Starting phenix.real_space_refine on Sun Aug 24 13:13:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tsi_41593/08_2025/8tsi_41593_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tsi_41593/08_2025/8tsi_41593.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tsi_41593/08_2025/8tsi_41593_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tsi_41593/08_2025/8tsi_41593_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tsi_41593/08_2025/8tsi_41593.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tsi_41593/08_2025/8tsi_41593.map" } resolution = 4.4 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= 0.866 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: 7 Type Number sf(0) Gaussians Al 2 5.89 5 P 4 5.49 5 S 98 5.16 5 C 13140 2.51 5 N 3450 2.21 5 O 3546 1.98 5 F 8 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20248 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1700 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 6, 'TRANS': 209} Chain: "C" Number of atoms: 2048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2048 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 16, 'TRANS': 240} Chain: "E" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1537 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 177} Chain breaks: 2 Chain: "F" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1606 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain breaks: 2 Chain: "G" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1611 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 187} Chain breaks: 2 Chain: "H" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1590 Classifications: {'peptide': 194} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 185} Chain breaks: 2 Chain: "I" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1537 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 177} Chain breaks: 2 Chain: "J" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1606 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain breaks: 2 Chain: "K" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1611 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 187} Chain breaks: 2 Chain: "L" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1590 Classifications: {'peptide': 194} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 185} Chain breaks: 2 Chain: "D" Number of atoms: 2048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2048 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 16, 'TRANS': 240} Chain: "B" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1700 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 6, 'TRANS': 209} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.44, per 1000 atoms: 0.22 Number of scatterers: 20248 At special positions: 0 Unit cell: (135, 130.68, 137.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 98 16.00 P 4 15.00 Al 2 13.00 F 8 9.00 O 3546 8.00 N 3450 7.00 C 13140 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS F 138 " - pdb=" SG CYS G 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 138 " - pdb=" SG CYS H 77 " distance=2.03 Simple disulfide: pdb=" SG CYS I 138 " - pdb=" SG CYS J 77 " distance=2.03 Simple disulfide: pdb=" SG CYS J 138 " - pdb=" SG CYS K 77 " distance=2.03 Simple disulfide: pdb=" SG CYS K 138 " - pdb=" SG CYS L 77 " 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: 1.27 Conformation dependent library (CDL) restraints added in 814.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4716 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 12 sheets defined 65.0% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 43 through 53 Processing helix chain 'A' and resid 83 through 94 Processing helix chain 'A' and resid 98 through 113 removed outlier: 3.694A pdb=" N MET A 102 " --> pdb=" O SER A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.888A pdb=" N TYR A 126 " --> pdb=" O MET A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 140 removed outlier: 3.777A pdb=" N ARG A 131 " --> pdb=" O SER A 127 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER A 132 " --> pdb=" O SER A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 171 Processing helix chain 'A' and resid 183 through 191 removed outlier: 3.974A pdb=" N GLU A 189 " --> pdb=" O ASN A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 217 Processing helix chain 'C' and resid 15 through 36 removed outlier: 3.900A pdb=" N THR C 34 " --> pdb=" O ARG C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 69 removed outlier: 4.140A pdb=" N PHE C 44 " --> pdb=" O TRP C 40 " (cutoff:3.500A) Proline residue: C 50 - end of helix removed outlier: 6.432A pdb=" N LEU C 63 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ALA C 64 " --> pdb=" O LEU C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 94 removed outlier: 3.816A pdb=" N ILE C 79 " --> pdb=" O PRO C 75 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N THR C 80 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY C 81 " --> pdb=" O PHE C 77 " (cutoff:3.500A) Proline residue: C 84 - end of helix Processing helix chain 'C' and resid 96 through 101 removed outlier: 4.015A pdb=" N ASP C 100 " --> pdb=" O MET C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 106 Processing helix chain 'C' and resid 112 through 143 removed outlier: 3.866A pdb=" N ARG C 120 " --> pdb=" O THR C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 176 Processing helix chain 'C' and resid 177 through 178 No H-bonds generated for 'chain 'C' and resid 177 through 178' Processing helix chain 'C' and resid 179 through 180 No H-bonds generated for 'chain 'C' and resid 179 through 180' Processing helix chain 'C' and resid 181 through 190 removed outlier: 3.979A pdb=" N ILE C 185 " --> pdb=" O GLN C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 197 removed outlier: 3.729A pdb=" N TYR C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE C 195 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER C 197 " --> pdb=" O LEU C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 206 removed outlier: 3.878A pdb=" N THR C 205 " --> pdb=" O PRO C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 209 No H-bonds generated for 'chain 'C' and resid 207 through 209' Processing helix chain 'C' and resid 210 through 216 removed outlier: 3.817A pdb=" N LEU C 214 " --> pdb=" O TYR C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 231 Processing helix chain 'C' and resid 242 through 263 Processing helix chain 'E' and resid 13 through 19 removed outlier: 3.596A pdb=" N VAL E 19 " --> pdb=" O GLN E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 31 Processing helix chain 'E' and resid 74 through 84 removed outlier: 4.026A pdb=" N HIS E 84 " --> pdb=" O GLN E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 97 Processing helix chain 'E' and resid 97 through 102 Processing helix chain 'E' and resid 118 through 130 Processing helix chain 'E' and resid 149 through 180 Processing helix chain 'E' and resid 340 through 361 Processing helix chain 'F' and resid 12 through 19 removed outlier: 4.187A pdb=" N TRP F 16 " --> pdb=" O LYS F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 32 Processing helix chain 'F' and resid 73 through 84 removed outlier: 3.952A pdb=" N HIS F 84 " --> pdb=" O GLN F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 97 Processing helix chain 'F' and resid 97 through 103 removed outlier: 3.706A pdb=" N GLY F 