Starting phenix.real_space_refine on Tue Jun 17 15:24:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tsi_41593/06_2025/8tsi_41593_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tsi_41593/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tsi_41593/06_2025/8tsi_41593.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tsi_41593/06_2025/8tsi_41593.map" model { file = "/net/cci-nas-00/data/ceres_data/8tsi_41593/06_2025/8tsi_41593_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tsi_41593/06_2025/8tsi_41593_neut.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.866 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 12.37, per 1000 atoms: 0.61 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: 5.43 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 2.14 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: 6.43 Time building geometry restraints manager: 6.43 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: 0.04 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: 2.220 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: 0.820 Check model and map are aligned: 0.140 Set scattering table: 0.200 Process input model: 46.310 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.110 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: 0.010 Load rotamer database and sin/cos tables:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.010 ------------------------------------------------------------------------------- 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 : 8.10 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (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 TRP 0.018 0.001 TRP B 10 HIS 0.005 0.001 HIS F 369 PHE 0.015 0.001 PHE C 61 TYR 0.033 0.001 TYR B 215 ARG 0.008 0.000 ARG L 47 Details of bonding type rmsd hydrogen bonds : bond 0.14441 ( 1232) hydrogen bonds : angle 5.94615 ( 3579) SS BOND : bond 0.00220 ( 6) SS BOND : angle 1.05153 ( 12) covalent geometry : bond 0.00428 (20708) covalent geometry : angle 1.20127 (28116) *********************** 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 : 2.667 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: 0.3060 time to fit residues: 220.0057 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 : 2.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 204 optimal weight: 0.6980 chunk 183 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 123 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 chunk 189 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 141 optimal weight: 0.0270 chunk 219 optimal weight: 0.9980 overall best weight: 0.6638 ------------------------------------------------------------------------------- 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 53 HIS 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 53 HIS D 204 HIS D 221 HIS B 87 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.152813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.141868 restraints weight = 28009.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.126155 restraints weight = 62307.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.126935 restraints weight = 55463.688| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3278 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3276 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20714 Z= 0.133 Angle : 0.601 8.061 28128 Z= 0.291 Chirality : 0.041 0.163 3204 Planarity : 0.004 0.053 3518 Dihedral : 6.041 129.438 2794 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.18 % Allowed : 3.