Starting phenix.real_space_refine on Wed Feb 4 16:48:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iru_60821/02_2026/9iru_60821.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iru_60821/02_2026/9iru_60821.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9iru_60821/02_2026/9iru_60821.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iru_60821/02_2026/9iru_60821.map" model { file = "/net/cci-nas-00/data/ceres_data/9iru_60821/02_2026/9iru_60821.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iru_60821/02_2026/9iru_60821.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 68 5.16 5 C 7428 2.51 5 N 1925 2.21 5 O 2260 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 11681 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1632 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 201} Chain: "B" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1691 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 212} Chain: "a" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 260 Classifications: {'peptide': 33} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 31} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "b" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 227 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 27} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 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: "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: "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: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 888 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 110} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 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: 2245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2245 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 271} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "g" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.52, per 1000 atoms: 0.22 Number of scatterers: 11681 At special positions: 0 Unit cell: (108.36, 125.56, 158.24, 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 68 16.00 O 2260 8.00 N 1925 7.00 C 7428 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 108 " distance=2.04 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 214 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 115 " distance=2.03 Simple disulfide: pdb=" SG CYS B 166 " - pdb=" SG CYS B 222 " distance=2.03 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 e 49 " - pdb=" SG CYS e 98 " distance=2.04 Simple disulfide: pdb=" SG CYS f 49 " - pdb=" SG CYS f 98 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS m 45 " - pdb=" SG CYS m 111 " distance=2.03 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 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: 0.86 Conformation dependent library (CDL) restraints added in 547.1 milliseconds 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2780 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 28 sheets defined 19.8% alpha, 30.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 141 through 146 Processing helix chain 'A' and resid 203 through 207 Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 81 through 84 removed outlier: 4.262A pdb=" N LYS B 84 " --> pdb=" O GLU B 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 81 through 84' Processing helix chain 'B' and resid 213 through 215 No H-bonds generated for 'chain 'B' and resid 213 through 215' Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'a' and resid 28 through 54 removed outlier: 4.256A pdb=" N CYS a 32 " --> pdb=" O ASP a 28 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU a 35 " --> pdb=" O LEU a 31 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE a 38 " --> pdb=" O LEU a 34 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU a 39 " --> pdb=" O LEU a 35 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL a 53 " --> pdb=" O LEU a 49 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS a 54 " --> pdb=" O PHE a 50 " (cutoff:3.500A) Processing helix chain 'b' and resid 31 through 54 removed outlier: 3.532A pdb=" N ASP b 36 " --> pdb=" O CYS b 32 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY b 43 " --> pdb=" O LEU b 39 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR b 47 " --> pdb=" O GLY b 43 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL b 53 " --> pdb=" O LEU b 49 " (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 124 removed outlier: 3.541A pdb=" N VAL d 104 " --> pdb=" O ASP d 100 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA d 105 " --> pdb=" O PRO d 101 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY d 106 " --> pdb=" O ALA d 102 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR d 110 " --> pdb=" O GLY d 106 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE d 123 " --> pdb=" O ALA d 119 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N CYS d 124 " --> pdb=" O LEU d 120 " (cutoff:3.500A) Processing helix chain 'e' and resid 104 through 108 removed outlier: 3.610A pdb=" N ALA e 108 " --> pdb=" O PRO e 105 " (cutoff:3.500A) Processing helix chain 'e' and resid 126 through 153 Processing helix chain 'f' and resid 126 through 142 removed outlier: 3.564A pdb=" N ALA f 131 " --> pdb=" O VAL f 127 " (cutoff:3.500A) Processing helix chain 'f' and resid 145 through 154 Processing helix chain 'g' and resid 111 through 138 removed outlier: 3.776A pdb=" N VAL g 128 " --> pdb=" O VAL g 124 " (cutoff:3.500A) Processing helix chain 'm' and resid 102 through 106 removed outlier: 3.568A pdb=" N SER m 106 " --> pdb=" O PRO m 103 " (cutoff:3.500A) Processing helix chain 'm' and resid 228 through 233 Processing helix chain 'm' and resid 239 through 272 removed outlier: 3.581A pdb=" N ASN m 243 " --> pdb=" O ASP m 239 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE m 244 " --> pdb=" O THR m 240 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL m 249 " --> pdb=" O GLN m 245 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER m 272 " --> pdb=" O LEU m 268 " (cutoff:3.500A) Processing helix chain 'n' and resid 101 through 105 removed outlier: 3.965A pdb=" N THR n 105 " --> pdb=" O PRO n 102 " (cutoff:3.500A) Processing helix chain 'n' and resid 150 through 158 removed outlier: 3.541A 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 307 removed outlier: 4.140A pdb=" N GLN n 273 " --> pdb=" O GLU n 269 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE n 280 " --> pdb=" O LEU n 276 