103 " --> pdb=" O ARG F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 130 Processing helix chain 'F' and resid 149 through 175 removed outlier: 3.654A pdb=" N GLN F 154 " --> pdb=" O PRO F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 370 Processing helix chain 'G' and resid 13 through 18 Processing helix chain 'G' and resid 19 through 32 removed outlier: 3.634A pdb=" N MET G 23 " --> pdb=" O VAL G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 84 removed outlier: 4.136A pdb=" N HIS G 84 " --> pdb=" O GLN G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 97 Processing helix chain 'G' and resid 97 through 102 removed outlier: 3.760A pdb=" N HIS G 101 " --> pdb=" O LYS G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 130 Processing helix chain 'G' and resid 149 through 175 removed outlier: 3.940A pdb=" N MET G 175 " --> pdb=" O LEU G 171 " (cutoff:3.500A) Processing helix chain 'G' and resid 340 through 369 Processing helix chain 'H' and resid 11 through 19 Processing helix chain 'H' and resid 19 through 33 Processing helix chain 'H' and resid 72 through 84 removed outlier: 4.228A pdb=" N HIS H 84 " --> pdb=" O GLN H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 97 removed outlier: 3.792A pdb=" N LEU H 89 " --> pdb=" O SER H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 103 Processing helix chain 'H' and resid 118 through 129 Processing helix chain 'H' and resid 149 through 178 removed outlier: 3.744A pdb=" N GLN H 154 " --> pdb=" O PRO H 150 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLU H 178 " --> pdb=" O ARG H 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 340 through 366 Processing helix chain 'I' and resid 13 through 19 Processing helix chain 'I' and resid 19 through 31 removed outlier: 3.908A pdb=" N MET I 23 " --> pdb=" O VAL I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 84 removed outlier: 4.051A pdb=" N HIS I 84 " --> pdb=" O GLN I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 97 Processing helix chain 'I' and resid 97 through 102 Processing helix chain 'I' and resid 118 through 130 Processing helix chain 'I' and resid 149 through 180 Processing helix chain 'I' and resid 340 through 361 Processing helix chain 'J' and resid 7 through 11 removed outlier: 4.102A pdb=" N ALA J 11 " --> pdb=" O ARG J 8 " (cutoff:3.500A) Processing helix chain 'J' and resid 12 through 19 removed outlier: 4.197A pdb=" N TRP J 16 " --> pdb=" O LYS J 12 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 33 removed outlier: 3.506A pdb=" N MET J 23 " --> pdb=" O VAL J 19 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 84 removed outlier: 3.958A pdb=" N HIS J 84 " --> pdb=" O GLN J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 97 Processing helix chain 'J' and resid 97 through 103 removed outlier: 3.707A pdb=" N GLY J 103 " --> pdb=" O ARG J 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 118 through 130 Processing helix chain 'J' and resid 149 through 175 removed outlier: 3.660A pdb=" N GLN J 154 " --> pdb=" O PRO J 150 " (cutoff:3.500A) Processing helix chain 'J' and resid 340 through 370 Processing helix chain 'K' and resid 13 through 18 Processing helix chain 'K' and resid 19 through 32 removed outlier: 3.790A pdb=" N MET K 23 " --> pdb=" O VAL K 19 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 84 removed outlier: 4.108A pdb=" N HIS K 84 " --> pdb=" O GLN K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 86 through 97 Processing helix chain 'K' and resid 97 through 102 removed outlier: 3.754A pdb=" N HIS K 101 " --> pdb=" O LYS K 97 " (cutoff:3.500A) Processing helix chain 'K' and resid 118 through 130 Processing helix chain 'K' and resid 149 through 175 removed outlier: 3.934A pdb=" N MET K 175 " --> pdb=" O LEU K 171 " (cutoff:3.500A) Processing helix chain 'K' and resid 340 through 369 Processing helix chain 'L' and resid 11 through 19 Processing helix chain 'L' and resid 19 through 33 Processing helix chain 'L' and resid 72 through 84 removed outlier: 4.208A pdb=" N HIS L 84 " --> pdb=" O GLN L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 85 through 97 removed outlier: 3.810A pdb=" N LEU L 89 " --> pdb=" O SER L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 97 through 103 Processing helix chain 'L' and resid 118 through 129 Processing helix chain 'L' and resid 149 through 178 removed outlier: 3.887A pdb=" N GLN L 154 " --> pdb=" O PRO L 150 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLU L 178 " --> pdb=" O ARG L 174 " (cutoff:3.500A) Processing helix chain 'L' and resid 340 through 366 Processing helix chain 'D' and resid 15 through 36 removed outlier: 3.900A pdb=" N THR D 34 " --> pdb=" O ARG D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 69 removed outlier: 4.140A pdb=" N PHE D 44 " --> pdb=" O TRP D 40 " (cutoff:3.500A) Proline residue: D 50 - end of helix removed outlier: 6.433A pdb=" N LEU D 63 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ALA D 64 " --> pdb=" O LEU D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 94 removed outlier: 3.816A pdb=" N ILE D 79 " --> pdb=" O PRO D 75 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N THR D 80 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY D 81 " --> pdb=" O PHE D 77 " (cutoff:3.500A) Proline residue: D 84 - end of helix Processing helix chain 'D' and resid 96 through 101 removed outlier: 4.015A pdb=" N ASP D 100 " --> pdb=" O MET D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 106 Processing helix chain 'D' and resid 112 through 143 removed outlier: 3.866A pdb=" N ARG D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 176 Processing helix chain 'D' and resid 177 through 178 No H-bonds generated for 'chain 'D' and resid 177 through 178' Processing helix chain 'D' and resid 179 through 180 No H-bonds generated for 'chain 'D' and resid 179 through 180' Processing helix chain 'D' and resid 181 through 190 removed outlier: 3.979A pdb=" N ILE D 185 " --> pdb=" O GLN D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 197 removed outlier: 3.728A pdb=" N TYR D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE D 195 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER D 197 " --> pdb=" O LEU D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 206 removed outlier: 3.878A pdb=" N THR D 205 " --> pdb=" O PRO D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 209 No H-bonds generated for 'chain 'D' and resid 207 through 209' Processing helix chain 'D' and resid 210 through 216 removed outlier: 3.816A pdb=" N LEU D 214 " --> pdb=" O TYR D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 231 Processing helix chain 'D' and resid 242 through 263 Processing helix chain 'B' and resid 43 through 53 Processing helix chain 'B' and resid 83 through 94 Processing helix chain 'B' and resid 98 through 113 removed outlier: 3.695A pdb=" N MET B 102 " --> pdb=" O SER B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 121 Processing helix chain 'B' and resid 122 through 126 removed outlier: 3.888A pdb=" N TYR B 126 " --> pdb=" O MET B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 140 removed outlier: 3.777A pdb=" N ARG B 131 " --> pdb=" O SER B 127 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER B 132 " --> pdb=" O SER B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 171 Processing helix chain 'B' and resid 183 through 191 removed outlier: 3.974A pdb=" N GLU