Starting phenix.real_space_refine on Thu Jun 12 23:18:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zeu_60046/06_2025/8zeu_60046.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zeu_60046/06_2025/8zeu_60046.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zeu_60046/06_2025/8zeu_60046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zeu_60046/06_2025/8zeu_60046.map" model { file = "/net/cci-nas-00/data/ceres_data/8zeu_60046/06_2025/8zeu_60046.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zeu_60046/06_2025/8zeu_60046.cif" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.071 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 9154 2.51 5 N 2406 2.21 5 O 2902 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14534 Number of models: 1 Model: "" Number of chains: 10 Chain: "H" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1646 Classifications: {'peptide': 216} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 203} Chain breaks: 1 Chain: "L" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1645 Classifications: {'peptide': 215} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 202} Chain: "B" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1645 Classifications: {'peptide': 215} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 202} Chain: "C" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 766 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain breaks: 2 Chain: "A" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1565 Classifications: {'peptide': 210} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 195} Chain breaks: 1 Chain: "D" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1646 Classifications: {'peptide': 216} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 203} Chain breaks: 1 Chain: "E" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1645 Classifications: {'peptide': 215} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 202} Chain: "F" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1645 Classifications: {'peptide': 215} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 202} Chain: "G" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 766 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain breaks: 2 Chain: "I" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1565 Classifications: {'peptide': 210} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 195} Chain breaks: 1 Time building chain proxies: 9.36, per 1000 atoms: 0.64 Number of scatterers: 14534 At special positions: 0 Unit cell: (71.61, 140.43, 155.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 2902 8.00 N 2406 7.00 C 9154 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 148 " - pdb=" SG CYS H 204 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 89 " distance=2.04 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 34 " - pdb=" SG CYS C 110 " distance=2.03 Simple disulfide: pdb=" SG CYS C 69 " - pdb=" SG CYS C 75 " distance=2.03 Simple disulfide: pdb=" SG CYS C 90 " - pdb=" SG CYS C 137 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 95 " distance=2.03 Simple disulfide: pdb=" SG CYS A 143 " - pdb=" SG CYS A 199 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 148 " - pdb=" SG CYS D 204 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 89 " distance=2.04 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 195 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 89 " distance=2.04 Simple disulfide: pdb=" SG CYS F 135 " - pdb=" SG CYS F 195 " distance=2.03 Simple disulfide: pdb=" SG CYS G 34 " - pdb=" SG CYS G 110 " distance=2.03 Simple disulfide: pdb=" SG CYS G 69 " - pdb=" SG CYS G 75 " distance=2.03 Simple disulfide: pdb=" SG CYS G 90 " - pdb=" SG CYS G 137 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 95 " distance=2.03 Simple disulfide: pdb=" SG CYS I 143 " - pdb=" SG CYS I 199 " 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: 3.10 Conformation dependent library (CDL) restraints added in 1.8 seconds 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3556 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 40 sheets defined 15.2% alpha, 46.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.18 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.649A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.626A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 166 No H-bonds generated for 'chain 'H' and resid 164 through 166' Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.814A pdb=" N PHE L 84 " --> pdb=" O ALA L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 128 Processing helix chain 'L' and resid 184 through 189 Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'B' and resid 80 through 84 removed outlier: 4.102A pdb=" N PHE B 84 " --> pdb=" O ALA B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 129 Processing helix chain 'B' and resid 184 through 189 Processing helix chain 'C' and resid 35 through 46 Processing helix chain 'C' and resid 46 through 56 removed outlier: 3.731A pdb=" N MET C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER C 56 " --> pdb=" O ILE C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 85 Processing helix chain 'C' and resid 91 through 95 removed outlier: 3.964A pdb=" N ALA C 94 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS C 95 " --> pdb=" O SER C 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 91 through 95' Processing helix chain 'C' and resid 96 through 110 Processing helix chain 'C' and resid 136 through 152 Processing helix chain 'A' and resid 86 through 90 removed outlier: 3.737A pdb=" N THR A 90 " --> pdb=" O PRO A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 161 No H-bonds generated for 'chain 'A' and resid 159 through 161' Processing helix chain 'A' and resid 190 through 195 removed outlier: 4.512A pdb=" N THR A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.649A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.626A pdb=" N THR D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 166 No H-bonds generated for 'chain 'D' and resid 164 through 166' Processing helix chain 'E' and resid 30 through 32 No H-bonds generated for 'chain 'E' and resid 30 through 32' Processing helix chain 'E' and resid 80 through 84 removed outlier: 3.814A pdb=" N PHE E 84 " --> pdb=" O ALA E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 128 Processing helix chain 'E' and resid 184 through 189 Processing helix chain 'F' and resid 30 through 32 No H-bonds generated for 'chain 'F' and resid 30 through 32' Processing helix chain 'F' and resid 80 through 84 removed outlier: 4.101A pdb=" N PHE F 84 " --> pdb=" O ALA F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 129 Processing helix chain 'F' and resid 184 through 189 Processing helix chain 'G' and resid 35 through 46 Processing helix chain 'G' and resid 46 through 56 removed outlier: 3.732A pdb=" N MET G 55 " --> pdb=" O LEU G 51 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER G 56 " --> pdb=" O ILE G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 85 Processing helix chain 'G' and resid 91 through 95 removed outlier: 3.965A pdb=" N ALA G 94 " --> pdb=" O ALA G 91 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS G 95 " --> pdb=" O SER G 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 91 through 95' Processing helix chain 'G' and resid 96 through 110 Processing helix chain 'G' and resid 136 through 152 Processing helix chain 'I' and resid 86 through 90 removed outlier: 3.737A pdb=" N THR I 90 " --> pdb=" O PRO I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 161 No H-bonds generated for 'chain 'I' and resid 159 through 161' Processing helix chain 'I' and resid 190 through 195 removed outlier: 4.512A pdb=" N THR I 194 " --> pdb=" O SER I 190 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.759A pdb=" N GLU H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N TRP H 33 " --> pdb=" O ALA H 99 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N MET H 34 " --> pdb=" O GLN H 50 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLN