdb=" N GLY S 145 " --> pdb=" O LEU S 130 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL S 142 " --> pdb=" O VAL S 189 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N CYS S 146 " --> pdb=" O SER S 185 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'S' and resid 126 through 130 removed outlier: 3.852A pdb=" N GLY S 145 " --> pdb=" O LEU S 130 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N LYS S 149 " --> pdb=" O LEU S 183 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU S 183 " --> pdb=" O LYS S 149 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR S 151 " --> pdb=" O TYR S 181 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'S' and resid 157 through 160 Processing sheet with id=AE1, first strand: chain 'T' and resid 4 through 7 removed outlier: 3.532A pdb=" N TYR T 70 " --> pdb=" O CYS T 23 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'T' and resid 10 through 13 removed outlier: 5.901A pdb=" N GLN T 36 " --> pdb=" O ARG T 45 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ARG T 45 " --> pdb=" O GLN T 36 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'T' and resid 10 through 13 Processing sheet with id=AE4, first strand: chain 'T' and resid 113 through 117 removed outlier: 3.628A pdb=" N SER T 176 " --> pdb=" O CYS T 133 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N TYR T 172 " --> pdb=" O ASN T 137 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER T 161 " --> pdb=" O SER T 175 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR T 177 " --> pdb=" O LEU T 159 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'T' and resid 152 through 153 removed outlier: 3.602A pdb=" N LYS T 206 " --> pdb=" O CYS T 193 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA T 195 " --> pdb=" O ILE T 204 " (cutoff:3.500A) 617 hydrogen bonds defined for protein. 1623 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.83 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4766 1.34 - 1.46: 3747 1.46 - 1.58: 6685 1.58 - 1.70: 1 1.70 - 1.82: 130 Bond restraints: 15329 Sorted by residual: bond pdb=" CB PRO S 173 " pdb=" CG PRO S 173 " ideal model delta sigma weight residual 1.492 1.668 -0.176 5.00e-02 4.00e+02 1.24e+01 bond pdb=" N PRO S 173 " pdb=" CD PRO S 173 " ideal model delta sigma weight residual 1.473 1.500 -0.027 1.40e-02 5.10e+03 3.71e+00 bond pdb=" CB PRO H 155 " pdb=" CG PRO H 155 " ideal model delta sigma weight residual 1.506 1.572 -0.066 3.90e-02 6.57e+02 2.90e+00 bond pdb=" N PRO S 173 " pdb=" CA PRO S 173 " ideal model delta sigma weight residual 1.465 1.447 0.018 1.12e-02 7.97e+03 2.52e+00 bond pdb=" CA GLY f 68 " pdb=" C GLY f 68 " ideal model delta sigma weight residual 1.530 1.515 0.016 1.04e-02 9.25e+03 2.36e+00 ... (remaining 15324 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 20711 2.79 - 5.58: 109 5.58 - 8.37: 18 8.37 - 11.15: 2 11.15 - 13.94: 1 Bond angle restraints: 20841 Sorted by residual: angle pdb=" CA PRO S 173 " pdb=" N PRO S 173 " pdb=" CD PRO S 173 " ideal model delta sigma weight residual 112.00 98.06 13.94 1.40e+00 5.10e-01 9.92e+01 angle pdb=" N PRO S 173 " pdb=" CD PRO S 173 " pdb=" CG PRO S 173 " ideal model delta sigma weight residual 103.20 97.23 5.97 1.50e+00 4.44e-01 1.58e+01 angle pdb=" N PRO S 173 " pdb=" CA PRO S 173 " pdb=" C PRO S 173 " ideal model delta sigma weight residual 111.57 117.41 -5.84 1.52e+00 4.33e-01 1.48e+01 angle pdb=" CA GLU n 49 " pdb=" CB GLU n 49 " pdb=" CG GLU n 49 " ideal model delta sigma weight residual 114.10 121.67 -7.57 2.00e+00 2.50e-01 1.43e+01 angle pdb=" C GLU g 67 " pdb=" N ASP g 68 " pdb=" CA ASP g 68 " ideal model delta sigma weight residual 121.54 128.68 -7.14 1.91e+00 2.74e-01 1.40e+01 ... (remaining 20836 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 8465 17.68 - 35.37: 627 35.37 - 53.05: 147 53.05 - 70.73: 21 70.73 - 88.42: 11 Dihedral angle restraints: 9271 sinusoidal: 3676 harmonic: 5595 Sorted by residual: dihedral pdb=" CA GLU n 49 " pdb=" C GLU n 49 " pdb=" N TYR n 50 " pdb=" CA TYR n 50 " ideal model delta harmonic sigma weight residual 180.00 132.89 47.11 0 5.00e+00 4.00e-02 8.88e+01 dihedral pdb=" CB CYS g 104 " pdb=" SG CYS g 104 " pdb=" SG CYS g 107 " pdb=" CB CYS g 107 " ideal model delta sinusoidal sigma weight residual -86.00 -149.16 63.16 1 1.00e+01 1.00e-02 5.27e+01 dihedral pdb=" CB CYS f 119 " pdb=" SG CYS f 119 " pdb=" SG CYS f 122 " pdb=" CB CYS f 122 " ideal model delta sinusoidal sigma weight residual -86.00 -33.01 -52.99 1 1.00e+01 1.00e-02 3.82e+01 ... (remaining 9268 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1850 0.047 - 0.095: 375 0.095 - 0.142: 106 0.142 - 0.190: 2 0.190 - 0.237: 1 Chirality restraints: 2334 Sorted by residual: chirality pdb=" CA PRO S 173 " pdb=" N PRO S 173 " pdb=" C PRO S 173 " pdb=" CB PRO S 173 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB ILE m 134 " pdb=" CA ILE m 134 " pdb=" CG1 ILE m 134 " pdb=" CG2 ILE m 134 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.02e-01 chirality pdb=" CA ASP g 80 " pdb=" N ASP g 80 " pdb=" C ASP g 80 " pdb=" CB ASP g 80 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.61e-01 ... (remaining 2331 not shown) Planarity restraints: 2641 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE S 172 " -0.079 5.00e-02 4.00e+02 1.09e-01 1.89e+01 pdb=" N PRO S 173 " 0.187 5.00e-02 4.00e+02 pdb=" CA PRO S 173 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO S 173 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL n 79 " -0.056 5.00e-02 4.00e+02 8.60e-02 1.18e+01 pdb=" N PRO n 80 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO n 80 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO n 80 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU S 154 " 0.032 5.00e-02 4.00e+02 4.77e-02 3.65e+00 pdb=" N PRO S 155 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO S 155 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO S 155 " 0.024 5.00e-02 4.00e+02 ... (remaining 2638 