Starting phenix.real_space_refine on Tue May 20 14:37:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tsi_41593/05_2025/8tsi_41593_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tsi_41593/05_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_41593/05_2025/8tsi_41593.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tsi_41593/05_2025/8tsi_41593.map" model { file = "/net/cci-nas-00/data/ceres_data/8tsi_41593/05_2025/8tsi_41593_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tsi_41593/05_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-5687/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: 12.63, per 1000 atoms: 0.62 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: 5.75 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: 2.13 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: 5.92 Time building geometry restraints manager: 6.52 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: 2.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.790 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 46.140 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.020 ------------------------------------------------------------------------------- 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 : 2.217 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: 0.2894 time to fit residues: 206.2045 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 : 2.508 ------------------------------------------------------------------------------- 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 = 0.152812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.141867 restraints weight = 28009.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.126113 restraints weight = 62236.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.125166 restraints weight = 55202.588| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3273 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 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 = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3271 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 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 8.062 28128 Z= 0.291 Chirality : 0.041 0.163 3204 Planarity : 0.004 0.053 3518 Dihedral : 6.041 129.439 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 4.49233 ( 3579) SS BOND : bond 0.00234 ( 6) SS BOND : angle 1.78935 ( 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 : 2.087 Fit side-chains revert: symmetry clash REVERT: C 49 GLU cc_start: 0.6567 (tm-30) cc_final: 0.6017 (tm-30) REVERT: C 69 MET cc_start: 0.8611 (ppp) cc_final: 0.7836 (ptt) REVERT: E 356 TYR cc_start: 0.7755 (t80) cc_final: 0.7450 (t80) REVERT: G 369 HIS cc_start: 0.7676 (t-90) cc_final: 0.7137 (t-90) REVERT: H 138 CYS cc_start: 0.8000 (m) cc_final: 0.7152 (m) REVERT: K 361 LEU cc_start: 0.8640 (tt) cc_final: 0.8230 (tt) REVERT: K 369 HIS cc_start: 0.7645 (t-90) cc_final: 0.7242 (t-90) REVERT: L 80 GLN cc_start: 0.8224 (tm-30) cc_final: 0.8004 (tm-30) REVERT: L 138 CYS cc_start: 0.7994 (m) cc_final: 0.7261 (m) REVERT: L 335 ILE cc_start: 0.9018 (tp) cc_final: 0.8788 (tt) REVERT: D 31 GLU cc_start: 0.8462 (tp30) cc_final: 0.8231 (tp30) REVERT: D 49 GLU cc_start: 0.6658 (tm-30) cc_final: 0.6035 (tm-30) REVERT: D 69 MET cc_start: 0.8639 (ppp) cc_final: 0.7728 (ptt) REVERT: B 48 MET cc_start: 0.8159 (tpt) cc_final: 0.7807 (tpt) REVERT: B 89 LYS cc_start: 0.8852 (mptt) cc_final: 0.8629 (mmtm) outliers start: 4 outliers final: 2 residues processed: 554 average time/residue: 0.3067 time to fit residues: 255.3097 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 : 2.099 ------------------------------------------------------------------------------- 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: 0.9990 chunk 140 optimal weight: 4.9990 chunk 218 optimal weight: 0.0970 chunk 45 optimal weight: 0.6980 chunk 171 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 223 optimal weight: 9.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 = 0.3646 r_free = 0.3646 target = 0.147277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.138393 restraints weight = 28663.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.134974 restraints weight = 65994.