H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP H 57 " --> pdb=" O PHE H 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.759A pdb=" N GLU H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N CYS H 96 " --> pdb=" O TRP H 111 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TRP H 111 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ARG H 98 " --> pdb=" O ASP H 109 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 128 through 132 removed outlier: 5.145A pdb=" N ALA H 145 " --> pdb=" O VAL H 192 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL H 192 " --> pdb=" O ALA H 145 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N GLY H 147 " --> pdb=" O VAL H 190 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL H 190 " --> pdb=" O GLY H 147 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LEU H 149 " --> pdb=" O SER H 188 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N SER H 188 " --> pdb=" O LEU H 149 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N LYS H 151 " --> pdb=" O LEU H 186 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU H 186 " --> pdb=" O LYS H 151 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 128 through 132 removed outlier: 5.145A pdb=" N ALA H 145 " --> pdb=" O VAL H 192 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL H 192 " --> pdb=" O ALA H 145 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N GLY H 147 " --> pdb=" O VAL H 190 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL H 190 " --> pdb=" O GLY H 147 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LEU H 149 " --> pdb=" O SER H 188 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N SER H 188 " --> pdb=" O LEU H 149 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N LYS H 151 " --> pdb=" O LEU H 186 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU H 186 " --> pdb=" O LYS H 151 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 159 through 162 Processing sheet with id=AA7, first strand: chain 'L' and resid 4 through 7 removed outlier: 5.170A pdb=" N THR L 70 " --> pdb=" O VAL L 25 " (cutoff:3.500A) removed outlier: 9.421A pdb=" N SER L 27 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 9.454A pdb=" N SER L 68 " --> pdb=" O SER L 27 " (cutoff:3.500A) removed outlier: 12.135A pdb=" N ILE L 29 " --> pdb=" O SER L 66 " (cutoff:3.500A) removed outlier: 11.829A pdb=" N SER L 66 " --> pdb=" O ILE L 29 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.108A pdb=" N LEU L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TRP L 36 " --> pdb=" O TRP L 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.108A pdb=" N LEU L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 115 through 119 removed outlier: 5.265A pdb=" N SER L 132 " --> pdb=" O LEU L 182 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N LEU L 182 " --> pdb=" O SER L 132 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N VAL L 134 " --> pdb=" O LEU L 180 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU L 180 " --> pdb=" O VAL L 134 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N LEU L 136 " --> pdb=" O SER L 178 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N SER L 178 " --> pdb=" O LEU L 136 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ASN L 138 " --> pdb=" O LEU L 176 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU L 176 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 154 through 156 removed outlier: 4.621A pdb=" N TRP L 149 " --> pdb=" O GLN L 156 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 4 through 7 removed outlier: 5.191A pdb=" N THR B 70 " --> pdb=" O VAL B 25 " (cutoff:3.500A) removed outlier: 9.677A pdb=" N SER B 27 " --> pdb=" O SER B 68 " (cutoff:3.500A) removed outlier: 9.862A pdb=" N SER B 68 " --> pdb=" O SER B 27 " (cutoff:3.500A) removed outlier: 12.368A pdb=" N ILE B 29 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 12.083A pdb=" N SER B 66 " --> pdb=" O ILE B 29 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.012A pdb=" N LEU B 11 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU B 34 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N TYR B 50 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N TRP B 36 " --> pdb=" O TRP B 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 115 through 119 removed outlier: 5.259A pdb=" N SER B 132 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N LEU B 182 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N VAL B 134 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU B 180 " --> pdb=" O VAL B 134 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N LEU B 136 " --> pdb=" O SER B 178 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N SER B 178 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ASN B 138 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LEU B 176 " --> pdb=" O ASN B 138 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 154 through 156 removed outlier: 4.318A pdb=" N TRP B 149 " --> pdb=" O GLN B 156 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AB8, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.594A pdb=" N VAL A 10 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE A 34 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N VAL A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TRP A 36 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 123 through 127 removed outlier: 6.042A pdb=" N TYR A 179 " --> pdb=" O ASP A 147 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 123 through 127 removed outlier: 6.042A pdb=" N TYR A 179 " --> pdb=" O ASP A 147 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 154 through 157 removed outlier: 4.489A pdb=" N TYR A 197 " --> pdb=" O VAL A 214 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AC4, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.759A pdb=" N GLU D 10 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N TRP D 33 " --> pdb=" O ALA D 99 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N MET D 34 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLN D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP D 57 " --> pdb=" O PHE D 52 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.759A pdb=" N GLU D 10 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N CYS D 96 " --> pdb=" O TRP D 111 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TRP D 111 " --> pdb=" O CYS D 96 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ARG D 98 " --> pdb=" O ASP D 109 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 128 through 132 removed outlier: 5.145A pdb=" N ALA D 145 " --> pdb=" O VAL D 192 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL D 192 " --> pdb=" O ALA D 145 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N GLY D 147 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL D 190 " --> pdb=" O GLY D 147 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LEU D 149 " --> pdb=" O SER D 188 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N SER D 188 " --> pdb=" O LEU D 149 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N LYS D 151 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU D 186 " --> pdb=" O LYS D 151 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 128 through 132 removed outlier: 5.145A pdb=" N ALA D 145 " --> pdb=" O VAL D 192 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL D 192 " --> pdb=" O ALA D 145 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N GLY D 147 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL D 190 " --> pdb=" O GLY D 147 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LEU D 149 " --> pdb=" O SER D 188 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N SER D 188 " --> pdb=" O LEU D 149 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N LYS D 151 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU D 186 " --> pdb=" O LYS D 151 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 159 through 162 Processing sheet with id=AC9, first strand: chain 'E' and resid 4 through 7 removed outlier: 5.169A pdb=" N THR