Starting phenix.real_space_refine on Thu Sep 18 05:40:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zeu_60046/09_2025/8zeu_60046.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zeu_60046/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8zeu_60046/09_2025/8zeu_60046.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zeu_60046/09_2025/8zeu_60046.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zeu_60046/09_2025/8zeu_60046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zeu_60046/09_2025/8zeu_60046.map" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.071 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.57, per 1000 atoms: 0.25 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: 1.22 Conformation dependent library (CDL) restraints added in 563.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.71 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: 2.44 Time building geometry restraints manager: 1.58 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: 0.01 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: 3.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.230 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.440 ------------------------------------------------------------------------------- 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 : 7.85 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (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 ARG 0.005 0.000 ARG L 18 TYR 0.054 0.002 TYR B 50 PHE 0.010 0.001 PHE F 140 TRP 0.038 0.002 TRP L 92 HIS 0.003 0.001 HIS F 190 Details of bonding type rmsd covalent geometry : bond 0.00411 (14876) covalent geometry : angle 0.60989 (20252) SS BOND : bond 0.00222 ( 22) SS BOND : angle 0.74317 ( 44) hydrogen bonds : bond 0.11353 ( 578) hydrogen bonds : angle 6.70990 ( 1608) *********************** 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 : 0.548 Fit side-chains 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: 0.7379 (t80) REVERT: B 153 ASN cc_start: 0.7706 (OUTLIER) cc_final: 0.7502 (t0) REVERT: B 159 ASN cc_start: 0.7072 (p0) cc_final: 0.6816 (m110) REVERT: E 104 LYS cc_start: 0.7897 (tttt) cc_final: 0.7597 (tptt) REVERT: E 126 LEU cc_start: 0.7058 (mm) cc_final: 0.6753 (mt) REVERT: E 188 GLU cc_start: 0.7226 (mt-10) cc_final: 0.6969 (mm-30) REVERT: F 75 THR cc_start: 0.8781 (m) cc_final: 0.8496 (p) REVERT: F 106 GLU cc_start: 0.7325 (pp20) cc_final: 0.6743 (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: 0.1354 time to fit residues: 78.2650 Evaluate side-chains 220 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 219 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 207 ASN L 39 GLN L 54 ASN L 161 GLN ** L 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.169510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.145353 restraints weight = 17986.413| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 1.69 r_work: 0.3596 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3456 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 14898 Z= 0.153 Angle : 0.588 7.558 20296 Z= 0.310 Chirality : 0.044 0.148 2300 Planarity : 0.005 0.069 2566 Dihedral : 4.513 38.222 2030 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.66 % Allowed : 9.24 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.20), residues: 1870 helix: 1.33 (0.38), residues: 206 sheet: 0.69 (0.17), residues: 846 loop : 0.76 (0.24), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 66 TYR 0.017 0.002 TYR H 27 PHE 0.020 0.002 PHE I 125 TRP 0.019 0.001 TRP E 92 HIS 0.007 0.001 HIS L 190 Details of bonding type rmsd covalent geometry : bond 0.00365 (14876) covalent geometry : angle 0.58806 (20252) SS BOND : bond 0.00448 ( 22) SS BOND : angle 0.61468 ( 44) hydrogen bonds : bond 0.03168 ( 578) hydrogen bonds : angle 5.48278 ( 1608) *********************** 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 292 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 248 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 188 SER cc_start: 0.8919 (t) cc_final: 0.8662 (t) REVERT: L 91 GLN cc_start: 0.8792 (pp30) cc_final: 0.8577 (pp30) REVERT: B 106 GLU cc_start: 0.7436 (pp20) cc_final: 0.7186 (pp20) REVERT: B 153 ASN cc_start: 0.7822 (OUTLIER) cc_final: 0.7409 (t0) REVERT: B 159 ASN cc_start: 0.7269 (p0) cc_final: 0.6842 (m110) REVERT: D 10 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7550 (mt-10) REVERT: D 65 GLN cc_start: 0.6788 (mm-40) cc_final: 0.6365 (mm-40) REVERT: E 3 VAL cc_start: 0.7525 (OUTLIER) cc_final: 0.7304 (p) REVERT: E 104 LYS