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU n 281 " --> pdb=" O SER n 277 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS n 306 " --> pdb=" O MET n 302 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27 removed outlier: 3.586A pdb=" N SER A 27 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER A 42 " --> pdb=" O SER A 27 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE A 95 " --> pdb=" O VAL A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 32 removed outlier: 3.626A pdb=" N GLU A 125 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 68 removed outlier: 6.646A pdb=" N TRP A 55 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS A 54 " --> pdb=" O GLN A 109 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 134 through 138 removed outlier: 3.572A pdb=" N LEU A 156 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 195 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 165 through 170 Processing sheet with id=AA6, first strand: chain 'B' and resid 37 through 40 removed outlier: 3.606A pdb=" N THR B 97 " --> pdb=" O ASP B 92 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 76 through 79 removed outlier: 3.852A pdb=" N SER B 76 " --> pdb=" O LEU B 71 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TRP B 55 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU B 69 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE B 53 " --> pdb=" O GLU B 69 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N LEU B 71 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N TYR B 51 " --> pdb=" O LEU B 71 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR B 113 " --> pdb=" O THR B 133 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 150 removed outlier: 3.582A pdb=" N SER B 206 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N TYR B 202 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 176 through 180 removed outlier: 3.982A pdb=" N THR B 177 " --> pdb=" O ASN B 225 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N CYS B 222 " --> pdb=" O LYS B 235 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS B 235 " --> pdb=" O CYS B 222 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'd' and resid 26 through 28 removed outlier: 6.001A pdb=" N VAL d 33 " --> pdb=" O LEU d 60 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'd' and resid 42 through 46 removed outlier: 6.526A pdb=" N ILE d 70 " --> pdb=" O VAL d 44 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLY d 46 " --> pdb=" O ARG d 68 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ARG d 68 " --> pdb=" O GLY d 46 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS d 73 " --> pdb=" O SER d 84 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER d 84 " --> pdb=" O CYS d 73 " (cutoff:3.500A) removed outlier: 9.218A pdb=" N TYR e 111 " --> pdb=" O GLU d 83 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N THR d 85 " --> pdb=" O TYR e 111 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N TYR e 113 " --> pdb=" O THR d 85 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLN d 87 " --> pdb=" O TYR e 113 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ARG e 115 " --> pdb=" O GLN d 87 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N HIS d 89 " --> pdb=" O ARG e 115 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ARG e 117 " --> pdb=" O HIS d 89 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ARG d 91 " --> pdb=" O ARG e 117 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N TRP e 59 " --> pdb=" O ILE e 66 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'd' and resid 96 through 98 removed outlier: 3.617A pdb=" N VAL d 97 " --> pdb=" O MET e 123 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'e' and resid 37 through 40 removed outlier: 3.681A pdb=" N LYS e 37 " --> pdb=" O THR e 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'f' and resid 37 through 41 Processing sheet with id=AB6, first strand: chain 'f' and resid 57 through 61 removed outlier: 3.865A pdb=" N LEU f 114 " --> pdb=" O GLY f 94 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG g 102 " --> pdb=" O ARG f 115 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY g 83 " --> pdb=" O VAL g 99 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN g 86 " --> pdb=" O PHE g 56 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TRP g 55 " --> pdb=" O GLY g 63 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY g 63 " --> pdb=" O TRP g 55 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N LYS g 57 " --> pdb=" O MET g 61 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N MET g 61 " --> pdb=" O LYS g 57 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'f' and resid 122 through 124 removed outlier: 3.696A pdb=" N MET f 123 " --> pdb=" O ILE g 108 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE g 108 " --> pdb=" O MET f 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'g' and resid 31 through 34 Processing sheet with id=AB9, first strand: chain 'm' and resid 33 through 36 removed outlier: 3.567A pdb=" N TYR m 109 " --> pdb=" O THR m 126 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER m 114 " --> pdb=" O TYR m 54 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N MET m 70 " --> pdb=" O TRP m 57 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ARG m 59 " --> pdb=" O LEU m 68 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N LEU m 68 " --> pdb=" O ARG m 59 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'm' and resid 33 through 36 removed outlier: 3.567A pdb=" N TYR m 109 " --> pdb=" O THR m 126 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'm' and resid 41 through 46 Processing sheet with id=AC3, first strand: chain 'm' and resid 141 through 143 removed outlier: 3.571A pdb=" N SER m 153 " --> pdb=" O SER m 198 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER m 198 " --> pdb=" O SER m 153 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'm' and resid 141 through 143 removed outlier: 3.571A pdb=" N SER m 153 " --> pdb=" O SER m 198 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER m 198 " --> pdb=" O SER m 153 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'n' and resid 24 through 26 removed outlier: 3.716A pdb=" N THR n 26 " --> pdb=" O GLN n 41 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'n' and resid 32 through 33 removed outlier: 6.724A pdb=" N LEU n 32 " --> pdb=" O THR n 133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'n' and resid 73 through 