E 70 " --> pdb=" O VAL E 25 " (cutoff:3.500A) removed outlier: 9.420A pdb=" N SER E 27 " --> pdb=" O SER E 68 " (cutoff:3.500A) removed outlier: 9.454A pdb=" N SER E 68 " --> pdb=" O SER E 27 " (cutoff:3.500A) removed outlier: 12.136A pdb=" N ILE E 29 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 11.829A pdb=" N SER E 66 " --> pdb=" O ILE E 29 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.107A pdb=" N LEU E 11 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N LEU E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N TYR E 50 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N TRP E 36 " --> pdb=" O TRP E 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.107A pdb=" N LEU E 11 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N THR E 98 " --> pdb=" O GLN E 91 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 115 through 119 removed outlier: 5.264A pdb=" N SER E 132 " --> pdb=" O LEU E 182 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N LEU E 182 " --> pdb=" O SER E 132 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N VAL E 134 " --> pdb=" O LEU E 180 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU E 180 " --> pdb=" O VAL E 134 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N LEU E 136 " --> pdb=" O SER E 178 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N SER E 178 " --> pdb=" O LEU E 136 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ASN E 138 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU E 176 " --> pdb=" O ASN E 138 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 154 through 156 removed outlier: 4.621A pdb=" N TRP E 149 " --> pdb=" O GLN E 156 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 4 through 7 removed outlier: 5.191A pdb=" N THR F 70 " --> pdb=" O VAL F 25 " (cutoff:3.500A) removed outlier: 9.677A pdb=" N SER F 27 " --> pdb=" O SER F 68 " (cutoff:3.500A) removed outlier: 9.863A pdb=" N SER F 68 " --> pdb=" O SER F 27 " (cutoff:3.500A) removed outlier: 12.368A pdb=" N ILE F 29 " --> pdb=" O SER F 66 " (cutoff:3.500A) removed outlier: 12.083A pdb=" N SER F 66 " --> pdb=" O ILE F 29 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.013A pdb=" N LEU F 11 " --> pdb=" O GLU F 106 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU F 34 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N TYR F 50 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N TRP F 36 " --> pdb=" O TRP F 48 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 115 through 119 removed outlier: 5.259A pdb=" N SER F 132 " --> pdb=" O LEU F 182 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LEU F 182 " --> pdb=" O SER F 132 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N VAL F 134 " --> pdb=" O LEU F 180 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU F 180 " --> pdb=" O VAL F 134 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N LEU F 136 " --> pdb=" O SER F 178 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N SER F 178 " --> pdb=" O LEU F 136 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ASN F 138 " --> pdb=" O LEU F 176 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LEU F 176 " --> pdb=" O ASN F 138 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 154 through 156 removed outlier: 4.317A pdb=" N TRP F 149 " --> pdb=" O GLN F 156 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AE1, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.593A pdb=" N VAL I 10 " --> pdb=" O THR I 113 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE I 34 " --> pdb=" O VAL I 50 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N VAL I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 123 through 127 removed outlier: 6.042A pdb=" N TYR I 179 " --> pdb=" O ASP I 147 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 123 through 127 removed outlier: 6.042A pdb=" N TYR I 179 " --> pdb=" O ASP I 147 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 154 through 157 removed outlier: 4.489A pdb=" N TYR I 197 " --> pdb=" O VAL I 214 " (cutoff:3.500A) 636 hydrogen bonds defined for protein. 1608 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: 5.12 Time building geometry restraints manager: 3.77 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: 4600 1.34 - 1.46: 3626 1.46 - 1.58: 6554 1.58 - 1.69: 0 1.69 - 1.81: 96 Bond restraints: 14876 Sorted by residual: bond pdb=" CB TYR F 50 " pdb=" CG TYR F 50 " ideal model delta sigma weight residual 1.512 1.480 0.032 2.20e-02 2.07e+03 2.14e+00 bond pdb=" CB TYR B 50 " pdb=" CG TYR B 50 " ideal model delta sigma weight residual 1.512 1.480 0.032 2.20e-02 2.07e+03 2.13e+00 bond pdb=" CG1 ILE C 79 " pdb=" CD1 ILE C 79 " ideal model delta sigma weight residual 1.513 1.462 0.051 3.90e-02 6.57e+02 1.68e+00 bond pdb=" CG1 ILE G 79 " pdb=" CD1 ILE G 79 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.68e+00 bond pdb=" CA VAL D 192 " pdb=" CB VAL D 192 " ideal model delta sigma weight residual 1.547 1.536 0.011 1.10e-02 8.26e+03 1.06e+00 ... (remaining 14871 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 19243 1.20 - 2.40: 751 2.40 - 3.60: 203 3.60 - 4.80: 39 4.80 - 5.99: 16 Bond angle restraints: 20252 Sorted by residual: angle pdb=" N GLY A 49 " pdb=" CA GLY A 49 " pdb=" C GLY A 49 " ideal model delta sigma weight residual 110.63 115.97 -5.34 1.45e+00 4.76e-01 1.36e+01 angle pdb=" N GLY I 49 " pdb=" CA GLY I 49 " pdb=" C GLY I 49 " ideal model delta sigma weight residual 110.63 115.93 -5.30 1.45e+00 4.76e-01 1.34e+01 angle pdb=" C MET B 4 " pdb=" CA MET B 4 " pdb=" CB MET B 4 " ideal model delta sigma weight residual 109.70 113.95 -4.25 1.81e+00 3.05e-01 5.52e+00 angle pdb=" C MET F 4 " pdb=" CA MET F 4 " pdb=" CB MET F 4 " ideal model delta sigma weight residual 109.70 113.92 -4.22 1.81e+00 3.05e-01 5.43e+00 angle pdb=" CA GLY A 49 " pdb=" C GLY A 49 " pdb=" N VAL A 50 " ideal model delta sigma weight residual 114.48 117.20 -2.72 1.19e+00 7.06e-01 5.22e+00 ... (remaining 20247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 8225 17.15 - 34.30: 518 34.30 - 51.45: 139 51.45 - 68.59: 28 68.59 - 85.74: 14 Dihedral angle restraints: 8924 sinusoidal: 3392 harmonic: 5532 Sorted by residual: dihedral pdb=" CB CYS A 143 " pdb=" SG CYS A 143 " pdb=" SG CYS A 199 " pdb=" CB CYS A 199 " ideal model delta sinusoidal sigma weight residual 93.00 148.66 -55.66 1 1.00e+01 1.00e-02 4.18e+01 dihedral pdb=" CB CYS I 143 " pdb=" SG CYS I 143 " pdb=" SG CYS I 199 " pdb=" CB CYS I 199 " ideal model delta sinusoidal sigma weight residual 93.00 148.66 -55.66 1 1.00e+01 1.00e-02 4.18e+01 dihedral pdb=" CA TRP L 92 " pdb=" C TRP L 92 " pdb=" N SER L 93 " pdb=" CA SER L 93 " ideal model delta harmonic sigma weight residual -180.00 -160.94 -19.06 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 8921 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1344 0.030 - 0.059: 613 0.059 - 0.088: 176 0.088 - 0.118: 146 0.118 - 0.147: 21 Chirality restraints: 2300 Sorted by residual: chirality pdb=" CA ILE I 37 " pdb=" N ILE I 37 " pdb=" C ILE I 37 " pdb=" CB ILE I 37 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.43e-01 chirality pdb=" CA ILE A 37 " pdb=" N ILE A 37 " pdb=" C ILE A 37 " pdb=" CB ILE A 37 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.16e-01 chirality pdb=" CA ILE D 203 " pdb=" N ILE D 203 " pdb=" C ILE D 203 " pdb=" CB ILE D 203 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.97e-01 ... (remaining 2297 not shown) Planarity restraints: 2566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 50 " -0.023 2.00e-02 2.50e+03 2.32e-02 1.08e+01 pdb=" CG TYR B 50 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR B 50 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR B 50 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR B 50 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR B 50 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 50 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 50 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 50 " 0.022 2.00e-02 2.50e+03 2.31e-02 1.07e+01 pdb=" CG TYR F 50 