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.128727 restraints weight = 97779.016| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3353 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.1987 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= 0.156 Angle : 0.591 13.805 28128 Z= 0.289 Chirality : 0.041 0.204 3204 Planarity : 0.004 0.050 3518 Dihedral : 5.739 130.174 2794 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.09 % Allowed : 2.65 % Favored : 97.26 % 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: 1.43 (0.18), residues: 2432 helix: 1.95 (0.14), residues: 1432 sheet: 0.88 (0.34), residues: 264 loop : -1.05 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 10 HIS 0.008 0.001 HIS J 369 PHE 0.014 0.001 PHE G 30 TYR 0.022 0.001 TYR A 190 ARG 0.006 0.000 ARG H 47 Details of bonding type rmsd hydrogen bonds : bond 0.04079 ( 1232) hydrogen bonds : angle 4.35343 ( 3579) SS BOND : bond 0.00282 ( 6) SS BOND : angle 1.43911 ( 12) covalent geometry : bond 0.00355 (20708) covalent geometry : angle 0.59039 (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 513 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 511 time to evaluate : 2.177 Fit side-chains REVERT: A 86 GLU cc_start: 0.7979 (pm20) cc_final: 0.7697 (pm20) REVERT: C 33 LYS cc_start: 0.7672 (tptt) cc_final: 0.7288 (tppt) REVERT: C 49 GLU cc_start: 0.6731 (tm-30) cc_final: 0.6020 (tm-30) REVERT: C 69 MET cc_start: 0.8441 (ppp) cc_final: 0.7918 (ptt) REVERT: C 134 ILE cc_start: 0.8601 (tp) cc_final: 0.8260 (tp) REVERT: C 233 GLN cc_start: 0.7599 (tp40) cc_final: 0.7397 (tp40) REVERT: C 257 LEU cc_start: 0.8679 (mt) cc_final: 0.8463 (mt) REVERT: E 322 LYS cc_start: 0.8028 (mtmm) cc_final: 0.7797 (mttt) REVERT: E 356 TYR cc_start: 0.7552 (t80) cc_final: 0.7247 (t80) REVERT: F 41 GLU cc_start: 0.8581 (tt0) cc_final: 0.8286 (tt0) REVERT: G 369 HIS cc_start: 0.7484 (t-90) cc_final: 0.6829 (t-90) REVERT: H 138 CYS cc_start: 0.8061 (m) cc_final: 0.7697 (t) REVERT: I 15 GLN cc_start: 0.8146 (pm20) cc_final: 0.7847 (pm20) REVERT: K 361 LEU cc_start: 0.8433 (tt) cc_final: 0.7918 (tt) REVERT: K 369 HIS cc_start: 0.7533 (t-90) cc_final: 0.6853 (t-90) REVERT: L 138 CYS cc_start: 0.8061 (m) cc_final: 0.7657 (t) REVERT: L 335 ILE cc_start: 0.9072 (tp) cc_final: 0.8814 (tt) REVERT: D 49 GLU cc_start: 0.6536 (tm-30) cc_final: 0.5809 (tm-30) REVERT: D 69 MET cc_start: 0.8594 (ppp) cc_final: 0.7885 (ptt) REVERT: D 96 MET cc_start: 0.7856 (mmm) cc_final: 0.7646 (mmt) REVERT: D 233 GLN cc_start: 0.7676 (tp40) cc_final: 0.7452 (tp40) REVERT: D 257 LEU cc_start: 0.8537 (mt) cc_final: 0.8233 (mt) outliers start: 2 outliers final: 0 residues processed: 512 average time/residue: 0.2951 time to fit residues: 233.2296 Evaluate side-chains 418 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 418 time to evaluate : 2.307 ------------------------------------------------------------------------------- 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: 0.9990 chunk 9 optimal weight: 7.9990 chunk 126 optimal weight: 0.8980 chunk 3 optimal weight: 7.9990 chunk 39 optimal weight: 0.6980 chunk 82 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 151 optimal weight: 0.6980 chunk 165 optimal weight: 0.5980 chunk 189 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 B 87 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.148405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.140009 restraints weight = 28718.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.138237 restraints weight = 56831.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.137008 restraints weight = 73241.709| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3523 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3523 r_free = 0.3523 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3523 r_free = 0.3523 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3523 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.2181 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= 0.125 Angle : 0.556 6.791 28128 Z= 0.271 Chirality : 0.040 0.145 3204 Planarity : 0.004 0.048 3518 Dihedral : 5.525 126.738 2794 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.09 % Allowed : 3.28 % Favored : 96.62 % 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: 1.48 (0.17), residues: 2432 helix: 1.98 (0.14), residues: 1436 sheet: 0.93 (0.34), residues: 264 loop : -1.06 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 10 HIS 0.005 0.001 HIS C 53 PHE 0.016 0.001 PHE B 136 TYR 0.017 0.001 TYR B 190 ARG 0.005 0.000 ARG L 47 Details of bonding type rmsd hydrogen bonds : bond 0.03743 ( 1232) hydrogen bonds : angle 4.19016 ( 3579) SS BOND : bond 0.00237 ( 6) SS BOND : angle 1.23355 ( 12) covalent geometry : bond 0.00279 (20708) covalent geometry : angle 0.55548 (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 509 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 507 time to evaluate : 2.