B 189 " --> pdb=" O ASN B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 217 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 11 removed outlier: 7.497A pdb=" N TYR A 11 " --> pdb=" O TYR A 19 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N TYR A 19 " --> pdb=" O TYR A 11 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 146 through 150 removed outlier: 5.924A pdb=" N TYR A 147 " --> pdb=" O ILE A 178 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL A 180 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE A 149 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE A 34 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLY A 35 " --> pdb=" O VAL A 195 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL A 197 " --> pdb=" O GLY A 35 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 131 through 135 removed outlier: 7.155A pdb=" N THR E 45 " --> pdb=" O VAL E 326 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N VAL E 326 " --> pdb=" O THR E 45 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ARG E 47 " --> pdb=" O LEU E 324 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LEU E 324 " --> pdb=" O ARG E 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 131 through 134 removed outlier: 6.931A pdb=" N THR F 45 " --> pdb=" O VAL F 326 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N VAL F 326 " --> pdb=" O THR F 45 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ARG F 47 " --> pdb=" O LEU F 324 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LEU F 324 " --> pdb=" O ARG F 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 131 through 135 removed outlier: 6.743A pdb=" N VAL G 43 " --> pdb=" O VAL G 327 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 130 through 134 removed outlier: 6.465A pdb=" N VAL H 43 " --> pdb=" O VAL H 327 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG H 47 " --> pdb=" O SER H 323 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER H 323 " --> pdb=" O ARG H 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 131 through 135 removed outlier: 7.113A pdb=" N THR I 45 " --> pdb=" O VAL I 326 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N VAL I 326 " --> pdb=" O THR I 45 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ARG I 47 " --> pdb=" O LEU I 324 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N LEU I 324 " --> pdb=" O ARG I 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 131 through 134 removed outlier: 6.938A pdb=" N THR J 45 " --> pdb=" O VAL J 326 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N VAL J 326 " --> pdb=" O THR J 45 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ARG J 47 " --> pdb=" O LEU J 324 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N LEU J 324 " --> pdb=" O ARG J 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 131 through 135 removed outlier: 6.740A pdb=" N VAL K 43 " --> pdb=" O VAL K 327 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 130 through 134 removed outlier: 6.931A pdb=" N THR L 45 " --> pdb=" O VAL L 326 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N VAL L 326 " --> pdb=" O THR L 45 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ARG L 47 " --> pdb=" O LEU L 324 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N LEU L 324 " --> pdb=" O ARG L 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 8 through 11 removed outlier: 7.496A pdb=" N TYR B 11 " --> pdb=" O TYR B 19 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N TYR B 19 " --> pdb=" O TYR B 11 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 146 through 150 removed outlier: 5.924A pdb=" N TYR B 147 " --> pdb=" O ILE B 178 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL B 180 " --> pdb=" O TYR B 147 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE B 149 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE B 34 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLY B 35 " --> pdb=" O VAL B 195 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL B 197 " --> pdb=" O GLY B 35 " (cutoff:3.500A) 1232 hydrogen bonds defined for protein. 3579 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: 2.86 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6454 1.34 - 1.46: 4851 1.46 - 1.58: 9229 1.58 - 1.70: 6 1.70 - 1.82: 168 Bond restraints: 20708 Sorted by residual: bond pdb=" F1 ALF B 301 " pdb="AL ALF B 301 " ideal model delta sigma weight residual 1.684 1.784 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" F1 ALF A 302 " pdb="AL ALF A 302 " ideal model delta sigma weight residual 1.684 1.784 -0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" F2 ALF A 302 " pdb="AL ALF A 302 " ideal model delta sigma weight residual 1.685 1.785 -0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" F2 ALF B 301 " pdb="AL ALF B 301 " ideal model delta sigma weight residual 1.685 1.785 -0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" F3 ALF A 302 " pdb="AL ALF A 302 " ideal model delta sigma weight residual 1.685 1.784 -0.099 2.00e-02 2.50e+03 2.46e+01 ... (remaining 20703 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.25: 28104 14.25 - 28.51: 8 28.51 - 42.76: 0 42.76 - 57.02: 0 57.02 - 71.27: 4 Bond angle restraints: 28116 Sorted by residual: angle pdb=" F1 ALF A 302 " pdb="AL ALF A 302 " pdb=" F2 ALF A 302 " ideal model delta sigma weight residual 108.68 179.95 -71.27 3.00e+00 1.11e-01 5.64e+02 angle pdb=" F1 ALF B 301 " pdb="AL ALF B 301 " pdb=" F2 ALF B 301 " ideal model delta sigma weight residual 108.68 179.92 -71.24 3.00e+00 1.11e-01 5.64e+02 angle pdb=" F3 ALF A 302 " pdb="AL ALF A 302 " pdb=" F4 ALF A 302 " ideal model delta sigma weight residual 109.63 179.93 -70.30 3.00e+00 1.11e-01 5.49e+02 angle pdb=" F3 ALF B 301 " pdb="AL ALF B 301 " pdb=" F4 ALF B 301 " ideal model delta sigma weight residual 109.63 179.93 -70.30 3.00e+00 1.11e-01 5.49e+02 angle pdb=" F2 ALF A 302 " pdb="AL ALF A 302 " pdb=" F4 ALF A 302 " ideal model delta sigma weight residual 110.21 89.98 20.23 3.00e+00 1.11e-01 4.55e+01 ... (remaining 28111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.19: 11085 24.19 - 48.39: 1115 48.39 - 72.58: 100 72.58 - 96.77: 20 96.77 - 120.96: 6 Dihedral angle restraints: 12326 sinusoidal: 5036 harmonic: 7290 Sorted by residual: dihedral pdb=" CB CYS G 138 " pdb=" SG CYS G 138 " pdb=" SG CYS H 77 " pdb=" CB CYS H 77 " ideal model delta sinusoidal sigma weight residual 93.00 -179.02 -87.98 1 1.00e+01 1.00e-02 9.26e+01 dihedral pdb=" CB CYS K 138 " pdb=" SG CYS K 138 " pdb=" SG CYS L 77 " pdb=" CB CYS L 77 " ideal model delta sinusoidal sigma weight residual 93.00 -179.43 -87.57 1 1.00e+01 1.00e-02 9.19e+01 dihedral pdb=" C5' ADP B 302 " pdb=" O5' ADP B 302 " pdb=" PA ADP B 302 " pdb=" O2A ADP B 302 " ideal model delta sinusoidal sigma weight residual -60.00 60.97 -120.96 1 2.00e+01 2.50e-03 3.63e+01 ... (remaining 12323 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2495 0.052 - 0.104: 544 0.104 - 0.156: 131 0.156 - 0.208: 30 0.208 - 0.259: 4 Chirality restraints: 3204 Sorted by residual: chirality pdb=" CB THR J 27 " pdb=" CA THR J 27 " pdb=" OG1 THR J 27 " pdb=" CG2 THR J 27 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CG LEU F 24 " pdb=" CB LEU F 24 " pdb=" CD1 LEU F 24 " pdb=" CD2 LEU F 24 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA VAL A 197 " pdb=" N VAL A 197 " pdb=" C VAL A 197 " pdb=" CB VAL A 197 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 