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR F 50 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR F 50 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR F 50 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR F 50 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR F 50 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 50 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 92 " 0.007 2.00e-02 2.50e+03 1.68e-02 7.09e+00 pdb=" CG TRP L 92 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP L 92 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP L 92 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP L 92 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP L 92 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP L 92 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 92 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 92 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP L 92 " 0.000 2.00e-02 2.50e+03 ... (remaining 2563 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 43 2.40 - 3.03: 8538 3.03 - 3.65: 21739 3.65 - 4.28: 34479 4.28 - 4.90: 59257 Nonbonded interactions: 124056 Sorted by model distance: nonbonded pdb=" NZ LYS L 208 " pdb=" O GLY I 193 " model vdw 1.776 3.120 nonbonded pdb=" CG2 VAL L 206 " pdb=" CB THR I 194 " model vdw 1.938 3.890 nonbonded pdb=" ND2 ASN H 205 " pdb=" OD1 ASP H 216 " model vdw 2.110 3.120 nonbonded pdb=" ND2 ASN D 205 " pdb=" OD1 ASP D 216 " model vdw 2.110 3.120 nonbonded pdb=" CB THR A 194 " pdb=" CG2 VAL E 206 " model vdw 2.163 3.890 ... (remaining 124051 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.680 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: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 35.500 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.080 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 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 0.055 14898 Z= 0.178 Angle : 0.610 5.994 20296 Z= 0.327 Chirality : 0.043 0.147 2300 Planarity : 0.004 0.060 2566 Dihedral : 12.932 85.743 5302 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.12 % Allowed : 0.60 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.20), residues: 1870 helix: 1.01 (0.39), residues: 204 sheet: 0.66 (0.17), residues: 834 loop : 0.76 (0.24), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP L 92 HIS 0.003 0.001 HIS F 190 PHE 0.010 0.001 PHE F 140 TYR 0.054 0.002 TYR B 50 ARG 0.005 0.000 ARG L 18 Details of bonding type rmsd hydrogen bonds : bond 0.11353 ( 578) hydrogen bonds : angle 6.70990 ( 1608) SS BOND : bond 0.00222 ( 22) SS BOND : angle 0.74317 ( 44) covalent geometry : bond 0.00411 (14876) covalent geometry : angle 0.60989 (20252) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 401 time to evaluate : 1.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 188 SER cc_start: 0.8437 (t) cc_final: 0.7981 (t) REVERT: H 220 GLU cc_start: 0.6501 (mm-30) cc_final: 0.6161 (mm-30) REVERT: L 141 TYR cc_start: 0.7897 (t80) cc_final: 0.7380 (t80) REVERT: B 153 ASN cc_start: 0.7706 (OUTLIER) cc_final: 0.7501 (t0) REVERT: B 159 ASN cc_start: 0.7072 (p0) cc_final: 0.6819 (m110) REVERT: E 104 LYS cc_start: 0.7897 (tttt) cc_final: 0.7596 (tptt) REVERT: E 126 LEU cc_start: 0.7058 (mm) cc_final: 0.6752 (mt) REVERT: E 188 GLU cc_start: 0.7226 (mt-10) cc_final: 0.6967 (mm-30) REVERT: F 75 THR cc_start: 0.8781 (m) cc_final: 0.8497 (p) REVERT: F 106 GLU cc_start: 0.7325 (pp20) cc_final: 0.6749 (pp20) REVERT: G 97 MET cc_start: 0.7312 (tpp) cc_final: 0.6515 (tpp) REVERT: I 204 LYS cc_start: 0.7409 (mmpt) cc_final: 0.7168 (mmmt) outliers start: 2 outliers final: 0 residues processed: 403 average time/residue: 0.2888 time to fit residues: 166.8342 Evaluate side-chains 221 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 220 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 145 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN L 161 GLN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN D 39 GLN E 39 GLN F 139 ASN F 153 ASN F 161 GLN I 174 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.153561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.127319 restraints weight = 18336.797| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.14 r_work: 0.3257 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.160 14898 Z= 0.369 Angle : 0.780 10.306 20296 Z= 0.412 Chirality : 0.050 0.179 2300 Planarity : 0.006 0.074 2566 Dihedral : 5.166 39.182 2030 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.93 % Allowed : 10.51 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.19), residues: 1870 helix: 0.45 (0.35), residues: 208 sheet: 0.42 (0.17), residues: 844 loop : 0.22 (0.23), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP E 92 HIS 0.009 0.002 HIS B 35 PHE 0.027 0.003 PHE L 99 TYR 0.032 0.003 TYR I 103 ARG 0.017 0.001 ARG I 66 Details of bonding type rmsd hydrogen bonds : bond 0.04170 ( 578) hydrogen bonds : angle 6.16484 ( 1608) SS BOND : bond 0.00648 ( 22) SS BOND : angle 0.96800 ( 44) covalent geometry : bond 0.00887 (14876) covalent geometry : angle 0.77964 (20252) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 240 time to evaluate : 1.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 188 SER cc_start: 0.8961 (t) cc_final: 0.8760 (t) REVERT: L 17 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7580 (mm-30) REVERT: L 68 SER cc_start: 0.8381 (OUTLIER) cc_final: 0.8078 (t) REVERT: L 167 GLN cc_start: 0.8056 (tt0) cc_final: 0.7760 (mt0) REVERT: B 106 GLU cc_start: 0.7895 (pp20) cc_final: 0.7657 (pp20) REVERT: B 153 ASN cc_start: 0.8090 (OUTLIER) cc_final: 0.7684 (t0) REVERT: B 159 ASN cc_start: 0.7807 (p0) cc_final: 0.7129 (m110) REVERT: C 82 LEU cc_start: 0.8730 (tp) cc_final: 0.8386 (tp) REVERT: C 95 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.8053 (mtmm) REVERT: C 96 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8021 (mp0) REVERT: D 19 LYS cc_start: 0.8259 (tttt) cc_final: 0.8031 (ttmm) REVERT: D 65 GLN cc_start: 0.6926 (mm-40) cc_final: 0.6291 (mm-40) REVERT: E 104 LYS cc_start: 0.8652 (tttt) cc_final: 0.8123 (tptt) REVERT: E 159 ASN cc_start: 0.7646 (p0) cc_final: 0.7439 (p0) REVERT: E 212 ARG cc_start: 0.6324 (mtm110) cc_final: 0.6036 (mtm-85) REVERT: F 106 GLU cc_start: 0.8315 (pp20) cc_final: 0.8104 (pm20) REVERT: F 143 ARG cc_start: 0.8078 (tmt-80) cc_final: 0.7769 (tpt90) REVERT: F 162 GLU cc_start: 0.8480 (pm20) cc_final: 0.8264 (pt0) REVERT: G 32 THR cc_start: 0.8658 (p) cc_final: 0.8401 (t) REVERT: G 97 MET cc_start: 0.8307 (tpp) cc_final: 0.7889 (tpp) REVERT: I 174 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7368 (mp10) outliers start: 65 outliers final: 44 residues processed: 292 average time/residue: 0.3099 time to fit residues: 132.3923 Evaluate side-chains 222 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 174 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 165 THR Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain L residue 183 SER Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 106 GLU Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 122 SER Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain I residue 17 THR Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 33 ASP Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 174 GLN Chi-restraints excluded: chain I residue 210 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 68 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 155 optimal weight: 10.0000 chunk 2 optimal weight: 0.6980 chunk 167 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 207 ASN L 39 GLN L 161 GLN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 GLN I 77 GLN I 174 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.154133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.128238 restraints weight = 18090.105| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.04 r_work: 0.3267 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 14898 Z= 0.202 Angle : 0.604 7.715 20296 Z= 0.317 Chirality : 0.044 0.144 2300 Planarity : 0.005 0.079 2566 Dihedral : 4.760 37.472 