cc_start: 0.8493 (tttt) cc_final: 0.8067 (tptt) REVERT: E 126 LEU cc_start: 0.7522 (mm) cc_final: 0.7207 (mt) REVERT: E 156 GLN cc_start: 0.8086 (mm-40) cc_final: 0.7862 (mm-40) REVERT: E 188 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6901 (mm-30) REVERT: G 50 ASP cc_start: 0.7848 (m-30) cc_final: 0.7500 (m-30) REVERT: G 97 MET cc_start: 0.7789 (tpp) cc_final: 0.6806 (tpp) REVERT: I 174 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.7218 (mp10) outliers start: 44 outliers final: 29 residues processed: 276 average time/residue: 0.1392 time to fit residues: 54.5645 Evaluate side-chains 228 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 196 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain H residue 203 ILE 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 182 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 79 VAL 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 D residue 37 VAL Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 106 GLU 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 122 SER Chi-restraints excluded: chain F residue 138 ASN Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain I residue 17 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 174 GLN Chi-restraints excluded: chain I residue 185 VAL 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 93 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 161 optimal weight: 7.9990 chunk 57 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 152 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN L 161 GLN L 200 GLN D 6 GLN I 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.155407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.129148 restraints weight = 18247.608| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.06 r_work: 0.3300 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.119 14898 Z= 0.254 Angle : 0.663 7.669 20296 Z= 0.349 Chirality : 0.045 0.160 2300 Planarity : 0.005 0.075 2566 Dihedral : 4.780 35.781 2030 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.96 % Allowed : 12.14 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.20), residues: 1870 helix: 0.93 (0.36), residues: 208 sheet: 0.53 (0.17), residues: 854 loop : 0.54 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 218 TYR 0.028 0.002 TYR I 103 PHE 0.025 0.002 PHE D 29 TRP 0.020 0.002 TRP E 92 HIS 0.007 0.001 HIS L 190 Details of bonding type rmsd covalent geometry : bond 0.00605 (14876) covalent geometry : angle 0.66284 (20252) SS BOND : bond 0.00776 ( 22) SS BOND : angle 0.89215 ( 44) hydrogen bonds : bond 0.03647 ( 578) hydrogen bonds : angle 5.63139 ( 1608) *********************** 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 280 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 231 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 31 ASN cc_start: 0.8015 (m-40) cc_final: 0.7807 (m110) REVERT: L 17 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7590 (mm-30) REVERT: L 68 SER cc_start: 0.8354 (p) cc_final: 0.8075 (t) REVERT: L 141 TYR cc_start: 0.8212 (t80) cc_final: 0.7639 (t80) REVERT: B 106 GLU cc_start: 0.7654 (pp20) cc_final: 0.7446 (pp20) REVERT: B 153 ASN cc_start: 0.8023 (OUTLIER) cc_final: 0.7669 (t0) REVERT: C 79 ILE cc_start: 0.8741 (mt) cc_final: 0.8511 (mp) REVERT: C 96 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8223 (mp0) REVERT: A 163 THR cc_start: 0.7458 (m) cc_final: 0.7250 (p) REVERT: D 65 GLN cc_start: 0.6750 (mm-40) cc_final: 0.6082 (mm-40) REVERT: E 104 LYS cc_start: 0.8625 (tttt) cc_final: 0.8119 (tptt) REVERT: E 188 GLU cc_start: 0.7417 (mt-10) cc_final: 0.7009 (mm-30) REVERT: G 32 THR cc_start: 0.8647 (p) cc_final: 0.8385 (t) REVERT: I 87 PRO cc_start: 0.7789 (Cg_exo) cc_final: 0.7449 (Cg_endo) outliers start: 49 outliers final: 33 residues processed: 272 average time/residue: 0.1370 time to fit residues: 52.9261 Evaluate side-chains 217 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 183 time to evaluate : 0.549 ------------------------------------------------------------------------------- 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 30 SER Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 182 LEU 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 124 GLU Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 155 VAL 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 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 122 SER Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 122 SER Chi-restraints excluded: chain I residue 17 THR 