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2171 2.76 - 3.30: 12972 3.30 - 3.83: 22997 3.83 - 4.37: 25820 4.37 - 4.90: 47482 Nonbonded interactions: 111442 Sorted by model distance: nonbonded pdb=" OE2 GLU L 104 " pdb=" OH TYR L 172 " model vdw 2.231 3.040 nonbonded pdb=" OE1 GLN n 199 " pdb=" OG SER n 205 " model vdw 2.244 3.040 nonbonded pdb=" OE2 GLU d 28 " pdb=" OH TYR d 90 " model vdw 2.255 3.040 nonbonded pdb=" O TYR L 185 " pdb=" OH TYR L 191 " model vdw 2.256 3.040 nonbonded pdb=" OD1 ASP L 169 " pdb=" OG1 THR L 171 " model vdw 2.272 3.040 ... (remaining 111437 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'H' selection = chain 'S' } ncs_group { reference = chain 'L' selection = chain 'T' } ncs_group { reference = (chain 'e' and (resid 33 through 69 or resid 74 through 155)) selection = (chain 'f' and resid 33 through 155) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 20.500 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: 0.530 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.420 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 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 0.176 15351 Z= 0.142 Angle : 0.624 13.942 20885 Z= 0.347 Chirality : 0.041 0.237 2334 Planarity : 0.005 0.109 2641 Dihedral : 13.274 88.416 5621 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.06 % Allowed : 11.09 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.09 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.19), residues: 1895 helix: 0.39 (0.29), residues: 265 sheet: -0.53 (0.21), residues: 682 loop : -1.87 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG m 99 TYR 0.018 0.001 TYR g 34 PHE 0.026 0.001 PHE L 95 TRP 0.015 0.001 TRP n 53 HIS 0.005 0.001 HIS n 48 Details of bonding type rmsd covalent geometry : bond 0.00319 (15329) covalent geometry : angle 0.62171 (20841) SS BOND : bond 0.00277 ( 22) SS BOND : angle 1.26980 ( 44) hydrogen bonds : bond 0.29000 ( 572) hydrogen bonds : angle 9.74705 ( 1623) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 186 time to evaluate : 0.378 Fit side-chains REVERT: S 3 GLN cc_start: 0.8053 (tt0) cc_final: 0.7834 (tt0) REVERT: S 23 LYS cc_start: 0.7967 (tptt) cc_final: 0.7752 (mmmt) outliers start: 1 outliers final: 1 residues processed: 186 average time/residue: 0.1343 time to fit residues: 34.9696 Evaluate side-chains 170 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 169 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 21 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.0870 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 2.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 74 ASN n 76 GLN ** n 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN S 39 GLN ** S 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 202 ASN T 137 ASN ** T 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.219802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.189622 restraints weight = 18124.698| |-----------------------------------------------------------------------------| r_work (start): 0.4216 rms_B_bonded: 1.55 r_work: 0.3931 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3869 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 15351 Z= 0.143 Angle : 0.615 8.774 20885 Z= 0.324 Chirality : 0.044 0.208 2334 Planarity : 0.005 0.053 2641 Dihedral : 5.562 54.137 2213 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.86 % Allowed : 10.44 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.09 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.19), residues: 1895 helix: 2.18 (0.31), residues: 274 sheet: -0.25 (0.21), residues: 704 loop : -1.88 (0.19), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG T 62 TYR 0.019 0.001 TYR m 71 PHE 0.031 0.002 PHE L 95 TRP 0.024 0.001 TRP T 46 HIS 0.006 0.001 HIS n 173 Details of bonding type rmsd covalent geometry : bond 0.00320 (15329) covalent geometry : angle 0.61351 (20841) SS BOND : bond 0.00423 ( 22) SS BOND : angle 1.22336 ( 44) hydrogen bonds : bond 0.06091 ( 572) hydrogen bonds : angle 6.13285 ( 1623) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 173 time to evaluate : 0.574 Fit side-chains REVERT: d 117 LEU cc_start: 0.8363 (tm) cc_final: 0.8132 (tp) REVERT: n 44 GLN cc_start: 0.7401 (OUTLIER) cc_final: 0.7047 (tm130) REVERT: n 50 TYR cc_start: 0.6385 (OUTLIER) cc_final: 0.6145 (p90) REVERT: n 151 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7622 (mp0) REVERT: n 176 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8987 (tt) REVERT: n 221 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8030 (mt0) REVERT: e 109 ASN cc_start: 0.7945 (p0) cc_final: 0.7673 (m110) REVERT: e 114 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8250 (pt) REVERT: H 74 LYS cc_start: 0.7701 (tptt) cc_final: 0.7453 (mtmt) REVERT: S 34 MET cc_start: 0.8014 (mmt) cc_final: 0.7384 (mmt) REVERT: T 47 ILE cc_start: 0.8033 (mm) cc_final: 0.7709 (mt) outliers start: 48 outliers final: 17 residues processed: 207 average time/residue: 0.1270 time to fit residues: 37.6633 Evaluate side-chains 181 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 41 SER Chi-restraints excluded: chain f residue 74 ASN Chi-restraints excluded: chain g residue 41 SER Chi-restraints excluded: chain g residue 126 ILE Chi-restraints excluded: chain g residue 128 VAL Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain g residue 133 VAL Chi-restraints excluded: chain m residue 94 ILE Chi-restraints excluded: chain m residue 111 CYS Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain n residue 44 GLN Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 176 LEU Chi-restraints excluded: chain n residue 221 GLN Chi-restraints excluded: chain n residue 294 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain H residue 111 GLN Chi-restraints excluded: chain T residue 10 ILE Chi-restraints excluded: chain T residue 145 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 184 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 