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.18), residues: 2432 helix: 1.90 (0.14), residues: 1424 sheet: 0.93 (0.34), residues: 264 loop : -0.97 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 121 HIS 0.006 0.001 HIS F 173 PHE 0.019 0.001 PHE G 30 TYR 0.023 0.001 TYR A 190 ARG 0.003 0.000 ARG B 22 Details of bonding type rmsd hydrogen bonds : bond 0.04412 ( 1232) hydrogen bonds : angle 4.49234 ( 3579) SS BOND : bond 0.00234 ( 6) SS BOND : angle 1.78934 ( 12) covalent geometry : bond 0.00283 (20708) covalent geometry : angle 0.59978 (28116) *********************** 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 556 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 552 time to evaluate : 2.345 Fit side-chains revert: symmetry clash REVERT: C 49 GLU cc_start: 0.6636 (tm-30) cc_final: 0.6048 (tm-30) REVERT: C 69 MET cc_start: 0.8624 (ppp) cc_final: 0.7860 (ptt) REVERT: E 356 TYR cc_start: 0.7784 (t80) cc_final: 0.7475 (t80) REVERT: G 369 HIS cc_start: 0.7668 (t-90) cc_final: 0.7150 (t-90) REVERT: H 138 CYS cc_start: 0.8045 (m) cc_final: 0.7226 (m) REVERT: K 361 LEU cc_start: 0.8648 (tt) cc_final: 0.8241 (tt) REVERT: K 369 HIS cc_start: 0.7635 (t-90) cc_final: 0.7247 (t-90) REVERT: L 80 GLN cc_start: 0.8255 (tm-30) cc_final: 0.8022 (tm-30) REVERT: L 138 CYS cc_start: 0.8028 (m) cc_final: 0.7340 (m) REVERT: L 335 ILE cc_start: 0.9052 (tp) cc_final: 0.8808 (tt) REVERT: D 31 GLU cc_start: 0.8487 (tp30) cc_final: 0.8228 (tp30) REVERT: D 49 GLU cc_start: 0.6709 (tm-30) cc_final: 0.6061 (tm-30) REVERT: D 69 MET cc_start: 0.8670 (ppp) cc_final: 0.7782 (ptt) REVERT: B 48 MET cc_start: 0.8078 (tpt) cc_final: 0.7719 (tpt) REVERT: B 89 LYS cc_start: 0.8864 (mptt) cc_final: 0.8631 (mmtm) outliers start: 4 outliers final: 2 residues processed: 554 average time/residue: 0.3415 time to fit residues: 285.6660 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 : 2.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 103 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 231 optimal weight: 10.0000 chunk 107 optimal weight: 0.6980 chunk 140 optimal weight: 4.9990 chunk 218 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 171 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 223 optimal weight: 9.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 HIS J 94 GLN D 20 GLN B 118 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.146739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.137538 restraints weight = 28734.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.136046 restraints weight = 66509.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.134969 restraints weight = 76523.086| |-----------------------------------------------------------------------------| 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) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3498 r_free = 0.3498 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3498 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20714 Z= 0.167 Angle : 0.599 13.214 28128 Z= 0.293 Chirality : 0.042 0.205 3204 Planarity : 0.004 0.051 3518 Dihedral : 5.755 130.315 2794 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.09 % Allowed : 2.97 % Favored : 96.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.17), residues: 2432 helix: 1.95 (0.14), residues: 1422 sheet: 0.84 (0.34), residues: 264 loop : -1.11 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 10 HIS 0.007 0.001 HIS D 65 PHE 0.014 0.001 PHE G 30 TYR 0.022 0.001 TYR A 190 ARG 0.005 0.000 ARG H 47 Details of bonding type rmsd hydrogen bonds : bond 0.04157 ( 1232) hydrogen bonds : angle 4.38303 ( 3579) SS BOND : bond 0.00609 ( 6) SS BOND : angle 1.44585 ( 12) covalent geometry : bond 0.00382 (20708) covalent geometry : angle 0.59869 (28116) *********************** 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 511 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 509 time to evaluate : 2.186 Fit side-chains REVERT: A 86 GLU cc_start: 0.7398 (pm20) cc_final: 0.6794 (pt0) REVERT: C 33 LYS cc_start: 0.7177 (tptt) cc_final: 0.6885 (tppt) REVERT: C 49 GLU cc_start: 0.6419 (tm-30) cc_final: 0.5780 (tm-30) REVERT: C 69 MET cc_start: 0.8407 (ppp) cc_final: 0.7901 (ptt) REVERT: C 134 ILE cc_start: 0.8510 (tp) cc_final: 0.8165 (tp) REVERT: E 28 VAL cc_start: 0.8805 (m) cc_final: 0.8583 (t) REVERT: E 322 LYS cc_start: 0.8043 (mtmm) cc_final: 0.7794 (mttt) REVERT: E 356 TYR cc_start: 0.7325 (t80) cc_final: 0.7044 (t80) REVERT: F 19 VAL cc_start: 0.8838 (t) cc_final: 