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 154 THR Chi-restraints excluded: chain I residue 210 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 34 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 153 optimal weight: 0.7980 chunk 136 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 159 optimal weight: 0.7980 chunk 125 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 161 GLN A 195 GLN D 200 GLN E 139 ASN I 84 ASN I 174 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.156508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.130842 restraints weight = 18062.774| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.01 r_work: 0.3357 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 14898 Z= 0.156 Angle : 0.562 8.178 20296 Z= 0.294 Chirality : 0.043 0.139 2300 Planarity : 0.005 0.074 2566 Dihedral : 4.535 35.766 2030 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.14 % Allowed : 14.13 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.20), residues: 1870 helix: 1.24 (0.37), residues: 208 sheet: 0.56 (0.17), residues: 870 loop : 0.55 (0.24), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 103 TYR 0.015 0.002 TYR H 105 PHE 0.013 0.002 PHE E 99 TRP 0.012 0.001 TRP D 111 HIS 0.010 0.001 HIS L 190 Details of bonding type rmsd covalent geometry : bond 0.00372 (14876) covalent geometry : angle 0.56192 (20252) SS BOND : bond 0.00249 ( 22) SS BOND : angle 0.71134 ( 44) hydrogen bonds : bond 0.02961 ( 578) hydrogen bonds : angle 5.34138 ( 1608) *********************** 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 257 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 205 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 141 TYR cc_start: 0.8357 (t80) cc_final: 0.7584 (t80) REVERT: B 153 ASN cc_start: 0.7920 (OUTLIER) cc_final: 0.7593 (t0) REVERT: C 96 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8031 (mp0) REVERT: C 143 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7688 (tp40) REVERT: A 16 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.6887 (tm-30) REVERT: A 101 ASP cc_start: 0.8502 (t0) cc_final: 0.7851 (t0) REVERT: D 65 GLN cc_start: 0.6544 (mm-40) cc_final: 0.6247 (mm-40) REVERT: E 104 LYS cc_start: 0.8505 (tttt) cc_final: 0.8115 (tptt) REVERT: E 188 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7022 (mm-30) REVERT: E 212 ARG cc_start: 0.6348 (mtm110) cc_final: 0.5986 (mtp-110) REVERT: F 143 ARG cc_start: 0.8140 (ttp80) cc_final: 0.7425 (tmt170) REVERT: G 32 THR cc_start: 0.8605 (p) cc_final: 0.8348 (t) REVERT: G 50 ASP cc_start: 0.7934 (m-30) cc_final: 0.7701 (m-30) REVERT: I 85 MET cc_start: 0.7385 (mmm) cc_final: 0.7041 (mmt) REVERT: I 87 PRO cc_start: 0.7730 (Cg_exo) cc_final: 0.7518 (Cg_endo) outliers start: 52 outliers final: 39 residues processed: 245 average time/residue: 0.1244 time to fit residues: 44.1028 Evaluate side-chains 221 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 179 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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 203 ILE 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 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 192 VAL Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 143 GLN 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 D residue 11 VAL Chi-restraints excluded: chain D residue 37 VAL 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 122 SER 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 70 THR Chi-restraints excluded: chain F residue 122 SER Chi-restraints excluded: chain G residue 69 CYS Chi-restraints excluded: chain I residue 18 LEU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 65 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 164 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 163 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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** I 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.152289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.127119 restraints weight = 18263.333| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.04 r_work: 0.3305 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 14898 Z= 0.232 Angle : 0.612 7.943 20296 Z= 0.319 Chirality : 0.044 0.165 2300 Planarity : 0.005 0.072 2566 Dihedral : 4.648 35.603 2030 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.68 % Allowed : 16.24 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.20), residues: 1870 helix: 1.19 (0.37), residues: 210 sheet: 0.42 (0.17), residues: 864 loop : 0.44 (0.24), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 103 TYR 0.020 0.002 TYR I 103 PHE 0.014 0.002 PHE H 64 TRP 0.016 0.002 TRP D 111 HIS 0.007 0.001 HIS L 190 Details of bonding type rmsd covalent geometry : bond 0.00555 (14876) covalent geometry : angle 0.61212 (20252) SS BOND : bond 0.00222 ( 22) SS BOND : angle 0.75885 ( 44) hydrogen bonds : bond 0.03198 ( 578) hydrogen bonds : angle 5.52296 ( 1608) *********************** 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 272 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 211 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 141 TYR cc_start: 0.8312 (t80) cc_final: 0.7646 (t80) REVERT: L 168 ASP cc_start: 0.7656 (t0) cc_final: 0.7433 (t0) REVERT: B 153 ASN cc_start: 0.7912 (OUTLIER) cc_final: 0.7601 (t0) REVERT: B 171 ASP cc_start: 0.7831 (t0) cc_final: 0.7604 (t0) REVERT: B 200 GLN cc_start: 0.8278 (tm-30) cc_final: 0.7978 (tm-30) REVERT: C 143 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7854 (tp40) REVERT: A 16 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6949 (tm-30) REVERT: A 101 ASP cc_start: 0.8628 (t0) cc_final: 0.8338 (t0) REVERT: E 104 LYS cc_start: 0.8555 (tttt) cc_final: 0.8269 (tptt) REVERT: E 184 LYS cc_start: 0.8116 (ttpt) cc_final: 0.7680 (ttpt) REVERT: F 143 ARG cc_start: 0.8266 (ttp80) cc_final: 0.7613 (tmt170) REVERT: I 72 ASP cc_start: 0.6613 (p0) cc_final: 0.6049 (t0) REVERT: I 87 PRO cc_start: 0.7695 (Cg_exo) cc_final: 0.7478 (Cg_endo) outliers start: 61 outliers final: 47 residues processed: 262 average time/residue: 0.1323 time to fit residues: 49.7535 Evaluate side-chains 237 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 187 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 188 SER 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 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 192 VAL Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 143 GLN 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 186 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 86 VAL 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 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 18 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 45 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 167 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 166 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 184 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 39 GLN L 167 GLN B 125 GLN B 156 GLN I 77 GLN I 84 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.154766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.129529 restraints weight = 18029.112| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.01 r_work: 0.3287 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.5286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 14898 Z= 0.133 Angle : 0.544 8.105 20296 Z= 0.283 Chirality : 0.042 0.143 2300 Planarity : 0.005 0.068 2566 Dihedral : 4.451 35.842 2030 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.93 % Allowed : 16.91 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.20), residues: 1870 helix: 1.40 (0.38), residues: 208 sheet: 0.47 (0.17), residues: 874 loop : 0.58 (0.24), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 212 TYR 0.021 0.001 TYR H 105 PHE 0.023 0.001 PHE F 117 TRP 0.010 0.001 TRP A 157 HIS 0.005 0.000 HIS L 190 Details of bonding type rmsd covalent geometry : bond 0.00318 (14876) covalent geometry : angle 0.54403 (20252) SS BOND : bond 0.00178 ( 22) SS BOND : angle 0.53662 ( 44) hydrogen bonds : bond 0.02797 ( 578) hydrogen bonds : angle 5.24598 ( 1608) *********************** 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 263 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 198 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 209 LYS cc_start: 0.7781 (mmtt) cc_final: 0.7568 (mmtp) REVERT: L 141 TYR cc_start: 0.8272 (t80) cc_final: 0.7564 (t80) REVERT: L 168 ASP cc_start: 0.7365 (t0) cc_final: 0.7099 (t0) REVERT: L 190 HIS cc_start: 0.7955 (m-70) cc_final: 0.7619 (m-70) REVERT: B 153 ASN cc_start: 0.7994 (OUTLIER) cc_final: 0.7664 (t0) REVERT: B 162 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6726 (mp0) REVERT: B 171 ASP cc_start: 0.7901 (t0) cc_final: 0.7671 (t0) REVERT: B 200 GLN cc_start: 0.8166 (tm-30) cc_final: 0.7886 (tm-30) REVERT: C 79 ILE cc_start: 0.8724 (mt) cc_final: 0.8491 (mp) REVERT: C 143 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7737 (tp40) REVERT: A 5 LYS cc_start: 0.6331 (mmmt) cc_final: 0.5823 (mmtt) REVERT: A 16 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.6910 (tm-30) REVERT: A 101 ASP cc_start: 0.8628 (t0) cc_final: 0.8343 (t0) REVERT: D 90 ASP cc_start: 0.8175 (t0) cc_final: 0.7182 (t0) REVERT: E 104 LYS cc_start: 0.8452 (tttt) cc_final: 0.8014 (tptt) REVERT: F 143 ARG cc_start: 0.8245 (ttp80) cc_final: 0.7630 (tmt170) REVERT: I 72 ASP cc_start: 0.6620 (p0) cc_final: 0.6114 (t0) outliers start: 65 outliers final: 44 residues processed: 252 average time/residue: 0.1276 time to fit residues: 46.6526 Evaluate side-chains 236 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 188 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 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 86 VAL Chi-restraints excluded: chain L residue 165 THR Chi-restraints excluded: chain L residue 180 LEU 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 124 GLU Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 143 GLN 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 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 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 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 70 THR Chi-restraints excluded: chain F residue 122 SER Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain G residue 32 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 2 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 156 optimal weight: 7.9990 chunk 66 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 83 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 163 ASN L 39 GLN ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.153438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.128462 restraints weight = 18095.532| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.97 r_work: 0.3278 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.5527 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= 0.160 Angle : 0.566 7.987 20296 Z= 0.294 Chirality : 0.042 0.139 2300 Planarity : 0.005 0.069 2566 Dihedral : 4.433 35.626 2030 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.11 % Allowed : 16.85 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.20), residues: 1870 helix: 1.38 (0.38), residues: 208 sheet: 0.50 (0.17), residues: 864 loop : 0.54 (0.24), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 212 TYR 0.022 0.002 TYR G 43 PHE 0.031 0.002 PHE F 117 TRP 0.011 0.001 TRP I 47 HIS 0.004 0.001 HIS L 190 Details of bonding type rmsd covalent geometry : bond 0.00385 (14876) covalent geometry : angle 0.56605 (20252) SS BOND : bond 0.00159 ( 22) SS BOND : angle 0.59001 ( 44) hydrogen bonds : bond 0.02873 ( 578) hydrogen bonds : angle 5.22619 ( 1608) *********************** 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: 68 poor density : 200 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 209 LYS cc_start: 0.7838 (mmtt) cc_final: 0.7609 (mmtp) REVERT: L 141 TYR cc_start: 0.8305 (t80) cc_final: 0.7612 (t80) REVERT: L 190 HIS cc_start: 0.7930 (m-70) cc_final: 0.7653 (m-70) REVERT: B 153 ASN cc_start: 0.8034 (OUTLIER) cc_final: 0.7701 (t0) REVERT: B 171 ASP cc_start: 0.7940 (t0) cc_final: 0.7737 (t0) REVERT: B 200 GLN cc_start: 0.8195 (tm-30) cc_final: 0.7919 (tm-30) REVERT: C 79 ILE cc_start: 0.8783 (mt) cc_final: 0.8526 (mp) REVERT: C 82 LEU cc_start: 0.8916 (tp) cc_final: 0.8539 (tp) REVERT: C 143 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7713 (tp40) REVERT: A 16 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.7028 (tm-30) REVERT: A 104 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7847 (mt) REVERT: D 90 ASP cc_start: 0.8278 (t0) cc_final: 0.7262 (t0) REVERT: E 104 LYS cc_start: 0.8492 (tttt) cc_final: 0.8045 (tptt) REVERT: E 126 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7467 (mt) REVERT: F 28 SER cc_start: 0.7929 (t) cc_final: 0.7674 (p) REVERT: F 143 ARG cc_start: 0.8218 (ttp80) cc_final: 0.7602 (tmt170) REVERT: I 72 ASP cc_start: 0.6642 (p0) cc_final: 0.6294 (t0) outliers start: 68 outliers final: 47 residues processed: 257 average time/residue: 0.1316 time to fit residues: 48.9943 Evaluate side-chains 241 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 189 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 163 ASN Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 188 SER 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 86 VAL Chi-restraints excluded: chain L residue 165 THR Chi-restraints excluded: chain L residue 180 LEU 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 C residue 69 CYS Chi-restraints excluded: chain C residue 143 GLN 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 