175 optimal weight: 10.0000 chunk 159 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 126 optimal weight: 0.8980 chunk 179 optimal weight: 7.9990 chunk 67 optimal weight: 8.9990 chunk 178 optimal weight: 20.0000 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: m 211 ASN ** n 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN ** S 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.214932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.187028 restraints weight = 18314.400| |-----------------------------------------------------------------------------| r_work (start): 0.4207 rms_B_bonded: 1.48 r_work: 0.3928 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3881 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 15351 Z= 0.238 Angle : 0.676 11.864 20885 Z= 0.355 Chirality : 0.047 0.212 2334 Planarity : 0.006 0.095 2641 Dihedral : 5.679 58.072 2210 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.80 % Favored : 94.14 % Rotamer: Outliers : 3.82 % Allowed : 11.63 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.09 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.19), residues: 1895 helix: 2.35 (0.31), residues: 274 sheet: -0.19 (0.20), residues: 686 loop : -1.92 (0.19), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG d 91 TYR 0.023 0.002 TYR n 282 PHE 0.046 0.002 PHE L 95 TRP 0.024 0.002 TRP T 46 HIS 0.012 0.002 HIS n 173 Details of bonding type rmsd covalent geometry : bond 0.00583 (15329) covalent geometry : angle 0.67439 (20841) SS BOND : bond 0.00565 ( 22) SS BOND : angle 1.31294 ( 44) hydrogen bonds : bond 0.06410 ( 572) hydrogen bonds : angle 5.77878 ( 1623) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 173 time to evaluate : 0.555 Fit side-chains REVERT: a 27 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8739 (mp) REVERT: d 117 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8194 (tp) REVERT: f 56 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8304 (tt0) REVERT: g 135 PHE cc_start: 0.6853 (OUTLIER) cc_final: 0.6559 (t80) REVERT: m 159 ASP cc_start: 0.7312 (OUTLIER) cc_final: 0.6955 (p0) REVERT: n 50 TYR cc_start: 0.6636 (OUTLIER) cc_final: 0.6358 (p90) REVERT: n 151 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7785 (mp0) REVERT: n 176 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.9031 (tt) REVERT: n 221 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8164 (mt0) REVERT: n 243 THR cc_start: 0.7946 (OUTLIER) cc_final: 0.7663 (m) REVERT: n 252 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.8120 (pt0) REVERT: e 109 ASN cc_start: 0.8101 (p0) cc_final: 0.7717 (m110) REVERT: e 114 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8376 (pt) REVERT: H 74 LYS cc_start: 0.7703 (tptt) cc_final: 0.7431 (mtmt) REVERT: T 46 TRP cc_start: 0.7591 (t-100) cc_final: 0.7364 (t60) outliers start: 64 outliers final: 31 residues processed: 219 average time/residue: 0.1297 time to fit residues: 40.8930 Evaluate side-chains 212 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 170 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 27 LEU Chi-restraints excluded: chain b residue 31 LEU Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain d residue 64 ILE Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain f residue 41 SER Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 56 GLU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain g residue 45 THR Chi-restraints excluded: chain g residue 126 ILE Chi-restraints excluded: chain g residue 128 VAL Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain g residue 133 VAL Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain m residue 40 ILE Chi-restraints excluded: chain m residue 94 ILE Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 159 ASP Chi-restraints excluded: chain m residue 183 ASP Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 79 VAL Chi-restraints excluded: chain n residue 176 LEU Chi-restraints excluded: chain n residue 215 VAL Chi-restraints excluded: chain n residue 221 GLN Chi-restraints excluded: chain n residue 243 THR Chi-restraints excluded: chain n residue 252 GLN Chi-restraints excluded: chain n residue 291 LEU Chi-restraints excluded: chain n residue 294 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 111 GLN Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain S residue 71 THR Chi-restraints excluded: chain S residue 111 GLN Chi-restraints excluded: chain T residue 10 ILE Chi-restraints excluded: chain T residue 20 THR Chi-restraints excluded: chain T residue 145 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 96 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 74 ASN ** n 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 36 GLN ** T 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 209 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.217283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.189479 restraints weight = 18368.756| |-----------------------------------------------------------------------------| r_work (start): 0.4218 rms_B_bonded: 1.42 r_work: 0.3929 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3886 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15351 Z= 0.148 Angle : 0.578 11.027 20885 Z= 0.304 Chirality : 0.043 0.203 2334 Planarity : 0.005 0.057 2641 Dihedral : 5.383 56.393 2210 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.01 % Favored : 94.93 % Rotamer: Outliers : 3.52 % Allowed : 13.06 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.09 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.19), residues: 1895 helix: 2.87 (0.31), residues: 274 sheet: -0.04 (0.20), residues: 691 loop : -1.75 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG m 99 TYR 0.023 0.001 TYR n 292 PHE 0.032 0.002 PHE L 95 TRP 0.015 0.001 TRP T 46 HIS 0.007 0.001 HIS n 173 Details of bonding type rmsd covalent geometry : bond 0.00350 (15329) covalent geometry : angle 0.57723 (20841) SS BOND : bond 0.00391 ( 