0.8637 (t) REVERT: F 41 GLU cc_start: 0.8536 (tt0) cc_final: 0.8228 (tt0) REVERT: G 369 HIS cc_start: 0.7228 (t-90) cc_final: 0.6660 (t-90) REVERT: H 138 CYS cc_start: 0.8100 (m) cc_final: 0.7697 (t) REVERT: K 361 LEU cc_start: 0.8265 (tt) cc_final: 0.7770 (tt) REVERT: K 369 HIS cc_start: 0.7308 (t-90) cc_final: 0.6718 (t-90) REVERT: L 79 LEU cc_start: 0.8532 (mt) cc_final: 0.8331 (mt) REVERT: L 335 ILE cc_start: 0.9012 (tp) cc_final: 0.8786 (tt) REVERT: D 49 GLU cc_start: 0.6055 (tm-30) cc_final: 0.5556 (tm-30) REVERT: D 69 MET cc_start: 0.8480 (ppp) cc_final: 0.7911 (ptt) REVERT: D 96 MET cc_start: 0.7848 (mmm) cc_final: 0.7593 (mmt) REVERT: D 134 ILE cc_start: 0.8565 (tp) cc_final: 0.8251 (tp) REVERT: D 257 LEU cc_start: 0.8484 (mt) cc_final: 0.8215 (mt) outliers start: 2 outliers final: 0 residues processed: 510 average time/residue: 0.3032 time to fit residues: 238.9392 Evaluate side-chains 411 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 411 time to evaluate : 2.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 80 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 126 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 39 optimal weight: 0.3980 chunk 82 optimal weight: 7.9990 chunk 142 optimal weight: 3.9990 chunk 151 optimal weight: 0.6980 chunk 165 optimal weight: 0.9980 chunk 189 optimal weight: 0.8980 chunk 101 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 94 GLN J 94 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.149964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.138697 restraints weight = 28728.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.124602 restraints weight = 56988.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.122734 restraints weight = 52223.615| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3225 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20714 Z= 0.124 Angle : 0.555 7.899 28128 Z= 0.270 Chirality : 0.040 0.143 3204 Planarity : 0.004 0.048 3518 Dihedral : 5.520 126.307 2794 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.05 % Allowed : 2.92 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.18), residues: 2432 helix: 1.96 (0.14), residues: 1438 sheet: 0.92 (0.34), residues: 264 loop : -1.06 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 10 HIS 0.004 0.001 HIS J 101 PHE 0.016 0.001 PHE A 136 TYR 0.017 0.001 TYR B 190 ARG 0.003 0.000 ARG L 47 Details of bonding type rmsd hydrogen bonds : bond 0.03722 ( 1232) hydrogen bonds : angle 4.19023 ( 3579) SS BOND : bond 0.00621 ( 6) SS BOND : angle 1.18106 ( 12) covalent geometry : bond 0.00273 (20708) covalent geometry : angle 0.55435 (28116) *********************** 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 504 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 503 time to evaluate : 2.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 MET cc_start: 0.8093 (mmt) cc_final: 0.7852 (mmt) REVERT: C 69 MET cc_start: 0.8505 (ppp) cc_final: 0.8023 (ptt) REVERT: E 322 LYS cc_start: 0.8102 (mtmm) cc_final: 0.7892 (mttt) REVERT: E 356 TYR cc_start: 0.8040 (t80) cc_final: 0.7751 (t80) REVERT: G 369 HIS cc_start: 0.7901 (t-90) cc_final: 0.6663 (t-90) REVERT: I 79 LEU cc_start: 0.8563 (mt) cc_final: 0.8289 (mm) REVERT: I 322 LYS cc_start: 0.8120 (mtmm) cc_final: 0.7895 (mttt) REVERT: J 134 MET cc_start: 0.8535 (tpp) cc_final: 0.8145 (tpp) REVERT: K 361 LEU cc_start: 0.8424 (tt) cc_final: 0.7826 (tt) REVERT: K 369 HIS cc_start: 0.8028 (t-90) cc_final: 0.7340 (t-90) REVERT: L 106 LEU cc_start: 0.7751 (mm) cc_final: 0.7546 (pt) REVERT: L 335 ILE cc_start: 0.9119 (tp) cc_final: 0.8902 (tt) REVERT: D 49 GLU cc_start: 0.7322 (tm-30) cc_final: 0.5674 (tm-30) REVERT: D 53 HIS cc_start: 0.5483 (m90) cc_final: 0.4843 (m90) REVERT: D 69 MET cc_start: 0.8577 (ppp) cc_final: 0.7959 (ptt) REVERT: D 257 LEU cc_start: 0.8561 (mt) cc_final: 0.8310 (mt) outliers start: 1 outliers final: 0 residues processed: 503 average time/residue: 0.3292 time to fit residues: 255.7377 Evaluate side-chains 398 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 398 time to evaluate : 2.