2030 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.38 % Allowed : 14.37 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.20), residues: 1870 helix: 1.05 (0.37), residues: 208 sheet: 0.49 (0.17), residues: 860 loop : 0.31 (0.23), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 92 HIS 0.009 0.001 HIS L 190 PHE 0.020 0.002 PHE I 125 TYR 0.019 0.002 TYR A 103 ARG 0.004 0.001 ARG H 218 Details of bonding type rmsd hydrogen bonds : bond 0.03333 ( 578) hydrogen bonds : angle 5.65421 ( 1608) SS BOND : bond 0.00243 ( 22) SS BOND : angle 0.67786 ( 44) covalent geometry : bond 0.00483 (14876) covalent geometry : angle 0.60408 (20252) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 212 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 4 MET cc_start: 0.8451 (tpp) cc_final: 0.8032 (tpp) REVERT: L 17 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7755 (mm-30) REVERT: L 141 TYR cc_start: 0.8218 (t80) cc_final: 0.7536 (t80) REVERT: L 167 GLN cc_start: 0.7825 (tt0) cc_final: 0.7455 (mt0) REVERT: B 106 GLU cc_start: 0.7776 (pp20) cc_final: 0.7403 (pp20) REVERT: B 109 ARG cc_start: 0.8019 (ptm160) cc_final: 0.7757 (ptm160) REVERT: B 153 ASN cc_start: 0.8068 (OUTLIER) cc_final: 0.7743 (t0) REVERT: B 159 ASN cc_start: 0.7881 (p0) cc_final: 0.7141 (m110) REVERT: C 96 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8146 (mp0) REVERT: A 101 ASP cc_start: 0.8630 (t0) cc_final: 0.8283 (t0) REVERT: A 163 THR cc_start: 0.7555 (m) cc_final: 0.7348 (p) REVERT: D 19 LYS cc_start: 0.8167 (tttt) cc_final: 0.7783 (ttmm) REVERT: D 65 GLN cc_start: 0.6779 (mm-40) cc_final: 0.6063 (mm-40) REVERT: D 90 ASP cc_start: 0.8083 (m-30) cc_final: 0.7673 (t0) REVERT: E 104 LYS cc_start: 0.8578 (tttt) cc_final: 0.8056 (tptt) REVERT: F 106 GLU cc_start: 0.8173 (pp20) cc_final: 0.7757 (pm20) REVERT: G 32 THR cc_start: 0.8657 (p) cc_final: 0.8390 (t) REVERT: I 89 ASP cc_start: 0.8316 (t70) cc_final: 0.8082 (t70) REVERT: I 174 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7454 (mp10) REVERT: I 204 LYS cc_start: 0.7888 (mmpt) cc_final: 0.7568 (mmmt) outliers start: 56 outliers final: 43 residues processed: 257 average time/residue: 0.2754 time to fit residues: 102.1824 Evaluate side-chains 231 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 186 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 183 SER Chi-restraints excluded: chain L residue 200 GLN Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 204 CYS Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 122 SER Chi-restraints excluded: chain G residue 69 CYS Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 33 ASP Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 154 THR Chi-restraints excluded: chain I residue 174 GLN Chi-restraints excluded: chain I residue 210 VAL Chi-restraints excluded: chain I residue 213 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 169 optimal weight: 0.7980 chunk 163 optimal weight: 0.0970 chunk 181 optimal weight: 0.4980 chunk 7 optimal weight: 0.2980 chunk 62 optimal weight: 6.9990 chunk 137 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN H 31 ASN L 39 GLN L 161 GLN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN I 84 ASN I 174 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.155076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.129016 restraints weight = 17832.898| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.07 r_work: 0.3274 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.4791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 14898 Z= 0.148 Angle : 0.561 7.663 20296 Z= 0.292 Chirality : 0.043 0.183 2300 Planarity : 0.005 0.074 2566 Dihedral : 4.566 37.811 2030 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.44 % Allowed : 16.18 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.20), residues: 1870 helix: 1.27 (0.37), residues: 208 sheet: 0.47 (0.17), residues: 860 loop : 0.43 (0.24), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 157 HIS 0.010 0.001 HIS L 190 PHE 0.012 0.001 PHE E 99 TYR 0.020 0.002 TYR H 202 ARG 0.004 0.000 ARG H 67 Details of bonding type rmsd hydrogen bonds : bond 0.02950 ( 578) hydrogen bonds : angle 5.38952 ( 1608) SS BOND : bond 0.00178 ( 22) SS BOND : angle 0.56058 ( 44) covalent geometry : bond 0.00357 (14876) covalent geometry : angle 0.56124 (20252) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 196 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 31 ASN cc_start: 0.8207 (m-40) cc_final: 0.8002 (m110) REVERT: H 215 VAL cc_start: 0.8770 (OUTLIER) cc_final: 0.8433 (m) REVERT: L 17 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7843 (mm-30) REVERT: L 141 TYR cc_start: 0.8208 (t80) cc_final: 0.7945 (t80) REVERT: B 106 GLU cc_start: 0.7715 (pp20) cc_final: 0.7409 (pp20) REVERT: B 109 ARG cc_start: 0.8074 (ptm160) cc_final: 0.7859 (ptm160) REVERT: B 153 ASN cc_start: 0.8113 (OUTLIER) cc_final: 0.7730 (t0) REVERT: B 162 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6698 (mp0) REVERT: B 171 ASP cc_start: 0.7679 (t0) cc_final: 0.7430 (t0) REVERT: C 79 ILE cc_start: 0.8605 (mt) cc_final: 0.8381 (mp) REVERT: A 16 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.6886 (tm-30) REVERT: A 101 ASP cc_start: 0.8664 (t0) cc_final: 0.8308 (t0) REVERT: D 65 GLN cc_start: 0.6694 (mm-40) cc_final: 0.6064 (mm-40) REVERT: D 90 ASP cc_start: 0.8058 (m-30) cc_final: 0.7718 (t0) REVERT: E 104 LYS cc_start: 0.8501 (tttt) cc_final: 0.8024 (tptt) REVERT: E 188 GLU cc_start: 0.7377 (mm-30) cc_final: 0.6844 (mm-30) REVERT: F 106 GLU cc_start: 0.8217 (pp20) cc_final: 0.7715 (pt0) REVERT: G 32 THR cc_start: 0.8635 (p) cc_final: 0.8401 (t) REVERT: I 174 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7521 (mp10) REVERT: I 204 LYS cc_start: 0.7868 (mmpt) cc_final: 0.7576 (mmmt) outliers start: 57 outliers final: 40 residues processed: 243 average time/residue: 0.2845 time to fit residues: 99.3435 Evaluate side-chains 226 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 181 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 183 SER Chi-restraints excluded: chain L residue 200 GLN Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 122 SER Chi-restraints excluded: chain G residue 69 CYS Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 33 ASP Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 154 THR Chi-restraints excluded: chain I residue 174 GLN Chi-restraints excluded: chain I residue 210 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 30 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 184 optimal weight: 2.9990 chunk 26 optimal weight: 0.0050 chunk 174 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 54 ASN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 GLN E 156 GLN I 84 ASN I 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.147825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.120398 restraints weight = 18805.158| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.42 r_work: 0.3234 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.5319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.111 14898 Z= 0.250 Angle : 0.624 7.321 20296 Z= 0.326 Chirality : 0.045 0.158 2300 Planarity : 0.005 0.071 2566 Dihedral : 4.754 37.513 2030 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 5.37 % Allowed : 15.64 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.20), residues: 1870 helix: 1.11 (0.37), residues: 208 sheet: 0.30 (0.17), residues: 860 loop : 0.26 (0.23), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP I 47 HIS 0.008 0.001 HIS L 190 PHE 0.022 0.002 PHE F 117 TYR 0.023 0.002 TYR I 103 ARG 0.007 0.001 ARG E 212 Details of bonding type rmsd hydrogen bonds : bond 0.03329 ( 578) hydrogen bonds : angle 5.63398 ( 1608) SS BOND : bond 0.00224 ( 22) SS BOND : angle 0.69799 ( 44) covalent geometry : bond 0.00603 (14876) covalent geometry : angle 0.62396 (20252) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 211 time to evaluate : 1.