22) SS BOND : angle 0.88409 ( 44) hydrogen bonds : bond 0.05083 ( 572) hydrogen bonds : angle 5.23192 ( 1623) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 179 time to evaluate : 0.675 Fit side-chains REVERT: g 135 PHE cc_start: 0.6668 (OUTLIER) cc_final: 0.6455 (t80) REVERT: m 159 ASP cc_start: 0.7094 (OUTLIER) cc_final: 0.6671 (p0) REVERT: n 50 TYR cc_start: 0.6584 (OUTLIER) cc_final: 0.6312 (p90) REVERT: n 151 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7752 (mp0) REVERT: n 221 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.7595 (mt0) REVERT: e 109 ASN cc_start: 0.8082 (p0) cc_final: 0.7667 (m110) REVERT: e 114 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8301 (pt) REVERT: H 74 LYS cc_start: 0.7668 (tptt) cc_final: 0.7453 (mtmt) REVERT: S 5 GLN cc_start: 0.7173 (mm-40) cc_final: 0.6915 (tp-100) REVERT: S 34 MET cc_start: 0.8114 (mmt) cc_final: 0.7654 (mmt) REVERT: T 46 TRP cc_start: 0.7507 (t-100) cc_final: 0.7250 (t-100) outliers start: 59 outliers final: 26 residues processed: 222 average time/residue: 0.1314 time to fit residues: 42.0215 Evaluate side-chains 202 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 171 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain f residue 41 SER Chi-restraints excluded: chain g residue 45 THR Chi-restraints excluded: chain g residue 126 ILE Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain g residue 133 VAL Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain m residue 40 ILE Chi-restraints excluded: chain m residue 45 CYS Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 159 ASP Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 79 VAL Chi-restraints excluded: chain n residue 130 LEU Chi-restraints excluded: chain n residue 215 VAL Chi-restraints excluded: chain n residue 221 GLN Chi-restraints excluded: chain n residue 252 GLN Chi-restraints excluded: chain n residue 300 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 73 LYS Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain H residue 111 GLN Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain S residue 71 THR Chi-restraints excluded: chain S residue 111 GLN Chi-restraints excluded: chain T residue 10 ILE Chi-restraints excluded: chain T residue 21 MET Chi-restraints excluded: chain T residue 131 VAL Chi-restraints excluded: chain T residue 145 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 49 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 175 optimal weight: 5.9990 chunk 134 optimal weight: 20.0000 chunk 90 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 160 optimal weight: 8.9990 chunk 92 optimal weight: 0.6980 chunk 47 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 74 ASN n 44 GLN ** n 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.215195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.184266 restraints weight = 18230.900| |-----------------------------------------------------------------------------| r_work (start): 0.4173 rms_B_bonded: 1.58 r_work: 0.3854 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3810 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15351 Z= 0.198 Angle : 0.621 10.545 20885 Z= 0.326 Chirality : 0.045 0.207 2334 Planarity : 0.005 0.048 2641 Dihedral : 5.453 51.394 2210 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.70 % Favored : 94.25 % Rotamer: Outliers : 3.58 % Allowed : 13.18 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.09 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.19), residues: 1895 helix: 2.84 (0.31), residues: 274 sheet: 0.04 (0.21), residues: 632 loop : -1.75 (0.18), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG m 99 TYR 0.023 0.002 TYR n 292 PHE 0.037 0.002 PHE L 95 TRP 0.015 0.002 TRP d 43 HIS 0.010 0.002 HIS n 173 Details of bonding type rmsd covalent geometry : bond 0.00485 (15329) covalent geometry : angle 0.62003 (20841) SS BOND : bond 0.00489 ( 22) SS BOND : angle 1.03001 ( 44) hydrogen bonds : bond 0.05439 ( 572) hydrogen bonds : angle 5.16896 ( 1623) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 189 time to evaluate : 0.604 Fit side-chains revert: symmetry clash REVERT: m 143 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7739 (tp40) REVERT: m 211 ASN cc_start: 0.8175 (t0) cc_final: 0.7936 (t0) REVERT: n 50 TYR cc_start: 0.6653 (OUTLIER) cc_final: 0.6255 (p90) REVERT: n 151 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7907 (mp0) REVERT: n 221 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.7899 (mt0) REVERT: n 243 THR cc_start: 0.8043 (OUTLIER) cc_final: 0.7738 (m) REVERT: n 252 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.8048 (pt0) REVERT: n 257 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.7548 (mt-10) REVERT: e 109 ASN cc_start: 0.8178 (p0) cc_final: 0.7724 (m110) REVERT: e 114 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8361 (pt) REVERT: S 5 GLN cc_start: 0.7258 (mm-40) cc_final: 0.6918 (tp-100) REVERT: S 34 MET cc_start: 0.8240 (mmt) cc_final: 0.7815 (mmt) REVERT: T 46 TRP cc_start: 0.7562 (t-100) cc_final: 0.7303 (t-100) outliers start: 60 outliers final: 36 residues processed: 232 average time/residue: 0.1315 time to fit residues: 43.9000 Evaluate side-chains 226 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 183 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 31 LEU Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain f residue 41 SER Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain g residue 41 SER Chi-restraints excluded: chain g residue 45 THR Chi-restraints excluded: chain g residue 126 ILE Chi-restraints excluded: chain g residue 128 VAL Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain g residue 133 VAL Chi-restraints excluded: chain m residue 40 ILE Chi-restraints excluded: chain m residue 45 CYS Chi-restraints excluded: chain m residue 94 ILE Chi-restraints excluded: chain m residue 143 GLN Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain m residue 183 