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 129 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 219 optimal weight: 0.7980 chunk 216 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 154 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 204 optimal weight: 7.9990 chunk 139 optimal weight: 9.9990 chunk 162 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN C 221 HIS C 238 GLN F 94 GLN J 94 GLN D 221 HIS D 238 GLN B 87 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.147270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.138442 restraints weight = 28832.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 91)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.122105 restraints weight = 64576.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.120062 restraints weight = 57248.335| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20714 Z= 0.167 Angle : 0.590 6.854 28128 Z= 0.289 Chirality : 0.042 0.154 3204 Planarity : 0.004 0.047 3518 Dihedral : 5.421 125.068 2794 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.09 % Allowed : 2.46 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.17), residues: 2432 helix: 1.91 (0.14), residues: 1436 sheet: 0.86 (0.34), residues: 260 loop : -1.07 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 10 HIS 0.009 0.001 HIS D 53 PHE 0.014 0.001 PHE A 136 TYR 0.017 0.002 TYR K 343 ARG 0.005 0.000 ARG L 47 Details of bonding type rmsd hydrogen bonds : bond 0.03954 ( 1232) hydrogen bonds : angle 4.25744 ( 3579) SS BOND : bond 0.00247 ( 6) SS BOND : angle 1.06038 ( 12) covalent geometry : bond 0.00389 (20708) covalent geometry : angle 0.58994 (28116) *********************** 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 494 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 492 time to evaluate : 2.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 GLU cc_start: 0.8151 (pm20) cc_final: 0.7926 (pm20) REVERT: A 87 ASN cc_start: 0.8530 (OUTLIER) cc_final: 0.8233 (t0) REVERT: A 140 MET cc_start: 0.8470 (mmt) cc_final: 0.8034 (mmt) REVERT: C 69 MET cc_start: 0.8689 (ppp) cc_final: 0.8155 (ptt) REVERT: C 134 ILE cc_start: 0.8736 (tp) cc_final: 0.8329 (tp) REVERT: C 150 ARG cc_start: 0.6720 (mtm180) cc_final: 0.6062 (mpp80) REVERT: E 322 LYS cc_start: 0.8137 (mtmm) cc_final: 0.7846 (mttt) REVERT: E 356 TYR cc_start: 0.8087 (t80) cc_final: 0.7833 (t80) REVERT: F 14 LEU cc_start: 0.7413 (pt) cc_final: 0.7207 (tp) REVERT: G 369 HIS cc_start: 0.7863 (t-90) cc_final: 0.6603 (t-90) REVERT: H 344 ASN cc_start: 0.7764 (m-40) cc_final: 0.7481 (m-40) REVERT: I 322 LYS cc_start: 0.8205 (mtmm) cc_final: 0.7978 (mttt) REVERT: J 134 MET cc_start: 0.8600 (tpp) cc_final: 0.8154 (tpp) REVERT: K 361 LEU cc_start: 0.8480 (tt) cc_final: 0.8029 (tt) REVERT: K 369 HIS cc_start: 0.8117 (t-90) cc_final: 0.7238 (t-90) REVERT: L 79 LEU cc_start: 0.8572 (mt) cc_final: 0.8368 (mt) REVERT: L 335 ILE cc_start: 0.9130 (tp) cc_final: 0.8927 (tt) REVERT: D 49 GLU cc_start: 0.6704 (tm-30) cc_final: 0.5671 (tm-30) REVERT: D 53 HIS cc_start: 0.5660 (m90) cc_final: 0.5202 (m-70) REVERT: D 69 MET cc_start: 0.8746 (ppp) cc_final: 0.8113 (ptt) REVERT: D 134 ILE cc_start: 0.8765 (tp) cc_final: 0.8432 (tp) REVERT: D 150 ARG cc_start: 0.6727 (mtm180) cc_final: 0.6101 (mpp80) REVERT: D 257 LEU cc_start: 0.8515 (mt) cc_final: 0.8251 (mt) REVERT: B 87 ASN cc_start: 0.8460 (OUTLIER) cc_final: 0.8070 (t0) REVERT: B 89 LYS cc_start: 0.8766 (mmtm) cc_final: 0.8180 (mmtp) outliers start: 2 outliers final: 0 residues processed: 494 average time/residue: 0.3178 time to fit residues: 242.2001 Evaluate side-chains 386 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 384 time to evaluate : 2.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 160 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 238 GLN F 173 HIS D 238 GLN ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.142708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.133848 restraints weight = 29460.