104 LEU Chi-restraints excluded: chain A residue 124 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 28 SER Chi-restraints excluded: chain E residue 86 VAL 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 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 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 22 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 chunk 173 optimal weight: 5.9990 chunk 144 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 59 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 GLN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.152251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.127702 restraints weight = 18190.777| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.93 r_work: 0.3263 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.5729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 14898 Z= 0.185 Angle : 0.582 8.288 20296 Z= 0.303 Chirality : 0.043 0.135 2300 Planarity : 0.005 0.072 2566 Dihedral : 4.473 35.369 2030 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.93 % Allowed : 17.57 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.20), residues: 1870 helix: 1.30 (0.38), residues: 208 sheet: 0.44 (0.17), residues: 864 loop : 0.51 (0.24), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 212 TYR 0.019 0.002 TYR G 43 PHE 0.032 0.002 PHE F 117 TRP 0.011 0.001 TRP I 47 HIS 0.003 0.001 HIS L 190 Details of bonding type rmsd covalent geometry : bond 0.00445 (14876) covalent geometry : angle 0.58239 (20252) SS BOND : bond 0.00166 ( 22) SS BOND : angle 0.62187 ( 44) hydrogen bonds : bond 0.02949 ( 578) hydrogen bonds : angle 5.30647 ( 1608) *********************** 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 264 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 199 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 209 LYS cc_start: 0.7870 (mmtt) cc_final: 0.7565 (mmtp) REVERT: L 141 TYR cc_start: 0.8321 (t80) cc_final: 0.7662 (t80) REVERT: L 148 GLN cc_start: 0.7978 (tp40) cc_final: 0.7733 (tp40) REVERT: L 190 HIS cc_start: 0.7969 (m-70) cc_final: 0.7699 (m-70) REVERT: B 153 ASN cc_start: 0.8107 (OUTLIER) cc_final: 0.7794 (t0) REVERT: B 162 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6873 (mp0) REVERT: B 200 GLN cc_start: 0.8233 (tm-30) cc_final: 0.7953 (tm-30) REVERT: C 143 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7687 (tp40) REVERT: C 155 LEU cc_start: 0.7208 (OUTLIER) cc_final: 0.7005 (mt) REVERT: A 16 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7042 (tm-30) REVERT: A 101 ASP cc_start: 0.8597 (t0) cc_final: 0.8385 (t0) REVERT: A 104 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7916 (mt) REVERT: D 90 ASP cc_start: 0.8352 (t0) cc_final: 0.7330 (t0) REVERT: E 104 LYS cc_start: 0.8437 (tttt) cc_final: 0.8034 (tptt) REVERT: E 126 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7432 (mt) REVERT: F 28 SER cc_start: 0.7939 (t) cc_final: 0.7674 (p) REVERT: F 143 ARG cc_start: 0.8210 (ttp80) cc_final: 0.7591 (tmt170) REVERT: I 72 ASP cc_start: 0.6662 (p0) cc_final: 0.6389 (t0) outliers start: 65 outliers final: 54 residues processed: 254 average time/residue: 0.1408 time to fit residues: 51.1166 Evaluate side-chains 244 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 183 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 188 SER 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 86 VAL Chi-restraints excluded: chain L residue 165 THR Chi-restraints excluded: chain L residue 180 LEU 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 C residue 68 SER Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 155 LEU 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 113 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 196 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 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 86 VAL 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 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 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 63 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 51 optimal weight: 0.0050 chunk 125 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 chunk 163 optimal weight: 0.