ASP Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 215 VAL Chi-restraints excluded: chain n residue 221 GLN Chi-restraints excluded: chain n residue 243 THR Chi-restraints excluded: chain n residue 252 GLN Chi-restraints excluded: chain n residue 257 GLU Chi-restraints excluded: chain n residue 291 LEU Chi-restraints excluded: chain n residue 294 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 123 MET Chi-restraints excluded: chain e residue 140 ILE Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 111 GLN Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain S residue 71 THR Chi-restraints excluded: chain S residue 111 GLN Chi-restraints excluded: chain S residue 142 VAL Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain T residue 10 ILE Chi-restraints excluded: chain T residue 21 MET Chi-restraints excluded: chain T residue 131 VAL Chi-restraints excluded: chain T residue 145 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 154 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 116 optimal weight: 7.9990 chunk 146 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 169 optimal weight: 0.9980 chunk 152 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 118 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 44 GLN ** n 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 197 HIS ** 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 = 0.4431 r_free = 0.4431 target = 0.211441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.174447 restraints weight = 17839.221| |-----------------------------------------------------------------------------| r_work (start): 0.4095 rms_B_bonded: 1.92 r_work: 0.3758 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work: 0.3701 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 15351 Z= 0.269 Angle : 0.694 12.022 20885 Z= 0.362 Chirality : 0.047 0.221 2334 Planarity : 0.006 0.068 2641 Dihedral : 5.718 51.658 2210 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.49 % Favored : 93.46 % Rotamer: Outliers : 3.76 % Allowed : 14.43 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.09 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.19), residues: 1895 helix: 2.61 (0.30), residues: 273 sheet: 0.02 (0.21), residues: 619 loop : -1.86 (0.18), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG d 91 TYR 0.024 0.002 TYR n 292 PHE 0.046 0.002 PHE L 95 TRP 0.017 0.002 TRP n 178 HIS 0.012 0.002 HIS n 173 Details of bonding type rmsd covalent geometry : bond 0.00667 (15329) covalent geometry : angle 0.69202 (20841) SS BOND : bond 0.00589 ( 22) SS BOND : angle 1.28738 ( 44) hydrogen bonds : bond 0.06048 ( 572) hydrogen bonds : angle 5.23184 ( 1623) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 190 time to evaluate : 0.587 Fit side-chains REVERT: g 135 PHE cc_start: 0.6976 (t80) cc_final: 0.6709 (t80) REVERT: m 143 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.7971 (tp40) REVERT: m 211 ASN cc_start: 0.8287 (t0) cc_final: 0.8047 (t0) REVERT: m 256 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8286 (tt) REVERT: n 50 TYR cc_start: 0.6754 (OUTLIER) cc_final: 0.6239 (p90) REVERT: n 151 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8079 (mp0) REVERT: n 172 ASP cc_start: 0.8708 (p0) cc_final: 0.8437 (p0) REVERT: n 240 ASP cc_start: 0.7959 (m-30) cc_final: 0.7662 (t70) REVERT: n 243 THR cc_start: 0.8193 (OUTLIER) cc_final: 0.7860 (m) REVERT: n 257 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.7580 (mt-10) REVERT: e 64 LYS cc_start: 0.8372 (tttt) cc_final: 0.7832 (ptpt) REVERT: e 109 ASN cc_start: 0.8311 (p0) cc_final: 0.7770 (m110) REVERT: e 114 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8408 (pt) REVERT: S 5 GLN cc_start: 0.7351 (mm-40) cc_final: 0.6960 (tp-100) REVERT: S 34 MET cc_start: 0.8439 (mmt) cc_final: 0.8072 (mmt) REVERT: T 46 TRP cc_start: 0.7709 (t-100) cc_final: 0.7376 (t-100) outliers start: 63 outliers final: 39 residues processed: 235 average time/residue: 0.1320 time to fit residues: 44.4079 Evaluate side-chains 228 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 183 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain b residue 31 LEU Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain f residue 41 SER Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain g residue 45 THR Chi-restraints excluded: chain g residue 126 ILE Chi-restraints excluded: chain g residue 128 VAL Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain g residue 133 VAL Chi-restraints excluded: chain m residue 45 CYS Chi-restraints excluded: chain m residue 94 ILE Chi-restraints excluded: chain m residue 143 GLN Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 159 ASP Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain m residue 183 ASP Chi-restraints excluded: chain m residue 256 LEU Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 215 VAL Chi-restraints excluded: chain n residue 243 THR Chi-restraints excluded: chain n residue 257 GLU Chi-restraints excluded: chain n residue 291 LEU Chi-restraints excluded: chain n residue 294 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 73 LYS Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 123 MET Chi-restraints excluded: chain e residue 140 ILE Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 111 GLN Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain S residue 71 THR Chi-restraints excluded: chain S residue 111 GLN Chi-restraints excluded: chain S residue 142 VAL Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain T residue 10 ILE Chi-restraints excluded: chain T residue 131 VAL Chi-restraints excluded: chain T residue 145 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 45 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 180 optimal weight: 20.0000 chunk 108 optimal weight: 0.6980 chunk 155 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 chunk 172 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: n 44 GLN ** n 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 