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 69 MET cc_start: 0.8487 (ppp) cc_final: 0.7924 (ptt) REVERT: E 322 LYS cc_start: 0.8071 (mtmm) cc_final: 0.7821 (mttt) REVERT: E 356 TYR cc_start: 0.7373 (t80) cc_final: 0.7159 (t80) REVERT: G 369 HIS cc_start: 0.7491 (t-90) cc_final: 0.6519 (t-90) REVERT: H 138 CYS cc_start: 0.7943 (m) cc_final: 0.7671 (t) REVERT: I 322 LYS cc_start: 0.8112 (mtmm) cc_final: 0.7904 (mttt) REVERT: K 361 LEU cc_start: 0.8279 (tt) cc_final: 0.7718 (tt) REVERT: K 369 HIS cc_start: 0.7530 (t-90) cc_final: 0.6852 (t-90) REVERT: L 138 CYS cc_start: 0.8000 (m) cc_final: 0.7689 (t) REVERT: L 335 ILE cc_start: 0.9068 (tp) cc_final: 0.8854 (tt) REVERT: D 49 GLU cc_start: 0.6324 (tm-30) cc_final: 0.5124 (tm-30) REVERT: D 69 MET cc_start: 0.8567 (ppp) cc_final: 0.7953 (ptt) REVERT: D 96 MET cc_start: 0.7888 (mmm) cc_final: 0.7639 (mmt) REVERT: D 257 LEU cc_start: 0.8421 (mt) cc_final: 0.8196 (mt) REVERT: B 86 GLU cc_start: 0.7131 (pm20) cc_final: 0.6467 (pm20) outliers start: 2 outliers final: 1 residues processed: 508 average time/residue: 0.2950 time to fit residues: 232.2537 Evaluate side-chains 400 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 399 time to evaluate : 2.353 ------------------------------------------------------------------------------- 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: 0.0070 chunk 219 optimal weight: 0.9990 chunk 216 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 204 optimal weight: 7.9990 chunk 139 optimal weight: 0.0370 chunk 162 optimal weight: 0.6980 overall best weight: 0.5480 ------------------------------------------------------------------------------- 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 53 HIS D 221 HIS D 238 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.149805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.142611 restraints weight = 28618.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.141158 restraints weight = 50700.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.139884 restraints weight = 68603.431| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3553 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3553 r_free = 0.3553 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3553 r_free = 0.3553 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3553 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20714 Z= 0.114 Angle : 0.557 7.126 28128 Z= 0.269 Chirality : 0.040 0.153 3204 Planarity : 0.004 0.046 3518 Dihedral : 5.369 124.690 2794 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.05 % Allowed : 1.92 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.55 (0.18), residues: 2432 helix: 2.01 (0.14), residues: 1436 sheet: 0.98 (0.34), residues: 264 loop : -0.97 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 10 HIS 0.007 0.001 HIS D 53 PHE 0.012 0.001 PHE B 136 TYR 0.016 0.001 TYR K 343 ARG 0.006 0.000 ARG L 47 Details of bonding type rmsd hydrogen bonds : bond 0.03586 ( 1232) hydrogen bonds : angle 4.14876 ( 3579) SS BOND : bond 0.00209 ( 6) SS BOND : angle 1.02234 ( 12) covalent geometry : bond 0.00250 (20708) covalent geometry : angle 0.55637 (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 497 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 496 time to evaluate : 2.