3201 not shown) Planarity restraints: 3518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 211 " -0.038 5.00e-02 4.00e+02 5.68e-02 5.17e+00 pdb=" N PRO D 212 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO D 212 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 212 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 211 " 0.037 5.00e-02 4.00e+02 5.66e-02 5.13e+00 pdb=" N PRO C 212 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO C 212 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 212 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 215 " 0.005 2.00e-02 2.50e+03 1.44e-02 4.15e+00 pdb=" CG TYR B 215 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR B 215 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR B 215 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR B 215 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 215 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 215 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 215 " -0.004 2.00e-02 2.50e+03 ... (remaining 3515 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3217 2.76 - 3.30: 19119 3.30 - 3.83: 33265 3.83 - 4.37: 35672 4.37 - 4.90: 63872 Nonbonded interactions: 155145 Sorted by model distance: nonbonded pdb=" OG1 THR A 83 " pdb=" OE1 GLU A 86 " model vdw 2.225 3.040 nonbonded pdb=" OG1 THR B 83 " pdb=" OE1 GLU B 86 " model vdw 2.225 3.040 nonbonded pdb=" OG SER D 167 " pdb=" OG SER D 252 " model vdw 2.246 3.040 nonbonded pdb=" OG SER C 167 " pdb=" OG SER C 252 " model vdw 2.247 3.040 nonbonded pdb=" O PHE K 30 " pdb=" OG SER K 34 " model vdw 2.247 3.040 ... (remaining 155140 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 2 through 217) selection = (chain 'B' and resid 2 through 217) } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and (resid 12 through 175 or resid 322 through 361)) selection = (chain 'F' and (resid 12 through 48 or resid 73 through 361)) selection = (chain 'G' and (resid 12 through 48 or resid 73 through 175 or resid 322 through \ 361)) selection = (chain 'H' and (resid 12 through 48 or resid 73 through 175 or resid 322 through \ 361)) selection = (chain 'I' and (resid 12 through 175 or resid 322 through 361)) selection = (chain 'J' and (resid 12 through 48 or resid 73 through 361)) selection = (chain 'K' and (resid 12 through 48 or resid 73 through 175 or resid 322 through \ 361)) selection = (chain 'L' and (resid 12 through 48 or resid 73 through 175 or resid 322 through \ 361)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 16.450 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 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 0.100 20714 Z= 0.245 Angle : 1.201 71.270 28128 Z= 0.509 Chirality : 0.049 0.259 3204 Planarity : 0.004 0.065 3518 Dihedral : 17.518 120.963 7592 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.68 % Allowed : 26.73 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.86 (0.17), residues: 2432 helix: 1.42 (0.14), residues: 1422 sheet: 0.75 (0.33), residues: 264 loop : -1.13 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 47 TYR 0.033 0.001 TYR B 215 PHE 0.015 0.001 PHE C 61 TRP 0.018 0.001 TRP B 10 HIS 0.005 0.001 HIS F 369 Details of bonding type rmsd covalent geometry : bond 0.00428 (20708) covalent geometry : angle 1.20127 (28116) SS BOND : bond 0.00220 ( 6) SS BOND : angle 1.05153 ( 12) hydrogen bonds : bond 0.14441 ( 1232) hydrogen bonds : angle 5.94615 ( 3579) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 456 time to evaluate : 0.889 Fit side-chains revert: symmetry clash REVERT: A 140 MET cc_start: 0.7803 (mtt) cc_final: 0.7465 (mpp) REVERT: A 147 TYR cc_start: 0.7061 (m-10) cc_final: 0.6833 (m-80) REVERT: A 199 GLN cc_start: 0.6916 (OUTLIER) cc_final: 0.6395 (tp40) REVERT: C 49 GLU cc_start: 0.6135 (tm-30) cc_final: 0.5526 (tm-30) REVERT: C 69 MET cc_start: 0.8685 (ppp) cc_final: 0.8099 (ptt) REVERT: C 96 MET cc_start: 0.8123 (mmm) cc_final: 0.7638 (mmt) REVERT: D 49 GLU cc_start: 0.6145 (tm-30) cc_final: 0.5532 (tm-30) REVERT: D 69 MET cc_start: 0.8648 (ppp) cc_final: 0.8050 (ptt) REVERT: D 96 MET cc_start: 0.8132 (mmm) cc_final: 0.7725 (mmt) REVERT: B 140 MET cc_start: 0.7735 (mtt) cc_final: 0.7386 (mpp) REVERT: B 199 GLN cc_start: 0.7074 (OUTLIER) cc_final: 0.6464 (tp40) outliers start: 15 outliers final: 6 residues processed: 464 average time/residue: 0.1502 time to fit residues: 107.9813 Evaluate side-chains 448 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 440 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 0.0770 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 9.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 201 GLN C 204 HIS C 221 HIS F 119 GLN F 173 HIS H 84 HIS J 173 HIS K 15 GLN L 84 HIS D 204 HIS D 221 HIS B 87 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.151373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.141612 restraints weight = 28063.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.139413 restraints weight = 56229.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.138086 restraints weight = 77579.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.126351 restraints weight = 72614.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.122735 restraints weight = 55808.548| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3203 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20714 Z= 0.151 Angle : 0.616 8.535 28128 Z= 0.299 Chirality : 0.042 0.163 3204 Planarity : 0.004 0.054 3518 Dihedral : 6.011 130.548 2794 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.18 % Allowed : 3.24 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.39 (0.18), residues: 2432 helix: 1.88 (0.14), residues: 1424 sheet: 0.89 (0.34), residues: 264 loop : -0.96 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 22 TYR 0.019 0.001 TYR A 190 PHE 0.020 0.001 PHE G 30 TRP 0.008 0.001 TRP H 114 HIS 0.006 0.001 HIS F 369 Details of bonding type rmsd covalent geometry : bond 0.00335 (20708) covalent geometry : angle 0.61535 (28116) SS BOND : bond 0.00314 ( 6) SS BOND : angle 1.76842 ( 12) hydrogen bonds : bond 0.04414 ( 1232) hydrogen bonds : angle 4.48620 ( 3579) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 547 time to evaluate : 0.628 Fit side-chains REVERT: A 89 LYS cc_start: 0.8753 (mptt) cc_final: 0.8534 (mmtm) REVERT: C 49 GLU cc_start: 0.6786 (tm-30) cc_final: 0.6337 (tm-30) REVERT: C 69 MET cc_start: 0.8726 (ppp) cc_final: 0.8067 (ptt) REVERT: E 322 LYS cc_start: 0.8191 (mtmm) cc_final: 0.7965 (mttt) REVERT: E 356 TYR cc_start: 0.7862 (t80) cc_final: 0.7572 (t80) REVERT: F 41 GLU cc_start: 0.8609 (tt0) cc_final: 0.8314 (tt0) REVERT: G 369 HIS cc_start: 0.7675 (t-90) cc_final: 0.7111 (t-90) REVERT: H 138 CYS cc_start: 0.8024 (m) cc_final: 0.7320 (m) REVERT: K 361 LEU cc_start: 0.8674 (tt) cc_final: 0.8261 (tt) REVERT: K 369 HIS cc_start: 0.7722 (t-90) cc_final: 0.7242 (t-170) REVERT: L 80 GLN cc_start: 0.8205 (tm-30) cc_final: 0.7968 (tm-30) REVERT: L 138 CYS cc_start: 0.8031 (m) cc_final: 0.7252 (m) REVERT: L 335 ILE cc_start: 0.9067 (tp) cc_final: 0.8837 (tt) REVERT: D 49 GLU cc_start: 0.6871 (tm-30) cc_final: 0.6330 (tm-30) REVERT: D 69 MET cc_start: 0.8766 (ppp) cc_final: 0.8000 (ptt) REVERT: D 134 ILE cc_start: 0.8680 (tp) cc_final: 0.8274 (tp) REVERT: B 48 MET cc_start: 0.8362 (tpt) cc_final: 0.8015 (tpt) REVERT: B 89 LYS cc_start: 0.8852 (mptt) cc_final: 0.8623 (mmtm) outliers start: 4 outliers final: 2 residues processed: 549 average time/residue: 0.1502 time to fit residues: 125.7151 Evaluate side-chains 420 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 418 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 26 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 151 optimal weight: 0.7980 chunk 188 optimal weight: 2.9990 chunk 121 optimal weight: 8.9990 chunk 86 optimal weight: 0.7980 chunk 13 optimal weight: 10.0000 chunk 162 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS C 20 GLN C 53 HIS C 204 HIS F 94 GLN J 94 GLN D 20 GLN D 53 HIS B 118 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.146368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.138227 restraints weight = 28663.