197 HIS ** 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 = 0.4285 r_free = 0.4285 target = 0.205067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.177204 restraints weight = 17906.718| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 1.47 r_work: 0.3634 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3565 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15351 Z= 0.137 Angle : 0.577 10.677 20885 Z= 0.303 Chirality : 0.043 0.210 2334 Planarity : 0.005 0.045 2641 Dihedral : 5.384 49.004 2210 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.01 % Favored : 94.93 % Rotamer: Outliers : 3.04 % Allowed : 15.32 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.09 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.19), residues: 1895 helix: 3.01 (0.31), residues: 278 sheet: 0.20 (0.21), residues: 619 loop : -1.75 (0.18), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG m 99 TYR 0.022 0.001 TYR n 292 PHE 0.026 0.001 PHE L 95 TRP 0.015 0.001 TRP d 43 HIS 0.007 0.001 HIS n 173 Details of bonding type rmsd covalent geometry : bond 0.00322 (15329) covalent geometry : angle 0.57319 (20841) SS BOND : bond 0.00396 ( 22) SS BOND : angle 1.51146 ( 44) hydrogen bonds : bond 0.04752 ( 572) hydrogen bonds : angle 4.94220 ( 1623) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 183 time to evaluate : 0.568 Fit side-chains REVERT: g 135 PHE cc_start: 0.6777 (t80) cc_final: 0.6456 (t80) REVERT: m 143 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7699 (tp40) REVERT: m 168 GLN cc_start: 0.7407 (tp40) cc_final: 0.7177 (tp-100) REVERT: m 211 ASN cc_start: 0.8260 (t0) cc_final: 0.8010 (t0) REVERT: n 50 TYR cc_start: 0.6613 (OUTLIER) cc_final: 0.6177 (p90) REVERT: n 151 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7809 (mp0) REVERT: n 172 ASP cc_start: 0.8618 (p0) cc_final: 0.8390 (p0) REVERT: n 240 ASP cc_start: 0.7741 (m-30) cc_final: 0.7477 (t70) REVERT: n 243 THR cc_start: 0.7857 (OUTLIER) cc_final: 0.7564 (m) REVERT: e 109 ASN cc_start: 0.7890 (p0) cc_final: 0.7480 (m110) REVERT: e 114 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8290 (pt) REVERT: S 5 GLN cc_start: 0.7326 (mm-40) cc_final: 0.6949 (tp-100) REVERT: S 34 MET cc_start: 0.8270 (mmt) cc_final: 0.7931 (mmt) REVERT: T 46 TRP cc_start: 0.7682 (t-100) cc_final: 0.7325 (t-100) outliers start: 51 outliers final: 35 residues processed: 221 average time/residue: 0.1316 time to fit residues: 42.1749 Evaluate side-chains 220 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 181 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain d residue 82 LYS Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain f residue 41 SER Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain g residue 45 THR Chi-restraints excluded: chain g residue 126 ILE Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain g residue 133 VAL Chi-restraints excluded: chain m residue 40 ILE Chi-restraints excluded: chain m residue 45 CYS Chi-restraints excluded: chain m residue 143 GLN Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain m residue 183 ASP Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 215 VAL Chi-restraints excluded: chain n residue 243 THR Chi-restraints excluded: chain n residue 263 ASP Chi-restraints excluded: chain n residue 291 LEU Chi-restraints excluded: chain n residue 300 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 111 GLN Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain S residue 71 THR Chi-restraints excluded: chain S residue 111 GLN Chi-restraints excluded: chain S residue 142 VAL Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain T residue 10 ILE Chi-restraints excluded: chain T residue 21 MET Chi-restraints excluded: chain T residue 131 VAL Chi-restraints excluded: chain T residue 145 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 85 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 79 optimal weight: 0.0470 chunk 151 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 180 optimal weight: 9.9990 chunk 112 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 overall best weight: 0.9680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: n 44 GLN ** n 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 197 HIS ** 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 = 0.4267 r_free = 0.4267 target = 0.203405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.173409 restraints weight = 17942.752| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 1.57 r_work: 0.3474 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 15351 Z= 0.159 Angle : 0.601 10.052 20885 Z= 0.315 Chirality : 0.044 0.224 2334 Planarity : 0.005 0.046 2641 Dihedral : 5.392 49.040 2210 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.80 % Favored : 94.14 % Rotamer: Outliers : 3.40 % Allowed : 15.68 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.09 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.19), residues: 1895 helix: 3.07 (0.30), residues: 278 sheet: 0.13 (0.21), residues: 637 loop : -1.67 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG m 99 TYR 0.021 0.002 TYR n 292 PHE 0.031 0.002 PHE L 95 TRP 0.014 0.001 TRP d 43 HIS 0.009 0.001 HIS n 173 Details of bonding type rmsd covalent geometry : bond 0.00383 (15329) covalent geometry : angle 0.59858 (20841) SS BOND : bond 0.00420 ( 22) SS BOND : angle 1.32710 ( 44) hydrogen bonds : bond 0.04853 ( 572) hydrogen bonds : angle 4.86539 ( 1623) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 180 time to evaluate : 0.537 Fit side-chains REVERT: g 135 PHE cc_start: 0.6897 (t80) cc_final: 0.6535 (t80) REVERT: m 143 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7993 (tt0) REVERT: m 168 GLN cc_start: 0.7711 (tp40) cc_final: 0.7458 (tp-100) REVERT: n 50 TYR cc_start: 0.6668 (OUTLIER) cc_final: 0.6079 (p90) REVERT: n 151 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8222 (mp0) REVERT: n 240 ASP cc_start: 0.8065 (m-30) cc_final: 0.7717 (t70) REVERT: n 243 THR cc_start: 0.8145 (OUTLIER) cc_final: 0.7785 (m) REVERT: n 245 ASP cc_start: 0.6927 (p0) cc_final: 0.6709 (p0) REVERT: n 257 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.7592 (mt-10) REVERT: e 109 ASN cc_start: 0.8188 (p0) cc_final: 0.7656 (m110) REVERT: e 114 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8311 (pt) REVERT: S 5 GLN cc_start: 0.7682 (mm-40) cc_final: 0.7082 (tp-100) REVERT: S 34 MET cc_start: 0.8568 (mmt) cc_final: 0.8270 (mmt) REVERT: T 46 TRP cc_start: 0.7829 (t-100) cc_final: 0.7436 (t-100) outliers start: 57 outliers final: 39 residues processed: 222 average time/residue: 0.1255 time to fit residues: 40.3853 Evaluate side-chains 219 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 174 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain f residue 41 SER Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain g residue 41 SER Chi-restraints excluded: chain g residue 45 THR Chi-restraints excluded: chain g residue 126 ILE Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain g residue 133 VAL Chi-restraints excluded: chain m residue 40 ILE Chi-restraints excluded: chain m residue 45 CYS Chi-restraints excluded: chain m residue 143 GLN Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 159 ASP Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain m residue 183 ASP Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 151 GLU Chi-restraints excluded: chain n residue 215 VAL Chi-restraints excluded: chain n residue 243 THR Chi-restraints excluded: chain n residue 257 GLU Chi-restraints excluded: chain n residue 263 ASP Chi-restraints excluded: chain n residue 291 LEU Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 123 MET Chi-restraints excluded: chain e residue 140 ILE Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 111 GLN Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain S residue 71 THR Chi-restraints excluded: chain S residue 111 GLN Chi-restraints excluded: chain S residue 142 VAL Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain T residue 10 ILE Chi-restraints excluded: chain T residue 21 MET Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain T residue 131 VAL Chi-restraints excluded: chain T residue 145 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 54 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 122 optimal weight: 6.9990 chunk 67 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 171 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 185 optimal weight: 30.0000 chunk 139 optimal weight: 0.0040 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** n 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN ** S 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 197 HIS ** 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 = 0.4280 r_free = 0.4280 target = 0.204733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.177595 restraints weight = 17957.806| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 1.35 r_work: 0.3561 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15351 Z= 0.125 Angle : 0.562 9.528 20885 Z= 0.294 Chirality : 0.042 0.202 2334 Planarity : 0.004 0.048 2641 Dihedral : 5.288 48.744 2210 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.01 % Favored : 94.93 % Rotamer: Outliers : 2.74 % Allowed : 15.80 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.09 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.19), residues: 1895 helix: 3.29 (0.30), residues: 278 sheet: 0.26 (0.21), residues: 626 loop : -1.59 (0.18), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG m 99 TYR 0.020 0.001 TYR n 292 PHE 0.024 0.001 PHE L 95 TRP 0.013 0.001 TRP d 43 HIS 0.007 0.001 HIS n 173 Details of bonding type rmsd covalent geometry : bond 0.00295 (15329) covalent geometry : angle 0.56050 (20841) SS BOND : bond 0.00315 ( 22) SS BOND : angle 1.10958 ( 44) hydrogen bonds : bond 0.04352 ( 572) hydrogen bonds : angle 4.68431 ( 1623) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 180 time to evaluate : 0.591 Fit side-chains REVERT: g 135 PHE cc_start: 0.6537 (t80) cc_final: 0.6261 (t80) REVERT: m 159 ASP cc_start: 0.7067 (OUTLIER) cc_final: 0.5818 (p0) REVERT: m 168 GLN cc_start: 0.7582 (tp40) cc_final: 0.7337 (tp-100) REVERT: n 44 GLN cc_start: 0.7811 (OUTLIER) cc_final: 0.7142 (tm130) REVERT: n 50 TYR cc_start: 0.6592 (OUTLIER) cc_final: 0.6130 (p90) REVERT: n 151 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7953 (mp0) REVERT: n 240 ASP cc_start: 0.7914 (m-30) cc_final: 0.7607 (t70) REVERT: e 109 ASN cc_start: 0.7992 (p0) cc_final: 0.7526 (m110) REVERT: e 114 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8275 (pt) REVERT: S 5 GLN cc_start: 0.7525 (mm-40) cc_final: 0.7011 (tp-100) REVERT: S 34 MET cc_start: 0.8400 (mmt) cc_final: 0.8084 (mmt) REVERT: T 46 TRP cc_start: 0.7743 (t-100) cc_final: 0.7421 (t-100) outliers start: 46 outliers final: 36 residues processed: 216 average time/residue: 0.1295 time to fit residues: 40.1092 Evaluate side-chains 215 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 174 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain d residue 82 LYS Chi-restraints excluded: chain f residue 41 SER Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain g residue 41 SER Chi-restraints excluded: chain g residue 45 THR Chi-restraints excluded: chain g residue 126 ILE Chi-restraints excluded: chain g residue 128 VAL Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain m residue 40 ILE Chi-restraints excluded: chain m residue 45 CYS Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 159 ASP Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain m residue 183 ASP Chi-restraints excluded: chain n residue 44 GLN Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 151 GLU Chi-restraints excluded: chain n residue 215 VAL Chi-restraints excluded: chain n residue 263 ASP Chi-restraints excluded: chain n residue 291 LEU Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 88 