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.118502 restraints weight = 65520.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.115641 restraints weight = 56242.418| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 20714 Z= 0.307 Angle : 0.721 7.712 28128 Z= 0.359 Chirality : 0.046 0.150 3204 Planarity : 0.005 0.048 3518 Dihedral : 5.630 126.686 2794 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.17), residues: 2432 helix: 1.61 (0.14), residues: 1436 sheet: 0.54 (0.34), residues: 260 loop : -1.21 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L 114 HIS 0.011 0.002 HIS D 65 PHE 0.017 0.002 PHE F 30 TYR 0.024 0.002 TYR F 343 ARG 0.004 0.001 ARG C 183 Details of bonding type rmsd hydrogen bonds : bond 0.04796 ( 1232) hydrogen bonds : angle 4.57555 ( 3579) SS BOND : bond 0.00341 ( 6) SS BOND : angle 1.47682 ( 12) covalent geometry : bond 0.00720 (20708) covalent geometry : angle 0.72070 (28116) *********************** 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 462 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 462 time to evaluate : 2.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 GLU cc_start: 0.7897 (pm20) cc_final: 0.7309 (pm20) REVERT: E 356 TYR cc_start: 0.8110 (t80) cc_final: 0.7802 (t80) REVERT: F 14 LEU cc_start: 0.7369 (pt) cc_final: 0.7075 (tp) REVERT: G 369 HIS cc_start: 0.7579 (t-90) cc_final: 0.7227 (t-90) REVERT: H 335 ILE cc_start: 0.9084 (tp) cc_final: 0.8864 (tt) REVERT: K 361 LEU cc_start: 0.8506 (tt) cc_final: 0.7995 (tt) REVERT: K 369 HIS cc_start: 0.7764 (t-90) cc_final: 0.7399 (t-90) REVERT: L 335 ILE cc_start: 0.9102 (tp) cc_final: 0.8870 (tt) REVERT: D 49 GLU cc_start: 0.6425 (tm-30) cc_final: 0.5783 (tm-30) REVERT: D 257 LEU cc_start: 0.8459 (mt) cc_final: 0.8178 (mt) REVERT: B 89 LYS cc_start: 0.8859 (mmtm) cc_final: 0.8424 (mmtp) outliers start: 0 outliers final: 0 residues processed: 462 average time/residue: 0.3297 time to fit residues: 237.0611 Evaluate side-chains 378 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 378 time to evaluate : 2.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 26 optimal weight: 0.7980 chunk 21 optimal weight: 0.4980 chunk 82 optimal weight: 0.9990 chunk 172 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 178 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 chunk 127 optimal weight: 0.9990 chunk 139 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN C 204 HIS C 221 HIS ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 173 HIS K 169 ASN D 204 HIS D 221 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.145599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.137881 restraints weight = 28786.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.136520 restraints weight = 61966.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.135610 restraints weight = 75080.871| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3503 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3503 r_free = 0.3503 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3503 r_free = 0.3503 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3503 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20714 Z= 0.153 Angle : 0.618 17.679 28128 Z= 0.296 Chirality : 0.042 0.142 3204 Planarity : 0.004 0.045 3518 Dihedral : 5.319 122.433 2794 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.05 % Allowed : 1.73 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.18), residues: 2432 helix: 1.80 (0.14), residues: 1436 sheet: 0.76 (0.34), residues: 262 loop : -1.15 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 10 HIS 0.008 0.001 HIS D 65 PHE 0.015 0.001 PHE A 136 TYR 0.013 0.001 TYR A 190 ARG 0.008 0.000 ARG L 47 Details of bonding type rmsd hydrogen bonds : bond 0.04005 ( 1232) hydrogen bonds : angle 4.28925 ( 3579) SS BOND : bond 0.00252 ( 6) SS BOND : angle 1.12289 ( 12) covalent geometry : bond 0.00353 (20708) covalent geometry : angle 0.61756 (28116) *********************** 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 477 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 476 time to evaluate : 2.