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.136930 restraints weight = 58786.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.135842 restraints weight = 66856.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.134994 restraints weight = 72963.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.134353 restraints weight = 73161.120| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3499 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3499 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20714 Z= 0.186 Angle : 0.608 6.935 28128 Z= 0.300 Chirality : 0.042 0.149 3204 Planarity : 0.004 0.051 3518 Dihedral : 5.795 130.415 2794 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.14 % Allowed : 3.10 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.35 (0.17), residues: 2432 helix: 1.93 (0.14), residues: 1422 sheet: 0.76 (0.34), residues: 264 loop : -1.12 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 47 TYR 0.021 0.002 TYR B 190 PHE 0.014 0.001 PHE G 30 TRP 0.012 0.001 TRP A 10 HIS 0.010 0.001 HIS J 369 Details of bonding type rmsd covalent geometry : bond 0.00429 (20708) covalent geometry : angle 0.60690 (28116) SS BOND : bond 0.00304 ( 6) SS BOND : angle 1.49063 ( 12) hydrogen bonds : bond 0.04245 ( 1232) hydrogen bonds : angle 4.38695 ( 3579) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 492 time to evaluate : 0.764 Fit side-chains REVERT: A 86 GLU cc_start: 0.7542 (pm20) cc_final: 0.7221 (pt0) REVERT: A 89 LYS cc_start: 0.8348 (mptt) cc_final: 0.7927 (mmmm) REVERT: C 33 LYS cc_start: 0.7355 (tptt) cc_final: 0.7053 (tppt) REVERT: C 49 GLU cc_start: 0.5522 (tm-30) cc_final: 0.4927 (tm-30) REVERT: C 69 MET cc_start: 0.8527 (ppp) cc_final: 0.8026 (ptt) REVERT: C 96 MET cc_start: 0.7909 (mmm) cc_final: 0.7539 (mmt) REVERT: C 134 ILE cc_start: 0.8506 (tp) cc_final: 0.8182 (tp) REVERT: E 28 VAL cc_start: 0.8833 (m) cc_final: 0.8613 (t) REVERT: E 356 TYR cc_start: 0.7372 (t80) cc_final: 0.7100 (t80) REVERT: F 19 VAL cc_start: 0.8828 (t) cc_final: 0.8624 (t) REVERT: G 369 HIS cc_start: 0.7387 (t-90) cc_final: 0.6648 (t-90) REVERT: K 361 LEU cc_start: 0.8356 (tt) cc_final: 0.7770 (tt) REVERT: K 369 HIS cc_start: 0.7548 (t-90) cc_final: 0.6715 (t-90) REVERT: L 335 ILE cc_start: 0.9011 (tp) cc_final: 0.8784 (tt) REVERT: D 33 LYS cc_start: 0.7333 (tptt) cc_final: 0.6932 (tppt) REVERT: D 49 GLU cc_start: 0.5638 (tm-30) cc_final: 0.4899 (tm-30) REVERT: D 69 MET cc_start: 0.8519 (ppp) cc_final: 0.7984 (ptt) REVERT: D 96 MET cc_start: 0.7952 (mmm) cc_final: 0.7649 (mmt) REVERT: D 134 ILE cc_start: 0.8565 (tp) cc_final: 0.8260 (tp) REVERT: D 257 LEU cc_start: 0.8427 (mt) cc_final: 0.8128 (mt) REVERT: B 86 GLU cc_start: 0.7646 (pm20) cc_final: 0.7206 (pt0) outliers start: 3 outliers final: 0 residues processed: 492 average time/residue: 0.1504 time to fit residues: 114.5317 Evaluate side-chains 399 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 399 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 220 optimal weight: 2.9990 chunk 85 optimal weight: 0.3980 chunk 153 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 chunk 223 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 32 optimal weight: 0.7980 chunk 233 optimal weight: 0.0980 chunk 65 optimal weight: 4.9990 chunk 232 optimal weight: 10.0000 chunk 167 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 53 HIS C 204 HIS F 94 GLN J 94 GLN D 53 HIS D 204 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.146653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.138858 restraints weight = 28679.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.137176 restraints weight = 61494.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.136130 restraints weight = 80003.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.121370 restraints weight = 76318.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.118539 restraints weight = 70980.160| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3149 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20714 Z= 0.163 Angle : 0.595 16.259 28128 Z= 0.291 Chirality : 0.042 0.207 3204 Planarity : 0.004 0.048 3518 Dihedral : 5.641 126.559 2794 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.09 % Allowed : 3.10 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.35 (0.17), residues: 2432 helix: 1.89 (0.14), residues: 1434 sheet: 0.83 (0.34), residues: 260 loop : -1.09 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 47 TYR 0.020 0.001 TYR A 190 PHE 0.018 0.001 PHE F 30 TRP 0.012 0.001 TRP A 10 HIS 0.005 0.001 HIS J 101 Details of bonding type rmsd covalent geometry : bond 0.00376 (20708) covalent geometry : angle 0.59451 (28116) SS BOND : bond 0.00319 ( 6) SS BOND : angle 1.29904 ( 12) hydrogen bonds : bond 0.04025 ( 1232) hydrogen bonds : angle 4.26684 ( 3579) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 494 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 49 GLU cc_start: 0.6753 (tm-30) cc_final: 0.5602 (tm-30) REVERT: C 69 MET cc_start: 0.8750 (ppp) cc_final: 0.8189 (ptt) REVERT: C 96 MET cc_start: 0.8264 (mmm) cc_final: 0.7980 (mmt) REVERT: E 322 LYS cc_start: 0.8230 (mtmm) cc_final: 0.7927 (mttt) REVERT: E 356 TYR cc_start: 0.8125 (t80) cc_final: 0.7885 (t80) REVERT: G 77 CYS cc_start: 0.5936 (m) cc_final: 0.5692 (m) REVERT: G 369 HIS cc_start: 0.8020 (t-90) cc_final: 0.6590 (t-90) REVERT: J 134 MET cc_start: 0.8492 (tpp) cc_final: 0.8088 (tpp) REVERT: K 361 LEU cc_start: 0.8650 (tt) cc_final: 0.8168 (tt) REVERT: K 369 HIS cc_start: 0.8088 (t-90) cc_final: 0.6768 (t-90) REVERT: L 335 ILE cc_start: 0.9137 (tp) cc_final: 0.8922 (tt) REVERT: D 49 GLU cc_start: 0.6848 (tm-30) cc_final: 0.5598 (tm-30) REVERT: D 69 MET cc_start: 0.8773 (ppp) cc_final: 0.8093 (ptt) REVERT: D 96 MET cc_start: 0.8094 (mmm) cc_final: 0.7847 (mmt) REVERT: D 134 ILE cc_start: 0.8805 (tp) cc_final: 0.8438 (tp) REVERT: D 233 GLN cc_start: 0.7884 (tp40) cc_final: 0.7671 (tp40) REVERT: D 257 LEU cc_start: 0.8580 (mt) cc_final: 0.8362 (mt) outliers start: 2 outliers final: 0 residues processed: 495 average time/residue: 0.1474 time to fit residues: 113.0211 Evaluate side-chains 405 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 405 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 121 optimal weight: 7.9990 chunk 117 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 128 optimal weight: 3.9990 chunk 184 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 225 optimal weight: 9.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN C 53 HIS C 204 HIS C 221 HIS C 238 GLN F 94 GLN J 94 GLN D 53 HIS D 221 HIS D 238 GLN B 87 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.144685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.136116 restraints weight = 28640.