SER Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 111 GLN Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain S residue 71 THR Chi-restraints excluded: chain S residue 111 GLN Chi-restraints excluded: chain S residue 142 VAL Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain T residue 21 MET Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain T residue 131 VAL Chi-restraints excluded: chain T residue 145 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 79 optimal weight: 0.0020 chunk 20 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 184 optimal weight: 20.0000 chunk 76 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** n 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 197 HIS ** 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 = 0.4286 r_free = 0.4286 target = 0.205381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.178304 restraints weight = 17982.044| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 1.36 r_work: 0.3632 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3499 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15351 Z= 0.122 Angle : 0.558 9.137 20885 Z= 0.291 Chirality : 0.042 0.208 2334 Planarity : 0.004 0.051 2641 Dihedral : 5.158 48.557 2210 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.22 % Favored : 94.72 % Rotamer: Outliers : 2.50 % Allowed : 16.46 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.09 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.20), residues: 1895 helix: 3.43 (0.30), residues: 278 sheet: 0.34 (0.21), residues: 626 loop : -1.53 (0.19), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG m 99 TYR 0.020 0.001 TYR n 292 PHE 0.025 0.001 PHE L 95 TRP 0.013 0.001 TRP d 43 HIS 0.007 0.001 HIS n 173 Details of bonding type rmsd covalent geometry : bond 0.00286 (15329) covalent geometry : angle 0.55583 (20841) SS BOND : bond 0.00332 ( 22) SS BOND : angle 1.11691 ( 44) hydrogen bonds : bond 0.04208 ( 572) hydrogen bonds : angle 4.56656 ( 1623) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 167 time to evaluate : 0.614 Fit side-chains REVERT: g 135 PHE cc_start: 0.6458 (t80) cc_final: 0.6238 (t80) REVERT: m 47 TYR cc_start: 0.6323 (p90) cc_final: 0.6083 (p90) REVERT: m 159 ASP cc_start: 0.6987 (OUTLIER) cc_final: 0.5735 (p0) REVERT: m 168 GLN cc_start: 0.7541 (tp40) cc_final: 0.7292 (tp-100) REVERT: n 50 TYR cc_start: 0.6575 (OUTLIER) cc_final: 0.6152 (p90) REVERT: n 151 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7838 (mp0) REVERT: n 257 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7610 (mt-10) REVERT: e 109 ASN cc_start: 0.7974 (p0) cc_final: 0.7530 (m110) REVERT: e 114 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8274 (pt) REVERT: S 5 GLN cc_start: 0.7385 (mm-40) cc_final: 0.6969 (tp-100) REVERT: S 34 MET cc_start: 0.8396 (mmt) cc_final: 0.8078 (mmt) REVERT: T 46 TRP cc_start: 0.7662 (t-100) cc_final: 0.7373 (t-100) outliers start: 42 outliers final: 32 residues processed: 198 average time/residue: 0.1334 time to fit residues: 37.9959 Evaluate side-chains 202 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 165 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain f residue 41 SER Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain g residue 41 SER Chi-restraints excluded: chain g residue 45 THR Chi-restraints excluded: chain g residue 126 ILE Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain m residue 40 ILE Chi-restraints excluded: chain m residue 45 CYS Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 159 ASP Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain m residue 183 ASP Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 151 GLU Chi-restraints excluded: chain n residue 215 VAL Chi-restraints excluded: chain n residue 257 GLU Chi-restraints excluded: chain n residue 263 ASP Chi-restraints excluded: chain n residue 291 LEU Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 111 GLN Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain S residue 71 THR Chi-restraints excluded: chain S residue 111 GLN Chi-restraints excluded: chain S residue 142 VAL Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain T residue 21 MET Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain T residue 131 VAL Chi-restraints excluded: chain T residue 145 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 96 optimal weight: 0.5980 chunk 134 optimal weight: 30.0000 chunk 112 optimal weight: 0.9990 chunk 163 optimal weight: 20.0000 chunk 81 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 174 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: n 44 GLN ** n 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN ** S 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.202881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.175518 restraints weight = 17869.431| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 1.34 r_work: 0.3410 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 15351 Z= 0.195 Angle : 0.625 10.152 20885 Z= 0.325 Chirality : 0.045 0.206 2334 Planarity : 0.005 0.057 2641 Dihedral : 5.391 49.422 2210 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.75 % Favored : 94.20 % Rotamer: Outliers : 2.74 % Allowed : 16.28 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.09 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.19), residues: 1895 helix: 3.14 (0.30), residues: 278 sheet: 0.26 (0.21), residues: 632 loop : -1.62 (0.18), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG m 99 TYR 0.020 0.002 TYR n 292 PHE 0.039 0.002 PHE L 95 TRP 0.013 0.002 TRP d 43 HIS 0.009 0.001 HIS n 173 Details of bonding type rmsd covalent geometry : bond 0.00480 (15329) covalent geometry : angle 0.62194 (20841) SS BOND : bond 0.00498 ( 22) SS BOND : angle 1.40622 ( 44) hydrogen bonds : bond 0.05030 ( 572) hydrogen bonds : angle 4.71067 ( 1623) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4422.87 seconds wall clock time: 76 minutes 37.01 seconds (4597.01 seconds total)