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 39 GLN L 148 GLN ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 ASN E 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.150390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.125261 restraints weight = 18343.922| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.98 r_work: 0.3231 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.5988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 14898 Z= 0.209 Angle : 0.612 8.612 20296 Z= 0.318 Chirality : 0.044 0.140 2300 Planarity : 0.005 0.072 2566 Dihedral : 4.602 35.461 2030 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.11 % Allowed : 17.93 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.20), residues: 1870 helix: 1.25 (0.38), residues: 206 sheet: 0.30 (0.17), residues: 878 loop : 0.40 (0.24), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 212 TYR 0.023 0.002 TYR C 43 PHE 0.031 0.002 PHE F 117 TRP 0.013 0.002 TRP I 47 HIS 0.003 0.001 HIS L 190 Details of bonding type rmsd covalent geometry : bond 0.00505 (14876) covalent geometry : angle 0.61153 (20252) SS BOND : bond 0.00181 ( 22) SS BOND : angle 0.65708 ( 44) hydrogen bonds : bond 0.03085 ( 578) hydrogen bonds : angle 5.44639 ( 1608) *********************** 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 262 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 194 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 84 SER cc_start: 0.7337 (m) cc_final: 0.6951 (p) REVERT: H 191 THR cc_start: 0.7971 (OUTLIER) cc_final: 0.7766 (p) REVERT: H 209 LYS cc_start: 0.7952 (mmtt) cc_final: 0.7625 (mmtp) REVERT: L 141 TYR cc_start: 0.8384 (t80) cc_final: 0.7752 (t80) REVERT: L 148 GLN cc_start: 0.7986 (tp-100) cc_final: 0.7770 (tp-100) REVERT: L 190 HIS cc_start: 0.7940 (m-70) cc_final: 0.7707 (m-70) REVERT: B 153 ASN cc_start: 0.8188 (OUTLIER) cc_final: 0.7872 (t0) REVERT: B 162 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6937 (mp0) REVERT: B 171 ASP cc_start: 0.7688 (t0) cc_final: 0.7425 (t0) REVERT: B 200 GLN cc_start: 0.8292 (tm-30) cc_final: 0.8031 (tm-30) REVERT: C 155 LEU cc_start: 0.7262 (OUTLIER) cc_final: 0.7043 (mt) REVERT: A 16 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7163 (tm-30) REVERT: A 101 ASP cc_start: 0.8625 (t0) cc_final: 0.8420 (t0) REVERT: A 104 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7981 (mt) REVERT: D 90 ASP cc_start: 0.8377 (t0) cc_final: 0.7357 (t0) REVERT: E 104 LYS cc_start: 0.8490 (tttt) cc_final: 0.7929 (ttmm) REVERT: E 126 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7526 (mt) REVERT: F 28 SER cc_start: 0.7927 (t) cc_final: 0.7644 (p) REVERT: F 143 ARG cc_start: 0.8204 (ttp80) cc_final: 0.7569 (tmt170) REVERT: I 72 ASP cc_start: 0.6775 (p0) cc_final: 0.6553 (t0) REVERT: I 211 ASP cc_start: 0.8755 (t0) cc_final: 0.8446 (t0) outliers start: 68 outliers final: 54 residues processed: 251 average time/residue: 0.1291 time to fit residues: 46.7228 Evaluate side-chains 246 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 185 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 187 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 86 VAL Chi-restraints excluded: chain L residue 165 THR Chi-restraints excluded: chain L residue 180 LEU 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 C residue 68 SER Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain A residue 5 LYS 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 104 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 196 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 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 86 VAL 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 50 TYR 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 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 29 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 116 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 174 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 180 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 39 GLN ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 GLN 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 = 0.153512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.128952 restraints weight = 18154.823| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.95 r_work: 0.3290 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.6076 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= 0.132 Angle : 0.565 8.587 20296 Z= 0.292 Chirality : 0.042 0.142 2300 Planarity : 0.005 0.072 2566 Dihedral : 4.409 35.797 2030 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.14 % Allowed : 18.66 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.20), residues: 1870 helix: 1.42 (0.39), residues: 206 sheet: 0.34 (0.17), residues: 878 loop : 0.48 (0.24), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 212 TYR 0.022 0.001 