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 GLU cc_start: 0.7252 (pm20) cc_final: 0.6943 (pm20) REVERT: A 140 MET cc_start: 0.7424 (mmt) cc_final: 0.7216 (mmt) REVERT: C 49 GLU cc_start: 0.5085 (tm-30) cc_final: 0.4146 (tm-30) REVERT: C 134 ILE cc_start: 0.8556 (tp) cc_final: 0.8093 (tp) REVERT: C 204 HIS cc_start: 0.6739 (m90) cc_final: 0.6517 (m-70) REVERT: E 322 LYS cc_start: 0.7834 (mtmt) cc_final: 0.7602 (mttt) REVERT: E 356 TYR cc_start: 0.7469 (t80) cc_final: 0.7037 (t80) REVERT: G 77 CYS cc_start: 0.5597 (m) cc_final: 0.5379 (m) REVERT: G 369 HIS cc_start: 0.7175 (t-90) cc_final: 0.6525 (t-90) REVERT: J 19 VAL cc_start: 0.8687 (t) cc_final: 0.8461 (t) REVERT: K 77 CYS cc_start: 0.5725 (m) cc_final: 0.5454 (m) REVERT: K 320 LYS cc_start: 0.6847 (mmpt) cc_final: 0.6535 (mmtt) REVERT: K 361 LEU cc_start: 0.8146 (tt) cc_final: 0.7702 (tt) REVERT: K 369 HIS cc_start: 0.7246 (t-90) cc_final: 0.7009 (t-90) REVERT: L 335 ILE cc_start: 0.9095 (tp) cc_final: 0.8870 (tt) REVERT: D 49 GLU cc_start: 0.5452 (tm-30) cc_final: 0.5124 (tm-30) REVERT: D 134 ILE cc_start: 0.8613 (tp) cc_final: 0.8225 (tp) outliers start: 1 outliers final: 0 residues processed: 476 average time/residue: 0.3932 time to fit residues: 292.3542 Evaluate side-chains 371 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 371 time to evaluate : 3.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 232 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 chunk 120 optimal weight: 9.9990 chunk 161 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 230 optimal weight: 0.2980 chunk 173 optimal weight: 0.0970 chunk 107 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 221 HIS ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 173 HIS 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 = 0.3613 r_free = 0.3613 target = 0.144791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.136860 restraints weight = 29064.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.120265 restraints weight = 66183.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.117698 restraints weight = 57936.612| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20714 Z= 0.170 Angle : 0.632 12.049 28128 Z= 0.308 Chirality : 0.042 0.172 3204 Planarity : 0.004 0.044 3518 Dihedral : 5.283 122.184 2794 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.05 % Allowed : 0.46 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.18), residues: 2432 helix: 1.74 (0.14), residues: 1438 sheet: 0.73 (0.35), residues: 260 loop : -1.15 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 10 HIS 0.010 0.001 HIS C 65 PHE 0.016 0.001 PHE A 136 TYR 0.017 0.001 TYR K 343 ARG 0.009 0.000 ARG K 166 Details of bonding type rmsd hydrogen bonds : bond 0.04047 ( 1232) hydrogen bonds : angle 4.29783 ( 3579) SS BOND : bond 0.00265 ( 6) SS BOND : angle 1.14094 ( 12) covalent geometry : bond 0.00397 (20708) covalent geometry : angle 0.63142 (28116) *********************** 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 470 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 469 time to evaluate : 2.488 Fit side-chains revert: symmetry clash REVERT: C 49 GLU cc_start: 0.6522 (tm-30) cc_final: 0.5777 (tm-30) REVERT: C 53 HIS cc_start: 0.5797 (m170) cc_final: 0.5585 (m90) REVERT: C 57 MET cc_start: 0.8425 (mmm) cc_final: 0.8211 (mmm) REVERT: C 134 ILE cc_start: 0.8729 (tp) cc_final: 0.8320 (tp) REVERT: C 150 ARG cc_start: 0.6733 (mtm180) cc_final: 0.6259 (mpp80) REVERT: E 356 TYR cc_start: 0.8036 (t80) cc_final: 0.7755 (t80) REVERT: J 19 VAL cc_start: 0.9031 (t) cc_final: 0.8780 (t) REVERT: J 149 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7935 (mt-10) REVERT: K 361 LEU cc_start: 0.8422 (tt) cc_final: 0.7888 (tt) REVERT: K 369 HIS cc_start: 0.7889 (t-90) cc_final: 0.7429 (t-90) REVERT: L 138 CYS cc_start: 0.8481 (m) cc_final: 0.8267 (m) REVERT: L 335 ILE cc_start: 0.9078 (tp) cc_final: 0.8847 (tt) REVERT: D 49 GLU cc_start: 0.6641 (tm-30) cc_final: 0.5456 (tm-30) REVERT: D 53 HIS cc_start: 0.6160 (m90) cc_final: 0.5920 (m90) REVERT: D 134 ILE cc_start: 0.8808 (tp) cc_final: 0.8417 (tp) REVERT: D 150 ARG cc_start: 0.6599 (mtm180) cc_final: 0.6017 (mpp80) outliers start: 1 outliers final: 1 residues processed: 469 average time/residue: 0.3982 time to fit residues: 292.2989 Evaluate side-chains 376 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 375 time to evaluate : 2.