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.120939 restraints weight = 67670.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.117729 restraints weight = 60130.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.116696 restraints weight = 49742.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.116532 restraints weight = 49178.528| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 20714 Z= 0.228 Angle : 0.658 6.933 28128 Z= 0.325 Chirality : 0.044 0.152 3204 Planarity : 0.004 0.047 3518 Dihedral : 5.636 125.174 2794 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.09 % Allowed : 3.51 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.15 (0.17), residues: 2432 helix: 1.73 (0.14), residues: 1436 sheet: 0.64 (0.34), residues: 260 loop : -1.12 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 47 TYR 0.020 0.002 TYR A 190 PHE 0.013 0.001 PHE B 136 TRP 0.012 0.001 TRP A 10 HIS 0.010 0.001 HIS G 173 Details of bonding type rmsd covalent geometry : bond 0.00533 (20708) covalent geometry : angle 0.65735 (28116) SS BOND : bond 0.00430 ( 6) SS BOND : angle 1.31387 ( 12) hydrogen bonds : bond 0.04408 ( 1232) hydrogen bonds : angle 4.42608 ( 3579) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 488 time to evaluate : 0.878 Fit side-chains REVERT: A 86 GLU cc_start: 0.8399 (pm20) cc_final: 0.8199 (pm20) REVERT: A 87 ASN cc_start: 0.8576 (OUTLIER) cc_final: 0.8275 (t0) REVERT: C 49 GLU cc_start: 0.6785 (tm-30) cc_final: 0.5531 (tm-30) REVERT: C 69 MET cc_start: 0.8835 (ppp) cc_final: 0.8114 (ptt) REVERT: C 96 MET cc_start: 0.8374 (mmm) cc_final: 0.8059 (mmt) REVERT: C 134 ILE cc_start: 0.8743 (tp) cc_final: 0.8351 (tp) REVERT: E 356 TYR cc_start: 0.8081 (t80) cc_final: 0.7788 (t80) REVERT: G 369 HIS cc_start: 0.7923 (t-90) cc_final: 0.6544 (t-90) REVERT: H 335 ILE cc_start: 0.9065 (tp) cc_final: 0.8809 (tt) REVERT: H 344 ASN cc_start: 0.7530 (m-40) cc_final: 0.7311 (m-40) REVERT: I 322 LYS cc_start: 0.8126 (mtmm) cc_final: 0.7891 (mttt) REVERT: J 19 VAL cc_start: 0.8964 (t) cc_final: 0.8730 (t) REVERT: J 134 MET cc_start: 0.8589 (tpp) cc_final: 0.8170 (tpp) REVERT: K 361 LEU cc_start: 0.8582 (tt) cc_final: 0.8175 (tt) REVERT: K 369 HIS cc_start: 0.7749 (t-90) cc_final: 0.7507 (t-90) REVERT: L 106 LEU cc_start: 0.7836 (mm) cc_final: 0.7627 (pt) REVERT: L 335 ILE cc_start: 0.9109 (tp) cc_final: 0.8893 (tt) REVERT: D 49 GLU cc_start: 0.6714 (tm-30) cc_final: 0.5368 (tm-30) REVERT: D 69 MET cc_start: 0.8881 (ppp) cc_final: 0.8192 (ptt) REVERT: D 89 ARG cc_start: 0.7275 (ttt180) cc_final: 0.6932 (ttt180) REVERT: D 134 ILE cc_start: 0.8785 (tp) cc_final: 0.8421 (tp) REVERT: D 257 LEU cc_start: 0.8503 (mt) cc_final: 0.8198 (mt) REVERT: B 86 GLU cc_start: 0.8347 (pm20) cc_final: 0.7985 (pm20) outliers start: 2 outliers final: 1 residues processed: 490 average time/residue: 0.1523 time to fit residues: 114.8905 Evaluate side-chains 384 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 382 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 16 optimal weight: 10.0000 chunk 131 optimal weight: 1.9990 chunk 218 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 127 optimal weight: 0.9990 chunk 209 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 203 optimal weight: 0.5980 chunk 157 optimal weight: 5.9990 chunk 133 optimal weight: 0.7980 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 204 HIS C 221 HIS C 238 GLN F 94 GLN J 94 GLN J 173 HIS D 204 HIS D 221 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.147375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.140296 restraints weight = 28107.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.138838 restraints weight = 56997.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.137712 restraints weight = 70157.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.124634 restraints weight = 71661.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.120941 restraints weight = 61825.039| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3227 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20714 Z= 0.140 Angle : 0.599 17.023 28128 Z= 0.289 Chirality : 0.041 0.236 3204 Planarity : 0.004 0.045 3518 Dihedral : 5.408 123.184 2794 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.31 (0.17), residues: 2432 helix: 1.85 (0.14), residues: 1436 sheet: 0.78 (0.34), residues: 260 loop : -1.08 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 47 TYR 0.020 0.001 TYR A 190 PHE 0.020 0.001 PHE F 30 TRP 0.013 0.001 TRP A 10 HIS 0.007 0.001 HIS D 53 Details of bonding type rmsd covalent geometry : bond 0.00318 (20708) covalent geometry : angle 0.59844 (28116) SS BOND : bond 0.00307 ( 6) SS BOND : angle 1.22142 ( 12) hydrogen bonds : bond 0.03938 ( 1232) hydrogen bonds : angle 4.24132 ( 3579) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 487 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 GLU cc_start: 0.8251 (pm20) cc_final: 0.7696 (pm20) REVERT: C 49 GLU cc_start: 0.6181 (tm-30) cc_final: 0.5578 (tm-30) REVERT: C 69 MET cc_start: 0.8643 (ppp) cc_final: 0.8063 (ptt) REVERT: C 96 MET cc_start: 0.8259 (mmm) cc_final: 0.8039 (mmt) REVERT: C 134 ILE cc_start: 0.8735 (tp) cc_final: 0.8306 (tp) REVERT: C 150 ARG cc_start: 0.6550 (mtm180) cc_final: 0.6037 (mpp80) REVERT: E 356 TYR cc_start: 0.8000 (t80) cc_final: 0.7755 (t80) REVERT: G 41 GLU cc_start: 0.9006 (tt0) cc_final: 0.8779 (tt0) REVERT: G 369 HIS cc_start: 0.7549 (t-90) cc_final: 0.7136 (t-90) REVERT: H 335 ILE cc_start: 0.9042 (tp) cc_final: 0.8817 (tt) REVERT: J 19 VAL cc_start: 0.8853 (t) cc_final: 0.8625 (t) REVERT: J 134 MET cc_start: 0.8485 (tpp) cc_final: 0.8030 (tpp) REVERT: K 41 GLU cc_start: 0.8982 (tt0) cc_final: 0.8678 (tt0) REVERT: K 361 LEU cc_start: 0.8408 (tt) cc_final: 0.8020 (tt) REVERT: K 369 HIS cc_start: 0.7694 (t-90) cc_final: 0.6850 (t-90) REVERT: L 106 LEU cc_start: 0.7772 (mm) cc_final: 0.7531 (pt) REVERT: L 335 ILE cc_start: 0.9162 (tp) cc_final: 0.8930 (tt) REVERT: D 49 GLU cc_start: 0.6143 (tm-30) cc_final: 0.5725 (tm-30) REVERT: D 69 MET cc_start: 0.8761 (ppp) cc_final: 0.8493 (ptt) REVERT: D 89 ARG cc_start: 0.7210 (ttt180) cc_final: 0.6881 (ttt180) REVERT: D 134 ILE cc_start: 0.8735 (tp) cc_final: 0.8336 (tp) REVERT: D 150 ARG cc_start: 0.6451 (mtm180) cc_final: 0.6000 (mpp80) REVERT: D 257 LEU cc_start: 0.8429 (mt) cc_final: 0.8221 (mt) REVERT: B 86 GLU cc_start: 0.8255 (pm20) cc_final: 0.7679 (pm20) outliers start: 0 outliers final: 0 residues processed: 487 average time/residue: 0.1481 time to fit residues: 111.7602 Evaluate side-chains 385 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 385 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 6 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 223 optimal weight: 3.9990 chunk 34 optimal weight: 0.0670 chunk 7 optimal weight: 2.9990 chunk 186 optimal weight: 0.8980 chunk 185 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 62 optimal weight: 0.0470 chunk 16 optimal weight: 5.9990 overall best weight: 0.5416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 53 HIS C 204 HIS C 221 HIS ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 221 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.148753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.140238 restraints weight = 28228.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.123751 restraints weight = 57080.