76 removed outlier: 7.777A pdb=" N ILE n 73 " --> pdb=" O VAL n 69 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL n 69 " --> pdb=" O ILE n 73 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TYR n 67 " --> pdb=" O ASP n 75 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LEU n 64 " --> pdb=" O ARG n 55 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ARG n 55 " --> pdb=" O LEU n 64 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N HIS n 66 " --> pdb=" O TRP n 53 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET n 51 " --> pdb=" O SER n 68 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL n 107 " --> pdb=" O GLN n 56 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'n' and resid 143 through 147 removed outlier: 5.849A pdb=" N TYR n 207 " --> pdb=" O GLY n 168 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'n' and resid 143 through 147 removed outlier: 5.849A pdb=" N TYR n 207 " --> pdb=" O GLY n 168 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'n' and resid 183 through 184 463 hydrogen bonds defined for protein. 1248 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: 1.66 Time building geometry restraints manager: 1.15 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: 3725 1.34 - 1.46: 2752 1.46 - 1.58: 5372 1.58 - 1.70: 1 1.70 - 1.82: 94 Bond restraints: 11944 Sorted by residual: bond pdb=" CG PRO m 32 " pdb=" CD PRO m 32 " ideal model delta sigma weight residual 1.503 1.384 0.119 3.40e-02 8.65e+02 1.22e+01 bond pdb=" CB PRO m 32 " pdb=" CG PRO m 32 " ideal model delta sigma weight residual 1.492 1.638 -0.146 5.00e-02 4.00e+02 8.53e+00 bond pdb=" N SER B 153 " pdb=" CA SER B 153 " ideal model delta sigma weight residual 1.454 1.489 -0.034 1.31e-02 5.83e+03 6.90e+00 bond pdb=" N ALA B 151 " pdb=" CA ALA B 151 " ideal model delta sigma weight residual 1.453 1.481 -0.028 1.25e-02 6.40e+03 5.09e+00 bond pdb=" C ALA B 151 " pdb=" N PRO B 152 " ideal model delta sigma weight residual 1.331 1.354 -0.022 1.21e-02 6.83e+03 3.45e+00 ... (remaining 11939 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.61: 16196 4.61 - 9.22: 17 9.22 - 13.82: 4 13.82 - 18.43: 0 18.43 - 23.04: 1 Bond angle restraints: 16218 Sorted by residual: angle pdb=" CA PRO m 32 " pdb=" N PRO m 32 " pdb=" CD PRO m 32 " ideal model delta sigma weight residual 112.00 88.96 23.04 1.40e+00 5.10e-01 2.71e+02 angle pdb=" N PRO m 32 " pdb=" CD PRO m 32 " pdb=" CG PRO m 32 " ideal model delta sigma weight residual 103.20 92.20 11.00 1.50e+00 4.44e-01 5.38e+01 angle pdb=" CA PRO m 32 " pdb=" CB PRO m 32 " pdb=" CG PRO m 32 " ideal model delta sigma weight residual 104.50 93.85 10.65 1.90e+00 2.77e-01 3.14e+01 angle pdb=" C LYS B 169 " pdb=" N ASP B 170 " pdb=" CA ASP B 170 " ideal model delta sigma weight residual 122.46 130.11 -7.65 1.41e+00 5.03e-01 2.94e+01 angle pdb=" C ALA m 204 " pdb=" N CYS m 205 " pdb=" CA CYS m 205 " ideal model delta sigma weight residual 122.95 116.52 6.43 1.66e+00 3.63e-01 1.50e+01 ... (remaining 16213 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.94: 6708 23.94 - 47.88: 440 47.88 - 71.82: 93 71.82 - 95.75: 9 95.75 - 119.69: 4 Dihedral angle restraints: 7254 sinusoidal: 2915 harmonic: 4339 Sorted by residual: dihedral pdb=" CB CYS d 37 " pdb=" SG CYS d 37 " pdb=" SG CYS d 73 " pdb=" CB CYS d 73 " ideal model delta sinusoidal sigma weight residual -86.00 -164.32 78.32 1 1.00e+01 1.00e-02 7.66e+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 93.00 168.47 -75.47 1 1.00e+01 1.00e-02 7.19e+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 -153.26 67.26 1 1.00e+01 1.00e-02 5.89e+01 ... (remaining 7251 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1295 0.040 - 0.081: 382 0.081 - 0.121: 128 0.121 - 0.161: 13 0.161 - 0.202: 2 Chirality restraints: 1820 Sorted by residual: 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 2.31 0.20 2.00e-01 2.50e+01 1.02e+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 9.45e-01 chirality pdb=" CA ASP B 170 " pdb=" N ASP B 170 " pdb=" C ASP B 170 " pdb=" CB ASP B 170 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.20e-01 ... (remaining 1817 not shown) Planarity restraints: 2058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY m 31 " 0.093 5.00e-02 4.00e+02 1.23e-01 2.43e+01 pdb=" N PRO m 32 " -0.212 5.00e-02 4.00e+02 pdb=" CA PRO m 32 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO m 32 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS e 49 " -0.042 5.00e-02 4.00e+02 6.48e-02 6.72e+00 pdb=" N PRO e 50 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO e 50 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO e 50 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO m 32 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.46e+00 pdb=" C PRO m 32 " -0.044 2.00e-02 2.50e+03 pdb=" O PRO m 32 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU m 33 " 0.015 2.00e-02 2.50e+03 ... (remaining 2055 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1906 2.77 - 3.30: 9941 3.30 - 3.83: 17460 3.83 - 4.37: 20020 4.37 - 4.90: 36496 Nonbonded interactions: 85823 Sorted by model distance: nonbonded pdb=" CB VAL g 128 " pdb=" C18 CLR g 202 " model vdw 2.234 3.890 nonbonded pdb=" OE2 GLU d 28 " pdb=" OH TYR d 90 " model vdw 2.248 3.040 nonbonded pdb=" O SER f 41 " pdb=" OG SER f 41 " model vdw 2.303 3.040 nonbonded pdb=" O VAL a 44 " pdb=" OG1 THR a 47 " model vdw 2.309 3.040 nonbonded pdb=" OE2 GLU f 106 " pdb=" OH TYR f 111 " model vdw 2.310 3.040 ... (remaining 85818 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'a' and (resid 26 through 29 or (resid 30 and (name N or name CA or name \ C or name O or name CB )) or resid 31 through 48 or (resid 49 and (name N or nam \ e CA or name C or name O or name CB )) or resid 50 through 54)) selection = chain 'b' } 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=0.73 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: 2.