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 99 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 116 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 97 optimal weight: 7.9990 chunk 209 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 187 optimal weight: 0.6980 chunk 79 optimal weight: 0.0980 chunk 165 optimal weight: 1.9990 chunk 120 optimal weight: 9.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.143703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.136387 restraints weight = 29010.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.135610 restraints weight = 62288.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.134758 restraints weight = 68244.903| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 20714 Z= 0.210 Angle : 0.682 21.079 28128 Z= 0.332 Chirality : 0.044 0.250 3204 Planarity : 0.004 0.044 3518 Dihedral : 5.379 123.095 2794 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.18), residues: 2432 helix: 1.65 (0.14), residues: 1436 sheet: 0.57 (0.34), residues: 260 loop : -1.20 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 10 HIS 0.010 0.001 HIS C 65 PHE 0.016 0.001 PHE A 136 TYR 0.018 0.002 TYR G 343 ARG 0.009 0.000 ARG K 166 Details of bonding type rmsd hydrogen bonds : bond 0.04295 ( 1232) hydrogen bonds : angle 4.39572 ( 3579) SS BOND : bond 0.00304 ( 6) SS BOND : angle 1.21898 ( 12) covalent geometry : bond 0.00494 (20708) covalent geometry : angle 0.68156 (28116) *********************** 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 457 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 457 time to evaluate : 2.687 Fit side-chains revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8484 (mptt) cc_final: 0.8277 (mmtm) REVERT: C 49 GLU cc_start: 0.5386 (tm-30) cc_final: 0.4715 (tm-30) REVERT: E 322 LYS cc_start: 0.7978 (mtmt) cc_final: 0.7758 (mttt) REVERT: E 356 TYR cc_start: 0.7281 (t80) cc_final: 0.7032 (t80) REVERT: H 138 CYS cc_start: 0.8444 (m) cc_final: 0.8142 (m) REVERT: J 19 VAL cc_start: 0.8804 (t) cc_final: 0.8565 (t) REVERT: J 343 TYR cc_start: 0.8711 (t80) cc_final: 0.8491 (t80) REVERT: K 361 LEU cc_start: 0.8207 (tt) cc_final: 0.7773 (tt) REVERT: K 369 HIS cc_start: 0.7188 (t-90) cc_final: 0.6528 (t-90) REVERT: L 138 CYS cc_start: 0.8258 (m) cc_final: 0.8056 (m) REVERT: L 335 ILE cc_start: 0.9060 (tp) cc_final: 0.8836 (tt) REVERT: D 49 GLU cc_start: 0.5534 (tm-30) cc_final: 0.4651 (tm-30) REVERT: D 96 MET cc_start: 0.7962 (mmm) cc_final: 0.7713 (mmt) REVERT: B 86 GLU cc_start: 0.6336 (pt0) cc_final: 0.5915 (pt0) REVERT: B 140 MET cc_start: 0.7391 (mmt) cc_final: 0.7157 (mtt) outliers start: 0 outliers final: 0 residues processed: 457 average time/residue: 0.4154 time to fit residues: 298.5941 Evaluate side-chains 372 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 3.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 174 optimal weight: 0.9980 chunk 199 optimal weight: 3.9990 chunk 202 optimal weight: 0.9980 chunk 138 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 chunk 127 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 241 optimal weight: 7.9990 chunk 92 optimal weight: 0.9980 overall best weight: 1.3982 ------------------------------------------------------------------------------- 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** L 169 ASN D 53 HIS D 204 HIS D 221 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.144097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.136626 restraints weight = 29267.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.120150 restraints weight = 64542.