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 GLU cc_start: 0.7522 (pm20) cc_final: 0.6864 (pm20) REVERT: C 69 MET cc_start: 0.8531 (ppp) cc_final: 0.7909 (ptt) REVERT: E 28 VAL cc_start: 0.8777 (m) cc_final: 0.8573 (t) REVERT: E 356 TYR cc_start: 0.7324 (t80) cc_final: 0.7068 (t80) REVERT: G 369 HIS cc_start: 0.7510 (t-90) cc_final: 0.6348 (t-90) REVERT: H 138 CYS cc_start: 0.7858 (m) cc_final: 0.7653 (t) REVERT: J 134 MET cc_start: 0.8515 (tpp) cc_final: 0.8249 (tpp) REVERT: J 349 LEU cc_start: 0.8451 (tt) cc_final: 0.8236 (tt) REVERT: K 361 LEU cc_start: 0.8123 (tt) cc_final: 0.7703 (tt) REVERT: K 369 HIS cc_start: 0.7585 (t-90) cc_final: 0.6781 (t-90) REVERT: L 138 CYS cc_start: 0.7904 (m) cc_final: 0.7595 (t) REVERT: L 335 ILE cc_start: 0.9044 (tp) cc_final: 0.8831 (tt) REVERT: D 69 MET cc_start: 0.8613 (ppp) cc_final: 0.7872 (ptt) REVERT: D 96 MET cc_start: 0.7870 (mmm) cc_final: 0.7664 (mmt) outliers start: 1 outliers final: 1 residues processed: 497 average time/residue: 0.3111 time to fit residues: 239.1620 Evaluate side-chains 407 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 406 time to evaluate : 2.348 ------------------------------------------------------------------------------- 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: 4.9990 chunk 23 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 121 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 173 HIS D 53 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.146788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.138237 restraints weight = 29132.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.136691 restraints weight = 63591.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.135562 restraints weight = 78550.545| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3498 |-occupancy refinement: start-------------------------------------------------| | 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: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3497 r_free = 0.3497 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3497 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20714 Z= 0.184 Angle : 0.608 9.860 28128 Z= 0.298 Chirality : 0.042 0.153 3204 Planarity : 0.004 0.045 3518 Dihedral : 5.367 124.791 2794 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % 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: 1.44 (0.17), residues: 2432 helix: 1.93 (0.14), residues: 1438 sheet: 0.91 (0.34), residues: 260 loop : -1.03 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 10 HIS 0.010 0.001 HIS C 65 PHE 0.014 0.001 PHE F 30 TYR 0.017 0.002 TYR K 343 ARG 0.009 0.000 ARG F 174 Details of bonding type rmsd hydrogen bonds : bond 0.03996 ( 1232) hydrogen bonds : angle 4.25236 ( 3579) SS BOND : bond 0.00569 ( 6) SS BOND : angle 1.18103 ( 12) covalent geometry : bond 0.00430 (20708) covalent geometry : angle 0.60803 (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 488 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 488 time to evaluate : 2.142 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 GLU cc_start: 0.7242 (pm20) cc_final: 0.6283 (pm20) REVERT: C 69 MET cc_start: 0.8728 (ppp) cc_final: 0.8062 (ptt) REVERT: C 134 ILE cc_start: 0.8565 (tp) cc_final: 0.8192 (tp) REVERT: C 150 ARG cc_start: 0.6767 (mtm180) cc_final: 0.6120 (mpp80) REVERT: G 77 CYS cc_start: 0.5466 (m) cc_final: 0.5251 (m) REVERT: G 369 HIS cc_start: 0.7498 (t-90) cc_final: 0.6414 (t-90) REVERT: H 79 LEU cc_start: 0.8509 (mt) cc_final: 0.8269 (mt) REVERT: H 138 CYS cc_start: 0.8033 (m) cc_final: 0.7768 (t) REVERT: H 335 ILE cc_start: 0.8976 (tp) cc_final: 0.8718 (tt) REVERT: J 134 MET cc_start: 0.8603 (tpp) cc_final: 0.8140 (tpp) REVERT: K 320 LYS cc_start: 0.6792 (mmpt) cc_final: 0.6374 (mmtt) REVERT: K 361 LEU cc_start: 0.8223 (tt) cc_final: 0.7852 (tt) REVERT: L 138 CYS cc_start: 0.8020 (m) cc_final: 0.7745 (t) REVERT: L 335 ILE cc_start: 0.9070 (tp) cc_final: 0.8857 (tt) REVERT: D 31 GLU cc_start: 0.7613 (tp30) cc_final: 0.7358 (tp30) REVERT: D 69 MET cc_start: 0.8726 (ppp) cc_final: 0.8003 (ptt) REVERT: D 96 MET cc_start: 0.8209 (mmm) cc_final: 0.7967 (mmt) REVERT: D 134 ILE cc_start: 0.8631 (tp) cc_final: 0.8222 (tp) REVERT: D 150 ARG cc_start: 0.6721 (mtm180) cc_final: 0.6117 (mpp80) outliers start: 0 outliers final: 0 residues processed: 488 average time/residue: 0.2964 time to fit residues: 223.3176 Evaluate side-chains 383 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 383 time to evaluate : 2.452 ------------------------------------------------------------------------------- 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: 6.9990 chunk 21 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 172 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 chunk 178 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 127 optimal weight: 2.9990 chunk 139 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN C 53 HIS C 204 HIS C 238 GLN K 169 ASN D 221 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.141628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.132885 restraints weight = 29505.