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.119794 restraints weight = 60673.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.119529 restraints weight = 75051.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.119266 restraints weight = 54214.659| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3141 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3141 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20714 Z= 0.120 Angle : 0.587 9.898 28128 Z= 0.285 Chirality : 0.041 0.181 3204 Planarity : 0.004 0.044 3518 Dihedral : 5.254 121.656 2794 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.41 (0.18), residues: 2432 helix: 1.90 (0.14), residues: 1436 sheet: 1.00 (0.34), residues: 262 loop : -1.06 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 174 TYR 0.020 0.001 TYR A 190 PHE 0.019 0.001 PHE H 30 TRP 0.015 0.001 TRP B 10 HIS 0.011 0.001 HIS D 65 Details of bonding type rmsd covalent geometry : bond 0.00264 (20708) covalent geometry : angle 0.58691 (28116) SS BOND : bond 0.00255 ( 6) SS BOND : angle 0.98389 ( 12) hydrogen bonds : bond 0.03660 ( 1232) hydrogen bonds : angle 4.15653 ( 3579) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 483 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 GLU cc_start: 0.8503 (pm20) cc_final: 0.8072 (pm20) REVERT: A 147 TYR cc_start: 0.7144 (m-10) cc_final: 0.6892 (m-10) REVERT: C 49 GLU cc_start: 0.7110 (tm-30) cc_final: 0.6387 (tm-30) REVERT: C 134 ILE cc_start: 0.8758 (tp) cc_final: 0.8316 (tp) REVERT: C 150 ARG cc_start: 0.6511 (mtm180) cc_final: 0.5960 (mpp80) REVERT: E 356 TYR cc_start: 0.8215 (t80) cc_final: 0.8003 (t80) REVERT: G 41 GLU cc_start: 0.8983 (tt0) cc_final: 0.8667 (tt0) REVERT: G 369 HIS cc_start: 0.7693 (t-90) cc_final: 0.7318 (t-90) REVERT: H 335 ILE cc_start: 0.9068 (tp) cc_final: 0.8864 (tt) REVERT: I 322 LYS cc_start: 0.8110 (mtmm) cc_final: 0.7859 (mttt) REVERT: J 19 VAL cc_start: 0.8872 (t) cc_final: 0.8651 (t) REVERT: J 134 MET cc_start: 0.8343 (tpp) cc_final: 0.7970 (tpp) REVERT: K 41 GLU cc_start: 0.8975 (tt0) cc_final: 0.8586 (tt0) REVERT: K 361 LEU cc_start: 0.8514 (tt) cc_final: 0.8093 (tt) REVERT: L 106 LEU cc_start: 0.7760 (mm) cc_final: 0.7535 (pt) REVERT: L 335 ILE cc_start: 0.9139 (tp) cc_final: 0.8894 (tt) REVERT: D 89 ARG cc_start: 0.7248 (ttt180) cc_final: 0.6911 (ttt180) REVERT: D 134 ILE cc_start: 0.8757 (tp) cc_final: 0.8348 (tp) REVERT: D 150 ARG cc_start: 0.6485 (mtm180) cc_final: 0.5916 (mpp80) REVERT: D 257 LEU cc_start: 0.8493 (mt) cc_final: 0.8230 (mt) REVERT: B 86 GLU cc_start: 0.8575 (pm20) cc_final: 0.8068 (pm20) outliers start: 0 outliers final: 0 residues processed: 483 average time/residue: 0.1425 time to fit residues: 107.4033 Evaluate side-chains 384 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 384 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 234 optimal weight: 9.9990 chunk 84 optimal weight: 0.6980 chunk 213 optimal weight: 8.9990 chunk 197 optimal weight: 4.9990 chunk 169 optimal weight: 0.9980 chunk 126 optimal weight: 0.5980 chunk 24 optimal weight: 0.3980 chunk 229 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 138 optimal weight: 0.9990 chunk 5 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 HIS C 221 HIS ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 169 ASN D 221 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.148237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.139525 restraints weight = 28626.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.123934 restraints weight = 66681.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.120630 restraints weight = 58559.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.119616 restraints weight = 49891.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.119500 restraints weight = 42806.995| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3178 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3178 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20714 Z= 0.128 Angle : 0.598 8.192 28128 Z= 0.291 Chirality : 0.041 0.174 3204 Planarity : 0.004 0.043 3518 Dihedral : 5.182 120.909 2794 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.42 (0.18), residues: 2432 helix: 1.91 (0.14), residues: 1436 sheet: 1.02 (0.34), residues: 262 loop : -1.08 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 166 TYR 0.020 0.001 TYR A 190 PHE 0.013 0.001 PHE A 136 TRP 0.015 0.001 TRP B 10 HIS 0.011 0.001 HIS D 65 Details of bonding type rmsd covalent geometry : bond 0.00289 (20708) covalent geometry : angle 0.59801 (28116) SS BOND : bond 0.00258 ( 6) SS BOND : angle 0.97049 ( 12) hydrogen bonds : bond 0.03649 ( 1232) hydrogen bonds : angle 4.14290 ( 3579) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 480 time to evaluate : 0.829 Fit side-chains revert: symmetry clash REVERT: A 147 TYR cc_start: 0.6929 (m-10) cc_final: 0.6687 (m-10) REVERT: C 49 GLU cc_start: 0.7230 (tm-30) cc_final: 0.6904 (tm-30) REVERT: C 69 MET cc_start: 0.9028 (ppp) cc_final: 0.8189 (ptt) REVERT: C 134 ILE cc_start: 0.8722 (tp) cc_final: 0.8304 (tp) REVERT: C 150 ARG cc_start: 0.6632 (mtm180) cc_final: 0.6027 (mpp80) REVERT: F 134 MET cc_start: 0.8500 (tpp) cc_final: 0.7967 (tpp) REVERT: G 41 GLU cc_start: 0.8927 (tt0) cc_final: 0.8525 (tt0) REVERT: G 369 HIS cc_start: 0.7589 (t-90) cc_final: 0.6735 (t-90) REVERT: H 335 ILE cc_start: 0.9063 (tp) cc_final: 0.8836 (tt) REVERT: J 19 VAL cc_start: 0.8935 (t) cc_final: 0.8706 (t) REVERT: K 41 GLU cc_start: 0.8945 (tt0) cc_final: 0.8589 (tt0) REVERT: K 361 LEU cc_start: 0.8474 (tt) cc_final: 0.8079 (tt) REVERT: L 335 ILE cc_start: 0.9097 (tp) cc_final: 0.8878 (tt) REVERT: D 49 GLU cc_start: 0.6869 (pp20) cc_final: 0.6444 (tm-30) REVERT: D 53 HIS cc_start: 0.6482 (m90) cc_final: 0.6229 (m90) REVERT: D 57 MET cc_start: 0.8430 (mmm) cc_final: 0.8209 (mmm) REVERT: D 69 MET cc_start: 0.8994 (ppp) cc_final: 0.8288 (ptt) REVERT: D 89 ARG cc_start: 0.7304 (ttt180) cc_final: 0.6975 (ttt180) REVERT: D 134 ILE cc_start: 0.8755 (tp) cc_final: 0.8326 (tp) REVERT: D 150 ARG cc_start: 0.6514 (mtm180) cc_final: 0.5961 (mpp80) REVERT: D 257 LEU cc_start: 0.8496 (mt) cc_final: 0.8247 (mt) REVERT: B 86 GLU cc_start: 0.8585 (pm20) cc_final: 0.8351 (pm20) outliers start: 0 outliers final: 0 residues processed: 480 average time/residue: 0.1477 time to fit residues: 110.4013 Evaluate side-chains 393 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 393 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 91 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 218 optimal weight: 0.2980 chunk 159 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 chunk 202 optimal weight: 3.9990 chunk 154 optimal weight: 0.9990 chunk 188 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 204 HIS C 221 HIS ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 221 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.147505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.139859 restraints weight = 28614.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.123350 restraints weight = 65212.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.119212 restraints weight = 66429.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.119147 restraints weight = 60878.