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.115977 restraints weight = 67788.089| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20714 Z= 0.181 Angle : 0.655 9.428 28128 Z= 0.320 Chirality : 0.043 0.183 3204 Planarity : 0.004 0.044 3518 Dihedral : 5.339 122.235 2794 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.18), residues: 2432 helix: 1.65 (0.14), residues: 1434 sheet: 0.56 (0.34), residues: 260 loop : -1.20 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 10 HIS 0.012 0.001 HIS C 65 PHE 0.013 0.001 PHE B 136 TYR 0.016 0.001 TYR K 343 ARG 0.010 0.000 ARG G 166 Details of bonding type rmsd hydrogen bonds : bond 0.04120 ( 1232) hydrogen bonds : angle 4.34535 ( 3579) SS BOND : bond 0.00303 ( 6) SS BOND : angle 1.20824 ( 12) covalent geometry : bond 0.00424 (20708) covalent geometry : angle 0.65472 (28116) ********************** 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 456 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 456 time to evaluate : 3.769 Fit side-chains revert: symmetry clash REVERT: C 49 GLU cc_start: 0.7006 (tm-30) cc_final: 0.6393 (tm-30) REVERT: C 69 MET cc_start: 0.8413 (ptp) cc_final: 0.8150 (ptp) REVERT: C 150 ARG cc_start: 0.6566 (mtm180) cc_final: 0.6003 (mpp80) REVERT: E 356 TYR cc_start: 0.8058 (t80) cc_final: 0.7819 (t80) REVERT: H 138 CYS cc_start: 0.8584 (m) cc_final: 0.8383 (m) REVERT: J 15 GLN cc_start: 0.8575 (pt0) cc_final: 0.8282 (pt0) REVERT: J 343 TYR cc_start: 0.8710 (t80) cc_final: 0.8343 (t80) REVERT: K 361 LEU cc_start: 0.8507 (tt) cc_final: 0.8030 (tt) REVERT: L 80 GLN cc_start: 0.8023 (tm-30) cc_final: 0.7774 (tm-30) REVERT: L 335 ILE cc_start: 0.9043 (tp) cc_final: 0.8803 (tt) REVERT: D 49 GLU cc_start: 0.6783 (tm-30) cc_final: 0.5861 (tm-30) REVERT: D 150 ARG cc_start: 0.6483 (mtm180) cc_final: 0.5798 (mpp80) REVERT: B 114 GLU cc_start: 0.5811 (mm-30) cc_final: 0.5535 (mm-30) outliers start: 0 outliers final: 0 residues processed: 456 average time/residue: 0.4372 time to fit residues: 313.2314 Evaluate side-chains 365 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 365 time to evaluate : 4.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 237 optimal weight: 3.9990 chunk 135 optimal weight: 0.0170 chunk 102 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 225 optimal weight: 10.0000 chunk 118 optimal weight: 0.9990 chunk 241 optimal weight: 9.9990 chunk 26 optimal weight: 0.0020 chunk 114 optimal weight: 0.5980 chunk 239 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.9230 ------------------------------------------------------------------------------- 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 ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 173 HIS D 204 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.145522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.138999 restraints weight = 28971.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.138115 restraints weight = 61546.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.136972 restraints weight = 69156.964| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.2812 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= 0.144 Angle : 0.629 8.810 28128 Z= 0.307 Chirality : 0.042 0.172 3204 Planarity : 0.004 0.044 3518 Dihedral : 5.251 121.337 2794 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.18), residues: 2432 helix: 1.70 (0.14), residues: 1436 sheet: 0.62 (0.34), residues: 260 loop : -1.13 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 10 HIS 0.011 0.001 HIS C 65 PHE 0.013 0.001 PHE B 136 TYR 0.017 0.001 TYR G 343 ARG 0.010 0.000 ARG G 166 Details of bonding type rmsd hydrogen bonds : bond 0.03901 ( 1232) hydrogen bonds : angle 4.28617 ( 3579) SS BOND : bond 0.00240 ( 6) SS BOND : angle 1.04557 ( 12) covalent geometry : bond 0.00330 (20708) covalent geometry : angle 0.62922 (28116) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9282.10 seconds wall clock time: 169 minutes 36.98 seconds (10176.98 seconds total)