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.131996 restraints weight = 69773.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.118653 restraints weight = 71178.279| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3153 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 20714 Z= 0.346 Angle : 0.784 19.988 28128 Z= 0.390 Chirality : 0.048 0.311 3204 Planarity : 0.005 0.054 3518 Dihedral : 5.709 126.552 2794 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.05 % Allowed : 1.96 % Favored : 97.99 % 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: 0.84 (0.17), residues: 2432 helix: 1.50 (0.14), residues: 1422 sheet: 0.48 (0.35), residues: 260 loop : -1.23 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 114 HIS 0.010 0.002 HIS D 53 PHE 0.017 0.002 PHE F 30 TYR 0.027 0.002 TYR F 343 ARG 0.005 0.001 ARG E 129 Details of bonding type rmsd hydrogen bonds : bond 0.05086 ( 1232) hydrogen bonds : angle 4.73579 ( 3579) SS BOND : bond 0.00335 ( 6) SS BOND : angle 1.49448 ( 12) covalent geometry : bond 0.00809 (20708) covalent geometry : angle 0.78319 (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 453 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 452 time to evaluate : 2.477 Fit side-chains REVERT: A 86 GLU cc_start: 0.8266 (pm20) cc_final: 0.7979 (pm20) REVERT: A 105 LYS cc_start: 0.8525 (mttt) cc_final: 0.8305 (mttt) REVERT: C 49 GLU cc_start: 0.6634 (tm-30) cc_final: 0.5706 (tm-30) REVERT: C 53 HIS cc_start: 0.6225 (m90) cc_final: 0.5772 (m90) REVERT: E 107 ARG cc_start: 0.6604 (mpp-170) cc_final: 0.6321 (mtm-85) REVERT: G 369 HIS cc_start: 0.7843 (t-90) cc_final: 0.7492 (t-90) REVERT: I 107 ARG cc_start: 0.6583 (mpp-170) cc_final: 0.6328 (mtm-85) REVERT: J 19 VAL cc_start: 0.9013 (t) cc_final: 0.8762 (t) REVERT: K 356 TYR cc_start: 0.8800 (t80) cc_final: 0.8561 (t80) REVERT: K 361 LEU cc_start: 0.8636 (tt) cc_final: 0.8048 (tt) REVERT: L 138 CYS cc_start: 0.8480 (m) cc_final: 0.8219 (t) REVERT: L 335 ILE cc_start: 0.9101 (tp) cc_final: 0.8864 (tt) REVERT: D 49 GLU cc_start: 0.6936 (tm-30) cc_final: 0.6504 (tm-30) REVERT: D 257 LEU cc_start: 0.8470 (mt) cc_final: 0.8193 (mt) REVERT: B 105 LYS cc_start: 0.8512 (mttt) cc_final: 0.8306 (mttt) outliers start: 1 outliers final: 0 residues processed: 453 average time/residue: 0.3262 time to fit residues: 222.7664 Evaluate side-chains 379 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 379 time to evaluate : 2.251 ------------------------------------------------------------------------------- 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: 9.9990 chunk 175 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 161 optimal weight: 0.7980 chunk 13 optimal weight: 10.0000 chunk 230 optimal weight: 7.9990 chunk 173 optimal weight: 0.4980 chunk 107 optimal weight: 0.8980 chunk 151 optimal weight: 0.9980 chunk 163 optimal weight: 0.6980 chunk 83 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 K 169 ASN D 204 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.146788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.140382 restraints weight = 28883.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.139592 restraints weight = 63313.