TYR C 43 PHE 0.033 0.001 PHE F 117 TRP 0.011 0.001 TRP A 157 HIS 0.002 0.000 HIS L 190 Details of bonding type rmsd covalent geometry : bond 0.00319 (14876) covalent geometry : angle 0.56475 (20252) SS BOND : bond 0.00178 ( 22) SS BOND : angle 0.58745 ( 44) hydrogen bonds : bond 0.02753 ( 578) hydrogen bonds : angle 5.23018 ( 1608) ********************** 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 245 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 193 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 191 THR cc_start: 0.7986 (OUTLIER) cc_final: 0.7777 (p) REVERT: H 209 LYS cc_start: 0.7915 (mmtt) cc_final: 0.7557 (mmtp) REVERT: L 52 THR cc_start: 0.7956 (m) cc_final: 0.7740 (m) REVERT: L 141 TYR cc_start: 0.8311 (t80) cc_final: 0.7726 (t80) REVERT: L 148 GLN cc_start: 0.7995 (tp-100) cc_final: 0.7751 (tt0) REVERT: L 196 GLU cc_start: 0.7754 (pt0) cc_final: 0.7202 (tt0) REVERT: B 153 ASN cc_start: 0.8180 (OUTLIER) cc_final: 0.7883 (t0) REVERT: B 162 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.7000 (mp0) REVERT: B 171 ASP cc_start: 0.7532 (t0) cc_final: 0.7293 (t0) REVERT: B 200 GLN cc_start: 0.8288 (tm-30) cc_final: 0.8062 (tm-30) REVERT: A 16 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.7057 (tm-30) REVERT: A 101 ASP cc_start: 0.8587 (t0) cc_final: 0.8379 (t0) REVERT: D 81 MET cc_start: 0.8197 (tmm) cc_final: 0.7575 (tmm) REVERT: D 90 ASP cc_start: 0.8245 (t0) cc_final: 0.7300 (t0) REVERT: E 62 ARG cc_start: 0.8196 (mtm-85) cc_final: 0.7991 (mtm-85) REVERT: E 104 LYS cc_start: 0.8445 (tttt) cc_final: 0.7887 (ttmm) REVERT: E 126 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7498 (mt) REVERT: F 28 SER cc_start: 0.7939 (t) cc_final: 0.7637 (p) REVERT: F 108 LYS cc_start: 0.7677 (ttpt) cc_final: 0.7408 (ttpp) REVERT: F 117 PHE cc_start: 0.8096 (m-10) cc_final: 0.7865 (m-80) REVERT: F 143 ARG cc_start: 0.8163 (ttp80) cc_final: 0.7567 (tmt170) outliers start: 52 outliers final: 45 residues processed: 236 average time/residue: 0.1328 time to fit residues: 45.1254 Evaluate side-chains 237 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 187 time to evaluate : 0.561 ------------------------------------------------------------------------------- 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 86 VAL Chi-restraints excluded: chain L residue 165 THR Chi-restraints excluded: chain L residue 180 LEU 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 C residue 68 SER Chi-restraints excluded: chain A residue 5 LYS 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 113 THR Chi-restraints excluded: chain A residue 124 VAL 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 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 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 50 TYR Chi-restraints excluded: chain F residue 70 THR 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 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 213 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 62 optimal weight: 0.0060 chunk 10 optimal weight: 0.2980 chunk 61 optimal weight: 6.9990 chunk 167 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 60 optimal weight: 0.4980 chunk 81 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 96 optimal weight: 4.9990 chunk 180 optimal weight: 6.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.155251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.130917 restraints weight = 18058.060| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.94 r_work: 0.3324 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.6135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14898 Z= 0.112 Angle : 0.549 8.672 20296 Z= 0.283 Chirality : 0.042 0.143 2300 Planarity : 0.005 0.071 2566 Dihedral : 4.229 35.366 2030 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.84 % Allowed : 18.72 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.20), residues: 1870 helix: 1.50 (0.39), residues: 206 sheet: 0.46 (0.17), residues: 882 loop : 0.60 (0.25), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 212 TYR 0.031 0.001 TYR C 43 PHE 0.032 0.001 PHE F 117 TRP 0.010 0.001 TRP A 157 HIS 0.003 0.001 HIS L 190 Details of bonding type rmsd covalent geometry : bond 0.00268 (14876) covalent geometry : angle 0.54890 (20252) SS BOND : bond 0.00160 ( 22) SS BOND : angle 0.46970 ( 44) hydrogen bonds : bond 0.02604 ( 578) hydrogen bonds : angle 5.04317 ( 1608) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3817.40 seconds wall clock time: 66 minutes 24.20 seconds (3984.20 seconds total)