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 87 ARG cc_start: 0.6793 (ptt-90) cc_final: 0.6533 (ptt-90) REVERT: H 89 GLU cc_start: 0.8274 (tp30) cc_final: 0.7908 (tp30) REVERT: H 215 VAL cc_start: 0.8767 (OUTLIER) cc_final: 0.8400 (m) REVERT: L 83 ASP cc_start: 0.8055 (m-30) cc_final: 0.7787 (t0) REVERT: L 141 TYR cc_start: 0.8350 (t80) cc_final: 0.7403 (t80) REVERT: L 148 GLN cc_start: 0.8165 (tp40) cc_final: 0.7827 (tp-100) REVERT: L 167 GLN cc_start: 0.8102 (tt0) cc_final: 0.7773 (mm-40) REVERT: L 168 ASP cc_start: 0.7408 (t0) cc_final: 0.7156 (t0) REVERT: B 106 GLU cc_start: 0.7954 (pp20) cc_final: 0.7533 (pp20) REVERT: B 153 ASN cc_start: 0.8302 (OUTLIER) cc_final: 0.7877 (t0) REVERT: B 162 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.7003 (mp0) REVERT: B 171 ASP cc_start: 0.7993 (t0) cc_final: 0.7737 (t0) REVERT: B 178 SER cc_start: 0.8616 (t) cc_final: 0.8337 (p) REVERT: B 200 GLN cc_start: 0.8111 (tm-30) cc_final: 0.7827 (tm-30) REVERT: C 95 LYS cc_start: 0.8289 (mtmm) cc_final: 0.8073 (mtmm) REVERT: C 96 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8052 (mp0) REVERT: A 5 LYS cc_start: 0.6576 (mmmt) cc_final: 0.5905 (mmtt) REVERT: A 16 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7063 (tm-30) REVERT: A 104 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7871 (mt) REVERT: D 65 GLN cc_start: 0.6891 (mm-40) cc_final: 0.6096 (mm-40) REVERT: D 90 ASP cc_start: 0.8291 (m-30) cc_final: 0.7714 (t0) REVERT: E 104 LYS cc_start: 0.8527 (tttt) cc_final: 0.7929 (tptt) REVERT: E 126 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7448 (mt) REVERT: F 28 SER cc_start: 0.8027 (t) cc_final: 0.7814 (p) REVERT: F 106 GLU cc_start: 0.8246 (pp20) cc_final: 0.7748 (pt0) REVERT: G 32 THR cc_start: 0.8721 (p) cc_final: 0.8503 (t) REVERT: I 72 ASP cc_start: 0.6909 (p0) cc_final: 0.6355 (t0) outliers start: 89 outliers final: 62 residues processed: 285 average time/residue: 0.2765 time to fit residues: 115.4666 Evaluate side-chains 253 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 185 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 165 THR Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 183 SER Chi-restraints excluded: chain L residue 200 GLN Chi-restraints excluded: chain B residue 4 MET Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 204 CYS Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 122 SER Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain G residue 69 CYS Chi-restraints excluded: chain I residue 17 THR Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 154 THR Chi-restraints excluded: chain I residue 210 VAL Chi-restraints excluded: chain I residue 213 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 67 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 141 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 185 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 39 GLN B 125 GLN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.150873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.124317 restraints weight = 18511.444| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.34 r_work: 0.3283 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.5517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 14898 Z= 0.146 Angle : 0.545 6.547 20296 Z= 0.284 Chirality : 0.043 0.138 2300 Planarity : 0.005 0.070 2566 Dihedral : 4.512 38.123 2030 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.29 % Allowed : 17.45 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.20), residues: 1870 helix: 1.43 (0.38), residues: 208 sheet: 0.32 (0.17), residues: 872 loop : 0.49 (0.24), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 157 HIS 0.004 0.000 HIS L 190 PHE 0.028 0.001 PHE F 117 TYR 0.016 0.002 TYR G 43 ARG 0.007 0.001 ARG F 212 Details of bonding type rmsd hydrogen bonds : bond 0.02841 ( 578) hydrogen bonds : angle 5.34576 ( 1608) SS BOND : bond 0.00173 ( 22) SS BOND : angle 0.56829 ( 44) covalent geometry : bond 0.00351 (14876) covalent geometry : angle 0.54479 (20252) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 206 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 87 ARG cc_start: 0.6671 (ptt-90) cc_final: 0.6372 (ptt-90) REVERT: H 215 VAL cc_start: 0.8753 (OUTLIER) cc_final: 0.8447 (m) REVERT: L 83 ASP cc_start: 0.7953 (m-30) cc_final: 0.7685 (t0) REVERT: L 141 TYR cc_start: 0.8314 (t80) cc_final: 0.7470 (t80) REVERT: L 190 HIS cc_start: 0.8019 (m-70) cc_final: 0.7671 (m-70) REVERT: B 106 GLU cc_start: 0.7812 (pp20) cc_final: 0.7486 (pp20) REVERT: B 153 ASN cc_start: 0.8353 (OUTLIER) cc_final: 0.7895 (t0) REVERT: B 162 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.7027 (mp0) REVERT: B 200 GLN cc_start: 0.8211 (tm-30) cc_final: 0.7931 (tm-30) REVERT: C 95 LYS cc_start: 0.8208 (mtmm) cc_final: 0.7955 (mtmm) REVERT: C 96 GLU cc_start: 0.8551 (mm-30) cc_final: 0.7678 (mp0) REVERT: A 5 LYS cc_start: 0.6381 (mmmt) cc_final: 0.5731 (mmtt) REVERT: A 16 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.6979 (tm-30) REVERT: A 101 ASP cc_start: 0.8491 (t0) cc_final: 0.7772 (t0) REVERT: A 104 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7745 (mt) REVERT: D 65 GLN cc_start: 0.6639 (mm-40) cc_final: 0.6093 (mm-40) REVERT: D 90 ASP cc_start: 0.8107 (m-30) cc_final: 0.7710 (t0) REVERT: E 104 LYS cc_start: 0.8380 (tttt) cc_final: 0.7843 (tptt) REVERT: E 126 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7216 (mt) REVERT: F 28 SER cc_start: 0.8004 (t) cc_final: 0.7755 (p) REVERT: F 106 GLU cc_start: 0.8216 (pp20) cc_final: 0.7661 (pt0) REVERT: G 32 THR cc_start: 0.8736 (p) cc_final: 0.8511 (t) REVERT: I 72 ASP cc_start: 0.6782 (p0) cc_final: 0.6271 (t0) outliers start: 71 outliers final: 53 residues processed: 262 average time/residue: 0.2973 time to fit residues: 112.7370 Evaluate side-chains 251 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 192 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 165 THR Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 183 SER Chi-restraints excluded: chain L residue 195 CYS Chi-restraints excluded: chain L residue 200 GLN Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 204 CYS Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 148 GLN Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 122 SER Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain G residue 69 CYS Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 105 ASN Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 154 THR Chi-restraints excluded: chain I residue 210 VAL Chi-restraints excluded: chain I residue 213 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 59 optimal weight: 9.9990 chunk 20 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 chunk 183 optimal weight: 0.8980 chunk 144 optimal weight: 0.6980 chunk 140 optimal weight: 1.9990 chunk 150 optimal weight: 7.9990 chunk 185 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 39 GLN L 161 GLN B 138 ASN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.152543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.128031 restraints weight = 18195.438| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.93 r_work: 0.3280 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.5711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 14898 Z= 0.154 Angle : 0.554 7.413 20296 Z= 0.289 Chirality : 0.042 0.145 2300 Planarity : 0.005 0.070 2566 Dihedral : 4.451 38.184 2030 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.71 % Allowed : 17.51 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.20), residues: 1870 helix: 1.46 (0.38), residues: 208 sheet: 0.35 (0.17), residues: 868 loop : 0.50 (0.24), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 157 HIS 0.003 0.001 HIS L 190 PHE 0.032 0.002 PHE F 117 TYR 0.027 0.002 TYR C 43 ARG 0.005 0.000 ARG E 212 Details of bonding type rmsd hydrogen bonds : bond 0.02855 ( 578) hydrogen bonds : angle 5.27676 ( 1608) SS BOND : bond 0.00158 ( 22) SS BOND : angle 0.57193 ( 44) covalent geometry : bond 0.00370 (14876) covalent geometry : angle 0.55375 (20252) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 190 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 87 ARG cc_start: 0.6786 (ptt-90) cc_final: 0.6427 (ptt-90) REVERT: H 191 THR cc_start: 0.7962 (OUTLIER) cc_final: 0.7756 (p) REVERT: H 215 VAL cc_start: 0.8740 (OUTLIER) cc_final: 0.8509 (m) REVERT: L 141 TYR cc_start: 0.8330 (t80) cc_final: 0.8119 (t80) REVERT: L 190 HIS cc_start: 0.7971 (m-70) cc_final: 0.7711 (m-70) REVERT: B 153 ASN cc_start: 0.8225 (OUTLIER) cc_final: 0.7805 (t0) REVERT: B 162 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6939 (mp0) REVERT: B 200 GLN cc_start: 0.8218 (tm-30) cc_final: 0.7677 (tm-30) REVERT: C 79 ILE cc_start: 0.8832 (mt) cc_final: 0.8614 (mp) REVERT: A 16 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6832 (tm-30) REVERT: A 101 ASP cc_start: 0.8578 (t0) cc_final: 0.8253 (t0) REVERT: A 104 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7763 (mt) REVERT: D 65 GLN cc_start: 0.6369 (mm-40) cc_final: 0.6010 (mm-40) REVERT: D 90 ASP cc_start: 0.8081 (m-30) cc_final: 0.7801 (t0) REVERT: E 104 LYS cc_start: 0.8441 (tttt) cc_final: 0.8017 (tptt) REVERT: E 126 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7419 (mt) REVERT: F 28 SER cc_start: 0.7867 (t) cc_final: 0.7609 (p) REVERT: F 106 GLU cc_start: 0.8150 (pp20) cc_final: 0.7675 (pt0) REVERT: G 32 THR cc_start: 0.8705 (p) cc_final: 0.8461 (t) REVERT: I 72 ASP cc_start: 0.6656 (p0) cc_final: 0.6354 (t0) outliers start: 78 outliers final: 63 residues processed: 252 average time/residue: 0.2899 time to fit residues: 106.2055 Evaluate side-chains 248 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 178 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 191 THR Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain H residue 205 ASN Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 165 THR Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 183 SER Chi-restraints excluded: chain L residue 195 CYS Chi-restraints excluded: chain L residue 200 GLN Chi-restraints excluded: chain B residue 4 MET Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 204 CYS Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 148 GLN Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 122 SER Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain G residue 69 CYS Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 154 THR Chi-restraints excluded: chain I residue 210 VAL Chi-restraints excluded: chain I residue 213 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 132 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 155 optimal weight: 7.9990 chunk 45 optimal weight: 0.3980 chunk 151 optimal weight: 0.4980 chunk 7 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN I 105 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.151495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.126784 restraints weight = 18184.394| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.94 r_work: 0.3269 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.5875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 14898 Z= 0.181 Angle : 0.569 7.497 20296 Z= 0.296 Chirality : 0.043 0.147 2300 Planarity : 0.005 0.072 2566 Dihedral : 4.497 37.886 2030 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.83 % Allowed : 17.51 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.20), residues: 1870 helix: 1.49 (0.38), residues: 206 sheet: 0.30 (0.17), residues: 868 loop : 0.46 (0.24), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 47 HIS 0.003 0.001 HIS L 190 PHE 0.030 0.002 PHE F 117 TYR 0.033 0.002 TYR C 43 ARG 0.007 0.001 ARG E 212 Details of bonding type rmsd hydrogen bonds : bond 0.02964 ( 578) hydrogen bonds : angle 5.34548 ( 1608) SS BOND : bond 0.00164 ( 22) SS BOND : angle 0.59493 ( 44) covalent geometry : bond 0.00436 (14876) covalent geometry : angle 0.56848 (20252) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 187 time to evaluate : 2.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 191 THR cc_start: 0.7974 (OUTLIER) cc_final: 0.7761 (p) REVERT: H 215 VAL cc_start: 0.8675 (OUTLIER) cc_final: 0.8471 (m) REVERT: L 141 TYR cc_start: 0.8341 (t80) cc_final: 0.7616 (t80) REVERT: B 153 ASN cc_start: 0.8247 (OUTLIER) cc_final: 0.7829 (t0) REVERT: B 162 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6951 (mp0) REVERT: B 171 ASP cc_start: 0.7651 (t0) cc_final: 0.7252 (t0) REVERT: B 200 GLN cc_start: 0.8303 (tm-30) cc_final: 0.7812 (tm-30) REVERT: C 79 ILE cc_start: 0.8841 (mt) cc_final: 0.8613 (mp) REVERT: A 16 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.6907 (tm-30) REVERT: A 104 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7861 (mt) REVERT: D 65 GLN cc_start: 0.6406 (mm-40) cc_final: 0.6034 (mm-40) REVERT: D 90 ASP cc_start: 0.8186 (m-30) cc_final: 0.7853 (t0) REVERT: E 104 LYS cc_start: 0.8455 (tttt) cc_final: 0.8028 (tptt) REVERT: E 126 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7480 (mt) REVERT: E 150 LYS cc_start: 0.7857 (ttmm) cc_final: 0.7200 (tttm) REVERT: F 28 SER cc_start: 0.7907 (t) cc_final: 0.7648 (p) REVERT: F 106 GLU cc_start: 0.8187 (pp20) cc_final: 0.7686 (pt0) REVERT: F 143 ARG cc_start: 0.8250 (ttp80) cc_final: 0.7492 (tmt170) REVERT: F 191 LYS cc_start: 0.7039 (ttpp) cc_final: 0.6726 (ttpp) REVERT: F 192 VAL cc_start: 0.7663 (OUTLIER) cc_final: 0.7358 (m) REVERT: G 32 THR cc_start: 0.8727 (p) cc_final: 0.8494 (t) REVERT: I 72 ASP cc_start: 0.6709 (p0) cc_final: 0.6475 (t0) outliers start: 80 outliers final: 65 residues processed: 252 average time/residue: 0.3443 time to fit residues: 128.8565 Evaluate side-chains 252 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 179 time to evaluate : 2.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 191 THR Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain H residue 205 ASN Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 165 THR Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 183 SER Chi-restraints excluded: chain L residue 195 CYS Chi-restraints excluded: chain L residue 200 GLN Chi-restraints excluded: chain B residue 4 MET Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 50 TYR Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 204 CYS Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 148 GLN Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 50 TYR Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 122 SER Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain G residue 69 CYS Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 154 THR Chi-restraints excluded: chain I residue 210 VAL Chi-restraints excluded: chain I residue 213 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 0.8980 chunk 93 optimal weight: 6.9990 chunk 37 optimal weight: 0.0970 chunk 164 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 169 optimal weight: 0.0040 chunk 26 optimal weight: 0.9990 chunk 173 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 39 GLN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.153551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.128988 restraints weight = 18120.478| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.92 r_work: 0.3313 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.5948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14898 Z= 0.113 Angle : 0.531 6.394 20296 Z= 0.277 Chirality : 0.042 0.141 2300 Planarity : 0.005 0.071 2566 Dihedral : 4.298 38.195 2030 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.99 % Allowed : 18.30 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.20), residues: 1870 helix: 1.71 (0.39), residues: 206 sheet: 0.36 (0.17), residues: 882 loop : 0.55 (0.25), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 157 HIS 0.002 0.000 HIS L 190 PHE 0.032 0.001 PHE F 117 TYR 0.027 0.001 TYR C 43 ARG 0.003 0.000 ARG L 18 Details of bonding type rmsd hydrogen bonds : bond 0.02680 ( 578) hydrogen bonds : angle 5.09972 ( 1608) SS BOND : bond 0.00155 ( 22) SS BOND : angle 0.47838 ( 44) covalent geometry : bond 0.00272 (14876) covalent geometry : angle 0.53093 (20252) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 192 time to evaluate : 2.