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 10.770 Find NCS groups from input model: 0.100 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.146 11961 Z= 0.183 Angle : 0.684 23.039 16252 Z= 0.394 Chirality : 0.043 0.202 1820 Planarity : 0.005 0.123 2058 Dihedral : 16.128 119.693 4423 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 0.54 % Allowed : 19.46 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.77 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.90 (0.21), residues: 1473 helix: -0.90 (0.30), residues: 267 sheet: -0.37 (0.25), residues: 487 loop : -2.05 (0.21), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 44 TYR 0.019 0.001 TYR n 50 PHE 0.019 0.001 PHE A 138 TRP 0.009 0.001 TRP m 197 HIS 0.003 0.001 HIS n 226 Details of bonding type rmsd covalent geometry : bond 0.00416 (11944) covalent geometry : angle 0.68217 (16218) SS BOND : bond 0.00368 ( 17) SS BOND : angle 1.15671 ( 34) hydrogen bonds : bond 0.29548 ( 437) hydrogen bonds : angle 9.11148 ( 1248) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 129 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: B 22 GLN cc_start: 0.8409 (tt0) cc_final: 0.8027 (tt0) REVERT: e 86 GLU cc_start: 0.7332 (tm-30) cc_final: 0.6946 (tm-30) REVERT: n 84 ASN cc_start: 0.7141 (t0) cc_final: 0.6499 (m-40) outliers start: 7 outliers final: 4 residues processed: 131 average time/residue: 0.1001 time to fit residues: 19.1932 Evaluate side-chains 129 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 125 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 41 SER Chi-restraints excluded: chain m residue 211 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.3980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 0.0670 overall best weight: 2.2924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 38 ASN e 61 HIS f 33 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.196338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.148245 restraints weight = 12974.272| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.26 r_work: 0.3193 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 11961 Z= 0.229 Angle : 0.675 10.402 16252 Z= 0.351 Chirality : 0.047 0.229 1820 Planarity : 0.005 0.058 2058 Dihedral : 6.963 71.003 1749 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 3.54 % Allowed : 19.00 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.77 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.34 (0.22), residues: 1473 helix: 0.93 (0.32), residues: 266 sheet: -0.18 (0.25), residues: 501 loop : -2.21 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 117 TYR 0.024 0.002 TYR n 50 PHE 0.015 0.002 PHE f 110 TRP 0.016 0.002 TRP B 52 HIS 0.005 0.001 HIS n 226 Details of bonding type rmsd covalent geometry : bond 0.00555 (11944) covalent geometry : angle 0.67265 (16218) SS BOND : bond 0.00490 ( 17) SS BOND : angle 1.37711 ( 34) hydrogen bonds : bond 0.07324 ( 437) hydrogen bonds : angle 5.91928 ( 1248) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 132 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: B 22 GLN cc_start: 0.8884 (tt0) cc_final: 0.8646 (tt0) REVERT: B 24 GLN cc_start: 0.8483 (mt0) cc_final: 0.8142 (mt0) REVERT: b 32 CYS cc_start: 0.7526 (t) cc_final: 0.7272 (t) REVERT: e 86 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7348 (tm-30) REVERT: e 90 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8518 (tt) REVERT: m 231 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7818 (tp) outliers start: 46 outliers final: 25 residues processed: 169 average time/residue: 0.0873 time to fit residues: 22.3789 Evaluate side-chains 151 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 43 CYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain b residue 44 VAL Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 98 CYS Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 40 ILE Chi-restraints excluded: chain m residue 113 MET Chi-restraints excluded: chain m residue 127 MET Chi-restraints excluded: chain m residue 148 LYS 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 m residue 231 LEU Chi-restraints excluded: chain n residue 26 THR Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 215 VAL Chi-restraints excluded: chain n residue 261 ARG Chi-restraints excluded: chain n residue 279 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 134 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 135 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 136 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 18 optimal weight: 20.0000 chunk 114 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.196348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.139224 restraints weight = 12789.261| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.44 r_work: 0.3157 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11961 Z= 0.129 Angle : 0.560 7.833 16252 Z= 0.291 Chirality : 0.043 0.208 1820 Planarity : 0.004 0.042 2058 Dihedral : 5.579 46.947 1744 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 4.15 % Allowed : 19.77 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.77 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.22), residues: 1473 helix: 1.69 (0.33), residues: 266 sheet: -0.17 (0.24), residues: 520 loop : -2.10 (0.22), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 117 TYR 0.022 0.001 TYR n 50 PHE 0.014 0.001 PHE g 64 TRP 0.013 0.001 TRP m 197 HIS 0.003 0.001 HIS n 226 Details of bonding type rmsd covalent geometry : bond 0.00298 (11944) covalent geometry : angle 0.55889 (16218) SS BOND : bond 0.00356 ( 17) SS BOND : angle 1.03484 ( 34) hydrogen bonds : bond 0.05415 ( 437) hydrogen bonds : angle 5.30996 ( 1248) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 134 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: B 22 GLN cc_start: 0.8668 (tt0) cc_final: 0.7912 (tp40) REVERT: B 24 GLN cc_start: 0.8288 (mt0) cc_final: 0.8038 (mt0) REVERT: d 27 GLU cc_start: 0.8950 (pt0) cc_final: 0.8665 (pt0) REVERT: e 39 SER cc_start: 0.8633 (OUTLIER) cc_final: 0.8282 (m) REVERT: e 86 GLU cc_start: 0.7552 (tm-30) cc_final: 0.7083 (tm-30) REVERT: f 33 GLN cc_start: 0.6485 (OUTLIER) cc_final: 0.6254 (pt0) REVERT: f 86 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7628 (mm-30) REVERT: m 231 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7418 (tp) outliers start: 54 outliers final: 30 residues processed: 173 average time/residue: 0.0873 time to fit residues: 22.8637 Evaluate side-chains 163 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain b residue 44 VAL Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain e residue 98 CYS Chi-restraints excluded: chain e residue 112 LEU Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain f residue 33 GLN Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 41 SER Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 126 ILE Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 40 ILE Chi-restraints excluded: chain m residue 113 MET Chi-restraints excluded: chain m residue 127 MET Chi-restraints excluded: chain m residue 148 LYS Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 