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.118501 restraints weight = 51840.997| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3143 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3142 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20714 Z= 0.149 Angle : 0.627 9.060 28128 Z= 0.303 Chirality : 0.042 0.184 3204 Planarity : 0.004 0.086 3518 Dihedral : 5.188 120.946 2794 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.38 (0.18), residues: 2432 helix: 1.88 (0.14), residues: 1436 sheet: 0.96 (0.34), residues: 262 loop : -1.09 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 174 TYR 0.019 0.001 TYR A 190 PHE 0.013 0.001 PHE A 136 TRP 0.017 0.001 TRP B 10 HIS 0.013 0.001 HIS D 65 Details of bonding type rmsd covalent geometry : bond 0.00345 (20708) covalent geometry : angle 0.62724 (28116) SS BOND : bond 0.00270 ( 6) SS BOND : angle 1.00755 ( 12) hydrogen bonds : bond 0.03773 ( 1232) hydrogen bonds : angle 4.18978 ( 3579) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 469 time to evaluate : 0.831 Fit side-chains REVERT: A 89 LYS cc_start: 0.8677 (mptt) cc_final: 0.8434 (mmtm) REVERT: C 49 GLU cc_start: 0.6981 (tm-30) cc_final: 0.5633 (tm-30) REVERT: C 57 MET cc_start: 0.8443 (mmm) cc_final: 0.8171 (mmm) REVERT: C 69 MET cc_start: 0.8877 (ppp) cc_final: 0.8327 (ptt) REVERT: C 134 ILE cc_start: 0.8697 (tp) cc_final: 0.8292 (tp) REVERT: C 150 ARG cc_start: 0.6462 (mtm180) cc_final: 0.5896 (mpp80) REVERT: G 41 GLU cc_start: 0.8930 (tt0) cc_final: 0.8580 (tt0) REVERT: G 369 HIS cc_start: 0.7427 (t-90) cc_final: 0.7175 (t-90) REVERT: H 335 ILE cc_start: 0.9048 (tp) cc_final: 0.8818 (tt) REVERT: I 322 LYS cc_start: 0.8116 (mtmm) cc_final: 0.7892 (mttt) REVERT: K 41 GLU cc_start: 0.8912 (tt0) cc_final: 0.8558 (tt0) REVERT: K 361 LEU cc_start: 0.8472 (tt) cc_final: 0.8079 (tt) REVERT: L 335 ILE cc_start: 0.9102 (tp) cc_final: 0.8879 (tt) REVERT: D 69 MET cc_start: 0.8952 (ppp) cc_final: 0.8495 (ptt) REVERT: D 89 ARG cc_start: 0.7235 (ttt180) cc_final: 0.6948 (ttt180) REVERT: D 134 ILE cc_start: 0.8743 (tp) cc_final: 0.8335 (tp) REVERT: D 150 ARG cc_start: 0.6481 (mtm180) cc_final: 0.5935 (mpp80) REVERT: D 257 LEU cc_start: 0.8538 (mt) cc_final: 0.8268 (mt) REVERT: B 37 ILE cc_start: 0.7054 (pt) cc_final: 0.6354 (mm) REVERT: B 89 LYS cc_start: 0.8758 (mptt) cc_final: 0.8548 (mmtm) outliers start: 0 outliers final: 0 residues processed: 469 average time/residue: 0.1319 time to fit residues: 96.9021 Evaluate side-chains 376 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 376 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 203 optimal weight: 0.3980 chunk 206 optimal weight: 0.0470 chunk 202 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 152 optimal weight: 0.8980 chunk 234 optimal weight: 9.9990 chunk 163 optimal weight: 0.9990 chunk 53 optimal weight: 0.2980 chunk 114 optimal weight: 0.6980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 HIS C 204 HIS ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 173 HIS L 169 ASN D 204 HIS D 221 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.149308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.140051 restraints weight = 28739.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.128442 restraints weight = 69901.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.125371 restraints weight = 63497.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.123637 restraints weight = 50630.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.123438 restraints weight = 41283.423| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3264 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20714 Z= 0.119 Angle : 0.631 23.328 28128 Z= 0.299 Chirality : 0.041 0.245 3204 Planarity : 0.004 0.043 3518 Dihedral : 5.083 120.492 2794 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.40 (0.18), residues: 2432 helix: 1.87 (0.14), residues: 1442 sheet: 1.04 (0.34), residues: 262 loop : -1.06 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG F 174 TYR 0.020 0.001 TYR A 190 PHE 0.011 0.001 PHE A 136 TRP 0.036 0.001 TRP D 45 HIS 0.013 0.001 HIS C 65 Details of bonding type rmsd covalent geometry : bond 0.00265 (20708) covalent geometry : angle 0.63122 (28116) SS BOND : bond 0.00274 ( 6) SS BOND : angle 0.87831 ( 12) hydrogen bonds : bond 0.03582 ( 1232) hydrogen bonds : angle 4.14529 ( 3579) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 460 time to evaluate : 0.741 Fit side-chains revert: symmetry clash REVERT: A 37 ILE cc_start: 0.6923 (pt) cc_final: 0.6218 (mm) REVERT: C 49 GLU cc_start: 0.7146 (tm-30) cc_final: 0.6527 (tm-30) REVERT: C 57 MET cc_start: 0.8379 (mmm) cc_final: 0.7956 (mmm) REVERT: C 134 ILE cc_start: 0.8655 (tp) cc_final: 0.8220 (tp) REVERT: C 150 ARG cc_start: 0.6410 (mtm180) cc_final: 0.5871 (mpp80) REVERT: G 41 GLU cc_start: 0.8848 (tt0) cc_final: 0.8541 (tt0) REVERT: G 369 HIS cc_start: 0.7331 (t-90) cc_final: 0.7075 (t-90) REVERT: I 322 LYS cc_start: 0.8100 (mtmm) cc_final: 0.7897 (mttt) REVERT: J 134 MET cc_start: 0.8291 (tpp) cc_final: 0.7950 (tpp) REVERT: K 41 GLU cc_start: 0.8844 (tt0) cc_final: 0.8514 (tt0) REVERT: K 361 LEU cc_start: 0.8415 (tt) cc_final: 0.8005 (tt) REVERT: D 69 MET cc_start: 0.8863 (ppp) cc_final: 0.8346 (ptt) REVERT: D 89 ARG cc_start: 0.7263 (ttt180) cc_final: 0.6914 (ttt180) REVERT: D 134 ILE cc_start: 0.8685 (tp) cc_final: 0.8339 (tp) REVERT: D 257 LEU cc_start: 0.8445 (mt) cc_final: 0.8176 (mt) REVERT: B 22 ARG cc_start: 0.7056 (mmm-85) cc_final: 0.6001 (tpt-90) REVERT: B 37 ILE cc_start: 0.6894 (pt) cc_final: 0.6188 (mm) REVERT: B 86 GLU cc_start: 0.7582 (pm20) cc_final: 0.7170 (pm20) outliers start: 0 outliers final: 0 residues processed: 460 average time/residue: 0.1432 time to fit residues: 102.5504 Evaluate side-chains 387 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 387 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 104 optimal weight: 1.9990 chunk 201 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 154 optimal weight: 0.9980 chunk 240 optimal weight: 3.9990 chunk 189 optimal weight: 0.7980 chunk 151 optimal weight: 1.9990 chunk 211 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 204 HIS ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 HIS D 221 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.145977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.138241 restraints weight = 28869.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.136998 restraints weight = 62848.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.136006 restraints weight = 71330.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.119593 restraints weight = 71184.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.116269 restraints weight = 68670.232| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 20714 Z= 0.194 Angle : 0.665 9.853 28128 Z= 0.323 Chirality : 0.043 0.203 3204 Planarity : 0.004 0.046 3518 Dihedral : 5.225 121.497 2794 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.29 (0.18), residues: 2432 helix: 1.85 (0.14), residues: 1426 sheet: 0.82 (0.34), residues: 262 loop : -1.11 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 174 TYR 0.019 0.001 TYR A 190 PHE 0.012 0.001 PHE A 136 TRP 0.041 0.001 TRP D 45 HIS 0.013 0.001 HIS C 65 Details of bonding type rmsd covalent geometry : bond 0.00456 (20708) covalent geometry : angle 0.66428 (28116) SS BOND : bond 0.00308 ( 6) SS BOND : angle 1.09941 ( 12) hydrogen bonds : bond 0.04013 ( 1232) hydrogen bonds : angle 4.26817 ( 3579) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3205.69 seconds wall clock time: 56 minutes 23.01 seconds (3383.01 seconds total)