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 87 ARG cc_start: 0.6790 (ptt-90) cc_final: 0.6576 (ptt-90) REVERT: H 89 GLU cc_start: 0.8023 (tp30) cc_final: 0.7821 (tp30) REVERT: H 191 THR cc_start: 0.7944 (OUTLIER) cc_final: 0.7737 (p) REVERT: L 141 TYR cc_start: 0.8272 (t80) cc_final: 0.7437 (t80) REVERT: L 168 ASP cc_start: 0.7471 (t0) cc_final: 0.7267 (t0) REVERT: L 196 GLU cc_start: 0.7743 (pt0) cc_final: 0.7355 (tt0) REVERT: B 106 GLU cc_start: 0.7747 (pp20) cc_final: 0.7422 (pp20) REVERT: B 153 ASN cc_start: 0.8204 (OUTLIER) cc_final: 0.7788 (t0) REVERT: B 171 ASP cc_start: 0.7700 (t0) cc_final: 0.7265 (t0) REVERT: A 16 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6873 (tm-30) REVERT: A 101 ASP cc_start: 0.8569 (t0) cc_final: 0.7988 (t0) REVERT: D 52 PHE cc_start: 0.8118 (t80) cc_final: 0.7765 (t80) REVERT: D 65 GLN cc_start: 0.6146 (mm-40) cc_final: 0.5936 (mm-40) REVERT: D 90 ASP cc_start: 0.8038 (m-30) cc_final: 0.7832 (t0) REVERT: E 104 LYS cc_start: 0.8391 (tttt) cc_final: 0.7993 (tptt) REVERT: E 126 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7399 (mt) REVERT: F 28 SER cc_start: 0.7813 (t) cc_final: 0.7562 (p) REVERT: F 106 GLU cc_start: 0.8077 (pp20) cc_final: 0.7645 (pt0) REVERT: F 143 ARG cc_start: 0.8258 (ttp80) cc_final: 0.7521 (tmt170) REVERT: F 191 LYS cc_start: 0.6961 (ttpp) cc_final: 0.6675 (ttpp) REVERT: F 192 VAL cc_start: 0.7585 (OUTLIER) cc_final: 0.7278 (m) REVERT: G 32 THR cc_start: 0.8701 (p) cc_final: 0.8465 (t) REVERT: I 72 ASP cc_start: 0.6754 (p0) cc_final: 0.6503 (t0) REVERT: I 211 ASP cc_start: 0.8733 (t0) cc_final: 0.8421 (t0) outliers start: 66 outliers final: 50 residues processed: 242 average time/residue: 0.3101 time to fit residues: 108.6854 Evaluate side-chains 234 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 179 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 191 THR Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain H residue 205 ASN Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 183 SER Chi-restraints excluded: chain L residue 200 GLN Chi-restraints excluded: chain B residue 4 MET Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 204 CYS Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 148 GLN Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 50 TYR Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 122 SER Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain G residue 69 CYS Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 154 THR Chi-restraints excluded: chain I residue 210 VAL Chi-restraints excluded: chain I residue 213 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 77 optimal weight: 0.4980 chunk 151 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 112 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 139 optimal weight: 0.5980 chunk 163 optimal weight: 0.0670 chunk 172 optimal weight: 3.9990 chunk 153 optimal weight: 8.9990 chunk 156 optimal weight: 5.9990 overall best weight: 1.4322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 39 GLN B 138 ASN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.149200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.124254 restraints weight = 18359.734| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.10 r_work: 0.3236 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.6121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 14898 Z= 0.191 Angle : 0.586 9.611 20296 Z= 0.304 Chirality : 0.043 0.144 2300 Planarity : 0.005 0.072 2566 Dihedral : 4.471 38.319 2030 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.93 % Allowed : 18.42 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.20), residues: 1870 helix: 1.54 (0.38), residues: 206 sheet: 0.31 (0.17), residues: 878 loop : 0.46 (0.24), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 47 HIS 0.002 0.001 HIS E 35 PHE 0.014 0.002 PHE C 98 TYR 0.035 0.002 TYR C 43 ARG 0.005 0.001 ARG E 212 Details of bonding type rmsd hydrogen bonds : bond 0.02989 ( 578) hydrogen bonds : angle 5.32594 ( 1608) SS BOND : bond 0.00158 ( 22) SS BOND : angle 0.59354 ( 44) covalent geometry : bond 0.00461 (14876) covalent geometry : angle 0.58630 (20252) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 182 time to evaluate : 2.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 87 ARG cc_start: 0.6823 (ptt-90) cc_final: 0.6597 (ptt-90) REVERT: H 191 THR cc_start: 0.8005 (OUTLIER) cc_final: 0.7799 (p) REVERT: L 141 TYR cc_start: 0.8306 (t80) cc_final: 0.7558 (t80) REVERT: L 148 GLN cc_start: 0.8071 (tp40) cc_final: 0.7768 (tp-100) REVERT: L 196 GLU cc_start: 0.7823 (pt0) cc_final: 0.7396 (tt0) REVERT: B 153 ASN cc_start: 0.8319 (OUTLIER) cc_final: 0.7890 (t0) REVERT: B 171 ASP cc_start: 0.7834 (t0) cc_final: 0.7340 (t0) REVERT: A 16 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.6909 (tm-30) REVERT: D 65 GLN cc_start: 0.6488 (mm-40) cc_final: 0.6024 (mm-40) REVERT: D 90 ASP cc_start: 0.8278 (m-30) cc_final: 0.7886 (t0) REVERT: E 104 LYS cc_start: 0.8452 (tttt) cc_final: 0.8019 (tptt) REVERT: E 126 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7482 (mt) REVERT: F 28 SER cc_start: 0.7930 (t) cc_final: 0.7653 (p) REVERT: F 106 GLU cc_start: 0.8011 (pp20) cc_final: 0.7682 (pt0) REVERT: F 143 ARG cc_start: 0.8282 (ttp80) cc_final: 0.7512 (tmt170) REVERT: F 191 LYS cc_start: 0.7043 (ttpp) cc_final: 0.6728 (ttpp) REVERT: F 192 VAL cc_start: 0.7597 (OUTLIER) cc_final: 0.7308 (m) REVERT: G 32 THR cc_start: 0.8741 (p) cc_final: 0.8520 (t) REVERT: I 72 ASP cc_start: 0.6858 (p0) cc_final: 0.6399 (t0) outliers start: 65 outliers final: 56 residues processed: 235 average time/residue: 0.2942 time to fit residues: 101.1399 Evaluate side-chains 241 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 180 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 191 THR Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain H residue 205 ASN Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 183 SER Chi-restraints excluded: chain L residue 195 CYS Chi-restraints excluded: chain L residue 200 GLN Chi-restraints excluded: chain B residue 4 MET Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 204 CYS Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 148 GLN Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 50 TYR Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 122 SER Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain G residue 69 CYS Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 154 THR Chi-restraints excluded: chain I residue 210 VAL Chi-restraints excluded: chain I residue 213 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 143 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 114 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 chunk 62 optimal weight: 0.0170 chunk 180 optimal weight: 6.9990 overall best weight: 0.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 39 GLN B 138 ASN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 ASN I 84 ASN I 105 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.151961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.127576 restraints weight = 18198.983| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.95 r_work: 0.3287 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.6188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14898 Z= 0.134 Angle : 0.546 7.563 20296 Z= 0.284 Chirality : 0.042 0.142 2300 Planarity : 0.005 0.072 2566 Dihedral : 4.337 38.287 2030 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.86 % Allowed : 18.72 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.20), residues: 1870 helix: 1.66 (0.38), residues: 206 sheet: 0.28 (0.17), residues: 886 loop : 0.58 (0.25), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 33 HIS 0.003 0.000 HIS L 190 PHE 0.010 0.001 PHE E 99 TYR 0.030 0.002 TYR C 43 ARG 0.003 0.000 ARG L 18 Details of bonding type rmsd hydrogen bonds : bond 0.02779 ( 578) hydrogen bonds : angle 5.16748 ( 1608) SS BOND : bond 0.00152 ( 22) SS BOND : angle 0.50340 ( 44) covalent geometry : bond 0.00322 (14876) covalent geometry : angle 0.54616 (20252) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8189.30 seconds wall clock time: 145 minutes 0.82 seconds (8700.82 seconds total)