181 VAL Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain m residue 183 ASP Chi-restraints excluded: chain m residue 231 LEU Chi-restraints excluded: chain m residue 249 VAL Chi-restraints excluded: chain n residue 26 THR Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 79 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 22 optimal weight: 8.9990 chunk 80 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN B 24 GLN B 181 ASN g 111 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.193259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.140245 restraints weight = 12754.331| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.10 r_work: 0.3100 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 11961 Z= 0.250 Angle : 0.671 10.577 16252 Z= 0.345 Chirality : 0.047 0.234 1820 Planarity : 0.005 0.061 2058 Dihedral : 5.936 50.472 1742 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.01 % Favored : 91.92 % Rotamer: Outliers : 5.46 % Allowed : 19.00 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.77 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.23 (0.22), residues: 1473 helix: 1.34 (0.32), residues: 270 sheet: -0.22 (0.24), residues: 512 loop : -2.23 (0.22), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG d 91 TYR 0.028 0.002 TYR n 50 PHE 0.015 0.002 PHE g 64 TRP 0.015 0.002 TRP B 52 HIS 0.005 0.001 HIS n 226 Details of bonding type rmsd covalent geometry : bond 0.00612 (11944) covalent geometry : angle 0.66885 (16218) SS BOND : bond 0.00530 ( 17) SS BOND : angle 1.42347 ( 34) hydrogen bonds : bond 0.06542 ( 437) hydrogen bonds : angle 5.30241 ( 1248) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 122 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: B 24 GLN cc_start: 0.8327 (mt0) cc_final: 0.7785 (mt0) REVERT: B 38 ARG cc_start: 0.7543 (OUTLIER) cc_final: 0.6989 (tmm-80) REVERT: B 54 GLU cc_start: 0.9074 (OUTLIER) cc_final: 0.7329 (mm-30) REVERT: B 174 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7051 (tm-30) REVERT: b 32 CYS cc_start: 0.7153 (t) cc_final: 0.6805 (t) REVERT: b 54 LYS cc_start: 0.4970 (OUTLIER) cc_final: 0.4731 (tttp) REVERT: d 27 GLU cc_start: 0.8902 (pt0) cc_final: 0.8605 (pt0) REVERT: e 39 SER cc_start: 0.8721 (OUTLIER) cc_final: 0.8358 (m) REVERT: e 86 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7157 (tm-30) REVERT: f 34 THR cc_start: 0.7322 (OUTLIER) cc_final: 0.7043 (p) REVERT: m 231 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7603 (tp) REVERT: n 199 GLN cc_start: 0.7202 (pt0) cc_final: 0.6903 (pt0) outliers start: 71 outliers final: 46 residues processed: 181 average time/residue: 0.0817 time to fit residues: 22.7000 Evaluate side-chains 174 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 121 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain b residue 44 VAL Chi-restraints excluded: chain b residue 54 LYS Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain e residue 84 LEU Chi-restraints excluded: chain e residue 98 CYS Chi-restraints excluded: chain e residue 112 LEU Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 126 ILE Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 33 LEU Chi-restraints excluded: chain m residue 40 ILE Chi-restraints excluded: chain m residue 113 MET Chi-restraints excluded: chain m residue 127 MET Chi-restraints excluded: chain m residue 146 ASP Chi-restraints excluded: chain m residue 148 LYS Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 181 VAL Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain m residue 183 ASP Chi-restraints excluded: chain m residue 231 LEU Chi-restraints excluded: chain m residue 249 VAL Chi-restraints excluded: chain n residue 24 THR Chi-restraints excluded: chain n residue 26 THR Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 79 VAL Chi-restraints excluded: chain n residue 261 ARG Chi-restraints excluded: chain n residue 276 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 80 optimal weight: 6.9990 chunk 21 optimal weight: 0.0970 chunk 2 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 27 optimal weight: 0.0070 chunk 110 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 chunk 120 optimal weight: 5.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.194652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.139996 restraints weight = 12754.565| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.14 r_work: 0.3158 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11961 Z= 0.126 Angle : 0.554 7.560 16252 Z= 0.288 Chirality : 0.043 0.207 1820 Planarity : 0.004 0.040 2058 Dihedral : 5.631 58.025 1742 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 4.00 % Allowed : 20.92 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.77 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.22), residues: 1473 helix: 1.90 (0.33), residues: 266 sheet: -0.16 (0.24), residues: 521 loop : -2.11 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 117 TYR 0.024 0.001 TYR n 50 PHE 0.014 0.001 PHE g 64 TRP 0.013 0.001 TRP m 197 HIS 0.003 0.001 HIS n 226 Details of bonding type rmsd covalent geometry : bond 0.00289 (11944) covalent geometry : angle 0.55179 (16218) SS BOND : bond 0.00378 ( 17) SS BOND : angle 1.18789 ( 34) hydrogen bonds : bond 0.04967 ( 437) hydrogen bonds : angle 4.98393 ( 1248) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 128 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: B 24 GLN cc_start: 0.8419 (mt0) cc_final: 0.7959 (mt0) REVERT: B 54 GLU cc_start: 0.9061 (OUTLIER) cc_final: 0.7264 (mm-30) REVERT: B 174 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7085 (tm-30) REVERT: d 27 GLU cc_start: 0.8928 (pt0) cc_final: 0.8634 (pt0) REVERT: e 39 SER cc_start: 0.8617 (OUTLIER) cc_final: 0.8275 (m) REVERT: e 86 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7197 (tm-30) REVERT: m 231 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7451 (tp) outliers start: 52 outliers final: 36 residues processed: 170 average time/residue: 0.0844 time to fit residues: 21.9124 Evaluate side-chains 164 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 124 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 48 VAL Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain e residue 84 LEU Chi-restraints excluded: chain e residue 91 GLU Chi-restraints excluded: chain e residue 98 CYS Chi-restraints excluded: chain e residue 112 LEU Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 126 ILE Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 33 LEU Chi-restraints excluded: chain m residue 40 ILE Chi-restraints excluded: chain m residue 113 MET Chi-restraints excluded: chain m residue 127 MET Chi-restraints excluded: chain m residue 148 LYS Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 181 VAL Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain m residue 183 ASP Chi-restraints excluded: chain m residue 231 LEU Chi-restraints excluded: chain m residue 249 VAL Chi-restraints excluded: chain n residue 26 THR Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 79 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 130 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 133 optimal weight: 2.9990 chunk 129 optimal weight: 0.2980 chunk 134 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 97 optimal weight: 20.0000 chunk 100 optimal weight: 6.9990 chunk 102 optimal weight: 9.9990 chunk 112 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.198838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.146257 restraints weight = 12924.218| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.32 r_work: 0.3351 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11961 Z= 0.109 Angle : 0.525 7.702 16252 Z= 0.273 Chirality : 0.042 0.201 1820 Planarity : 0.004 0.038 2058 Dihedral : 5.373 56.448 1742 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 4.46 % Allowed : 20.00 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.77 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.22), residues: 1473 helix: 2.22 (0.33), residues: 267 sheet: -0.03 (0.24), residues: 516 loop : -2.04 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 117 TYR 0.024 0.001 TYR n 50 PHE 0.013 0.001 PHE g 64 TRP 0.012 0.001 TRP m 197 HIS 0.003 0.001 HIS n 226 Details of bonding type rmsd covalent geometry : bond 0.00244 (11944) covalent geometry : angle 0.52359 (16218) SS BOND : bond 0.00312 ( 17) SS BOND : angle 0.95464 ( 34) hydrogen bonds : bond 0.04413 ( 437) hydrogen bonds : angle 4.76741 ( 1248) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 126 time to evaluate : 0.429 Fit side-chains revert: symmetry clash REVERT: B 22 GLN cc_start: 0.8781 (tt0) cc_final: 0.8258 (tp40) REVERT: B 24 GLN cc_start: 0.8605 (mt0) cc_final: 0.8401 (mt0) REVERT: B 54 GLU cc_start: 0.9012 (OUTLIER) cc_final: 0.7422 (mm-30) REVERT: B 174 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.7100 (tm-30) REVERT: d 27 GLU cc_start: 0.8847 (pt0) cc_final: 0.8615 (pt0) REVERT: e 39 SER cc_start: 0.8642 (OUTLIER) cc_final: 0.8335 (m) REVERT: e 86 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7459 (tm-30) REVERT: g 61 MET cc_start: 0.8250 (ttt) cc_final: 0.7990 (ttt) REVERT: n 50 TYR cc_start: 0.5849 (OUTLIER) cc_final: 0.3372 (p90) REVERT: n 199 GLN cc_start: 0.7153 (OUTLIER) cc_final: 0.6889 (pt0) REVERT: n 269 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7926 (mt-10) outliers start: 58 outliers final: 35 residues processed: 169 average time/residue: 0.0865 time to fit residues: 22.0830 Evaluate side-chains 161 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 120 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain e residue 84 LEU Chi-restraints excluded: chain e residue 98 CYS Chi-restraints excluded: chain e residue 112 LEU Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 155 ARG Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 126 ILE Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 33 LEU Chi-restraints excluded: chain m residue 40 ILE Chi-restraints excluded: chain m residue 113 MET Chi-restraints excluded: chain m residue 127 MET Chi-restraints excluded: chain m residue 148 LYS Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 181 VAL Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain m residue 249 VAL Chi-restraints excluded: chain n residue 26 THR Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 79 VAL Chi-restraints excluded: chain n residue 199 GLN Chi-restraints excluded: chain n residue 269 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 32 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 56 optimal weight: 0.0870 chunk 102 optimal weight: 9.9990 chunk 76 optimal weight: 0.9980 chunk 80 optimal weight: 7.9990 overall best weight: 2.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.193684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.143178 restraints weight = 12894.499| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.96 r_work: 0.3232 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 11961 Z= 0.249 Angle : 0.666 10.367 16252 Z= 0.343 Chirality : 0.047 0.230 1820 Planarity : 0.005 0.065 2058 Dihedral : 5.864 51.133 1742 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.35 % Favored : 91.58 % Rotamer: Outliers : 5.31 % Allowed : 19.54 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.77 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.22), residues: 1473 helix: 1.66 (0.32), residues: 268 sheet: -0.18 (0.24), residues: 512 loop : -2.19 (0.22), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG d 91 TYR 0.027 0.002 TYR n 50 PHE 0.018 0.002 PHE f 110 TRP 0.014 0.002 TRP B 52 HIS 0.005 0.001 HIS n 226 Details of bonding type rmsd covalent geometry : bond 0.00608 (11944) covalent geometry : angle 0.66263 (16218) SS BOND : bond 0.00529 ( 17) SS BOND : angle 1.51830 ( 34) hydrogen bonds : bond 0.06236 ( 437) hydrogen bonds : angle 5.04106 ( 1248) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 119 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: B 22 GLN cc_start: 0.8947 (tt0) cc_final: 0.8453 (tt0) REVERT: B 24 GLN cc_start: 0.8571 (mt0) cc_final: 0.8188 (mt0) REVERT: B 38 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.7052 (tmm-80) REVERT: B 54 GLU cc_start: 0.9033 (OUTLIER) cc_final: 0.7461 (mm-30) REVERT: B 174 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7117 (tm-30) REVERT: b 32 CYS cc_start: 0.7431 (t) cc_final: 0.7080 (t) REVERT: d 27 GLU cc_start: 0.8903 (pt0) cc_final: 0.8639 (pt0) REVERT: e 39 SER cc_start: 0.8741 (OUTLIER) cc_final: 0.8401 (m) REVERT: e 86 GLU cc_start: 0.7732 (tm-30) cc_final: 0.7350 (tm-30) REVERT: e 155 ARG cc_start: 0.6597 (OUTLIER) cc_final: 0.5360 (tmt-80) REVERT: g 61 MET cc_start: 0.8218 (ttt) cc_final: 0.7978 (ttt) REVERT: m 231 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7897 (tp) REVERT: n 50 TYR cc_start: 0.5926 (OUTLIER) cc_final: 0.3815 (p90) REVERT: n 176 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8694 (tt) REVERT: n 199 GLN cc_start: 0.7240 (OUTLIER) cc_final: 0.6987 (pt0) outliers start: 69 outliers final: 47 residues processed: 174 average time/residue: 0.0819 time to fit residues: 21.8850 Evaluate side-chains 175 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 119 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain b residue 44 VAL Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain e residue 84 LEU Chi-restraints excluded: chain e residue 91 GLU Chi-restraints excluded: chain e residue 98 CYS Chi-restraints excluded: chain e residue 112 LEU Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain e residue 155 ARG Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 126 ILE Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 33 LEU Chi-restraints excluded: chain m residue 40 ILE Chi-restraints excluded: chain m residue 113 MET Chi-restraints excluded: chain m residue 127 MET Chi-restraints excluded: chain m residue 146 ASP Chi-restraints excluded: chain m residue 148 LYS Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 181 VAL Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain m residue 231 LEU Chi-restraints excluded: chain m residue 249 VAL Chi-restraints excluded: chain n residue 24 THR Chi-restraints excluded: chain n residue 26 THR Chi-restraints excluded: chain n residue 40 LEU 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 199 GLN Chi-restraints excluded: chain n residue 215 VAL Chi-restraints excluded: chain n residue 261 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 84 optimal weight: 5.9990 chunk 129 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 144 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 13 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.197824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.145421 restraints weight = 12882.575| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.27 r_work: 0.3291 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11961 Z= 0.115 Angle : 0.545 8.480 16252 Z= 0.283 Chirality : 0.043 0.205 1820 Planarity : 0.004 0.039 2058 Dihedral : 5.459 48.154 1742 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.92 % Allowed : 21.46 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.77 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.22), residues: 1473 helix: 2.18 (0.33), residues: 267 sheet: -0.04 (0.24), residues: 514 loop : -2.05 (0.22), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG f 115 TYR 0.022 0.001 TYR n 50 PHE 0.014 0.001 PHE g 64 TRP 0.013 0.001 TRP m 197 HIS 0.003 0.001 HIS n 226 Details of bonding type rmsd covalent geometry : bond 0.00262 (11944) covalent geometry : angle 0.54335 (16218) SS BOND : bond 0.00324 ( 17) SS BOND : angle 0.98347 ( 34) hydrogen bonds : bond 0.04657 ( 437) hydrogen bonds : angle 4.81142 ( 1248) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 121 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: B 22 GLN cc_start: 0.8785 (tt0) cc_final: 0.8282 (tt0) REVERT: B 24 GLN cc_start: 0.8545 (mt0) cc_final: 0.8156 (mt0) REVERT: B 54 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.7268 (mm-30) REVERT: B 174 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6919 (tm-30) REVERT: d 27 GLU cc_start: 0.8749 (pt0) cc_final: 0.8482 (pt0) REVERT: e 39 SER cc_start: 0.8549 (OUTLIER) cc_final: 0.8230 (m) REVERT: e 86 GLU cc_start: 0.7494 (tm-30) cc_final: 0.7173 (tm-30) REVERT: g 61 MET cc_start: 0.8074 (ttt) cc_final: 0.7834 (ttt) REVERT: g 86 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7958 (tt0) REVERT: n 50 TYR cc_start: 0.5888 (OUTLIER) cc_final: 0.3760 (p90) REVERT: n 199 GLN cc_start: 0.7106 (OUTLIER) cc_final: 0.6846 (pt0) outliers start: 51 outliers final: 39 residues processed: 161 average time/residue: 0.0899 time to fit residues: 22.2590 Evaluate side-chains 163 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 118 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain b residue 44 VAL Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 37 CYS Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain e residue 70 GLU Chi-restraints excluded: chain e residue 84 LEU Chi-restraints excluded: chain e residue 91 GLU Chi-restraints excluded: chain e residue 98 CYS Chi-restraints excluded: chain e residue 112 LEU Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 86 GLN Chi-restraints excluded: chain g residue 126 ILE Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 33 LEU Chi-restraints excluded: chain m residue 113 MET Chi-restraints excluded: chain m residue 127 MET Chi-restraints excluded: chain m residue 148 LYS Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 181 VAL Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain n residue 26 THR Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 79 VAL Chi-restraints excluded: chain n residue 199 GLN Chi-restraints excluded: chain n residue 215 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 8 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 7 optimal weight: 0.3980 chunk 82 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 109 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.198418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.144782 restraints weight = 12814.781| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.18 r_work: 0.3367 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11961 Z= 0.114 Angle : 0.535 7.797 16252 Z= 0.278 Chirality : 0.042 0.201 1820 Planarity : 0.004 0.038 2058 Dihedral : 5.264 46.599 1742 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.46 % Allowed : 22.00 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.77 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.23), residues: 1473 helix: 2.34 (0.33), residues: 267 sheet: 0.01 (0.24), residues: 516 loop : -2.01 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG e 155 TYR 0.021 0.001 TYR n 50 PHE 0.013 0.001 PHE g 64 TRP 0.012 0.001 TRP m 197 HIS 0.003 0.001 HIS n 226 Details of bonding type rmsd covalent geometry : bond 0.00262 (11944) covalent geometry : angle 0.53437 (16218) SS BOND : bond 0.00315 ( 17) SS BOND : angle 0.92604 ( 34) hydrogen bonds : bond 0.04390 ( 437) hydrogen bonds : angle 4.67112 ( 1248) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 122 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: B 22 GLN cc_start: 0.8796 (tt0) cc_final: 0.8191 (tp40) REVERT: B 24 GLN cc_start: 0.8562 (mt0) cc_final: 0.8290 (mt0) REVERT: B 54 GLU cc_start: 0.9044 (OUTLIER) cc_final: 0.7418 (mm-30) REVERT: B 174 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7071 (tm-30) REVERT: d 27 GLU cc_start: 0.8843 (pt0) cc_final: 0.8594 (pt0) REVERT: e 39 SER cc_start: 0.8656 (OUTLIER) cc_final: 0.8338 (m) REVERT: e 86 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7277 (tm-30) REVERT: g 61 MET cc_start: 0.8159 (ttt) cc_final: 0.7920 (ttt) REVERT: g 86 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.8008 (tt0) REVERT: n 50 TYR cc_start: 0.5844 (OUTLIER) cc_final: 0.3709 (p90) REVERT: n 199 GLN cc_start: 0.7111 (OUTLIER) cc_final: 0.6828 (pt0) outliers start: 45 outliers final: 35 residues processed: 159 average time/residue: 0.0930 time to fit residues: 22.5976 Evaluate side-chains 157 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 116 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain b residue 44 VAL Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 37 CYS Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 84 LEU Chi-restraints excluded: chain e residue 98 CYS Chi-restraints excluded: chain e residue 112 LEU Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 86 GLN Chi-restraints excluded: chain g residue 126 ILE Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 33 LEU Chi-restraints excluded: chain m residue 113 MET Chi-restraints excluded: chain m residue 127 MET Chi-restraints excluded: chain m residue 148 LYS Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 181 VAL Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain n residue 26 THR Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 79 VAL Chi-restraints excluded: chain n residue 199 GLN Chi-restraints excluded: chain n residue 215 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 113 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 141 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.197599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.144570 restraints weight = 12851.776| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.15 r_work: 0.3268 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11961 Z= 0.128 Angle : 0.548 7.731 16252 Z= 0.283 Chirality : 0.043 0.199 1820 Planarity : 0.004 0.038 2058 Dihedral : 5.242 44.747 1742 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 3.62 % Allowed : 22.31 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.77 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.23), residues: 1473 helix: 2.34 (0.32), residues: 266 sheet: 0.03 (0.24), residues: 518 loop : -1.98 (0.22), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG e 155 TYR 0.022 0.001 TYR n 50 PHE 0.013 0.001 PHE g 64 TRP 0.011 0.001 TRP m 197 HIS 0.003 0.001 HIS n 226 Details of bonding type rmsd covalent geometry : bond 0.00301 (11944) covalent geometry : angle 0.54696 (16218) SS BOND : bond 0.00346 ( 17) SS BOND : angle 1.00946 ( 34) hydrogen bonds : bond 0.04564 ( 437) hydrogen bonds : angle 4.65833 ( 1248) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 118 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: B 22 GLN cc_start: 0.8849 (tt0) cc_final: 0.8229 (tp40) REVERT: B 24 GLN cc_start: 0.8615 (mt0) cc_final: 0.8330 (mt0) REVERT: B 54 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.7450 (mm-30) REVERT: B 174 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7098 (tm-30) REVERT: d 27 GLU cc_start: 0.8818 (pt0) cc_final: 0.8570 (pt0) REVERT: e 39 SER cc_start: 0.8666 (OUTLIER) cc_final: 0.8348 (m) REVERT: e 86 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7379 (tm-30) REVERT: g 61 MET cc_start: 0.8213 (ttt) cc_final: 0.7983 (ttt) REVERT: g 86 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8059 (tt0) REVERT: n 50 TYR cc_start: 0.5745 (OUTLIER) cc_final: 0.3643 (p90) REVERT: n 199 GLN cc_start: 0.7140 (OUTLIER) cc_final: 0.6865 (pt0) outliers start: 47 outliers final: 41 residues processed: 158 average time/residue: 0.0860 time to fit residues: 21.2010 Evaluate side-chains 163 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 116 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain b residue 44 VAL Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 37 CYS Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 47 LEU Chi-restraints excluded: chain e residue 70 GLU Chi-restraints excluded: chain e residue 84 LEU Chi-restraints excluded: chain e residue 98 CYS Chi-restraints excluded: chain e residue 112 LEU Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 86 GLN Chi-restraints excluded: chain g residue 126 ILE Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 33 LEU Chi-restraints excluded: chain m residue 113 MET Chi-restraints excluded: chain m residue 127 MET Chi-restraints excluded: chain m residue 148 LYS Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 181 VAL Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain m residue 186 SER Chi-restraints excluded: chain n residue 24 THR Chi-restraints excluded: chain n residue 26 THR Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 79 VAL Chi-restraints excluded: chain n residue 199 GLN Chi-restraints excluded: chain n residue 215 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 124 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 135 optimal weight: 5.9990 chunk 69 optimal weight: 0.5980 chunk 131 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 129 optimal weight: 0.5980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.197374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.142993 restraints weight = 12942.528| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.35 r_work: 0.3340 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 11961 Z= 0.187 Angle : 0.839 59.101 16252 Z= 0.481 Chirality : 0.050 1.077 1820 Planarity : 0.004 0.038 2058 Dihedral : 5.253 44.704 1742 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 3.92 % Allowed : 21.77 % Favored : 74.31 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 10.77 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.23), residues: 1473 helix: 2.33 (0.32), residues: 266 sheet: 0.04 (0.24), residues: 518 loop : -1.98 (0.22), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG d 91 TYR 0.022 0.001 TYR n 50 PHE 0.013 0.001 PHE g 64 TRP 0.011 0.001 TRP m 197 HIS 0.004 0.001 HIS n 226 Details of bonding type rmsd covalent geometry : bond 0.00400 (11944) covalent geometry : angle 0.83894 (16218) SS BOND : bond 0.00378 ( 17) SS BOND : angle 0.99697 ( 34) hydrogen bonds : bond 0.04658 ( 437) hydrogen bonds : angle 4.65787 ( 1248) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3783.37 seconds wall clock time: 65 minutes 9.20 seconds (3909.20 seconds total)