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.126398 restraints weight = 68455.135| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3299 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3299 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20714 Z= 0.136 Angle : 0.615 8.136 28128 Z= 0.299 Chirality : 0.042 0.182 3204 Planarity : 0.004 0.044 3518 Dihedral : 5.297 122.699 2794 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.05 % Allowed : 0.55 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.16 (0.17), residues: 2432 helix: 1.74 (0.14), residues: 1436 sheet: 0.51 (0.33), residues: 276 loop : -1.10 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 10 HIS 0.010 0.001 HIS D 65 PHE 0.014 0.001 PHE B 136 TYR 0.017 0.001 TYR G 343 ARG 0.013 0.000 ARG F 174 Details of bonding type rmsd hydrogen bonds : bond 0.03955 ( 1232) hydrogen bonds : angle 4.32681 ( 3579) SS BOND : bond 0.00288 ( 6) SS BOND : angle 1.11470 ( 12) covalent geometry : bond 0.00306 (20708) covalent geometry : angle 0.61510 (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 469 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 468 time to evaluate : 2.199 Fit side-chains REVERT: A 86 GLU cc_start: 0.8112 (pm20) cc_final: 0.7245 (pm20) REVERT: A 105 LYS cc_start: 0.8281 (mttt) cc_final: 0.8079 (mttt) REVERT: A 147 TYR cc_start: 0.7108 (m-10) cc_final: 0.6883 (m-10) REVERT: C 49 GLU cc_start: 0.6375 (tm-30) cc_final: 0.5466 (tm-30) REVERT: C 134 ILE cc_start: 0.8605 (tp) cc_final: 0.8187 (tp) REVERT: C 150 ARG cc_start: 0.6664 (mtm180) cc_final: 0.6136 (mpp80) REVERT: G 369 HIS cc_start: 0.7479 (t-90) cc_final: 0.7237 (t-90) REVERT: J 19 VAL cc_start: 0.8868 (t) cc_final: 0.8611 (t) REVERT: K 41 GLU cc_start: 0.9015 (tt0) cc_final: 0.8750 (tt0) REVERT: K 361 LEU cc_start: 0.8386 (tt) cc_final: 0.7902 (tt) REVERT: L 335 ILE cc_start: 0.9125 (tp) cc_final: 0.8881 (tt) REVERT: D 49 GLU cc_start: 0.6511 (tm-30) cc_final: 0.6090 (tm-30) REVERT: D 150 ARG cc_start: 0.6636 (mtm180) cc_final: 0.6188 (mpp80) outliers start: 1 outliers final: 0 residues processed: 468 average time/residue: 0.2964 time to fit residues: 212.9600 Evaluate side-chains 370 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 370 time to evaluate : 2.469 ------------------------------------------------------------------------------- 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: 6.9990 chunk 116 optimal weight: 0.0670 chunk 5 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 209 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 187 optimal weight: 0.0570 chunk 79 optimal weight: 0.8980 chunk 165 optimal weight: 0.7980 chunk 120 optimal weight: 10.0000 overall best weight: 0.7638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** C 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 HIS C 221 HIS J 173 HIS D 221 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.146468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.139087 restraints weight = 28649.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.123530 restraints weight = 71863.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.119115 restraints weight = 71229.827| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 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 = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2690 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= 0.134 Angle : 0.610 7.820 28128 Z= 0.296 Chirality : 0.041 0.183 3204 Planarity : 0.004 0.044 3518 Dihedral : 5.179 122.764 2794 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.05 % Allowed : 0.55 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.31 (0.18), residues: 2432 helix: 1.84 (0.14), residues: 1434 sheet: 0.86 (0.34), residues: 262 loop : -1.10 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 10 HIS 0.010 0.001 HIS C 53 PHE 0.012 0.001 PHE A 136 TYR 0.017 0.001 TYR K 343 ARG 0.011 0.000 ARG K 166 Details of bonding type rmsd hydrogen bonds : bond 0.03831 ( 1232) hydrogen bonds : angle 4.25510 ( 3579) SS BOND : bond 0.00217 ( 6) SS BOND : angle 1.06621 ( 12) covalent geometry : bond 0.00305 (20708) covalent geometry : angle 0.60940 (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 464 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 463 time to evaluate : 2.358 Fit side-chains revert: symmetry clash REVERT: A 114 GLU cc_start: 0.5700 (mm-30) cc_final: 0.5454 (mm-30) REVERT: C 49 GLU cc_start: 0.7272 (tm-30) cc_final: 0.6086 (tm-30) REVERT: C 134 ILE cc_start: 0.8691 (tp) cc_final: 0.8254 (tp) REVERT: C 150 ARG cc_start: 0.6585 (mtm180) cc_final: 0.5989 (mpp80) REVERT: F 174 ARG cc_start: 0.8283 (ttp80) cc_final: 0.8009 (tmm160) REVERT: G 369 HIS cc_start: 0.7535 (t-90) cc_final: 0.7138 (t-90) REVERT: J 19 VAL cc_start: 0.8879 (t) cc_final: 0.8604 (t) REVERT: K 361 LEU cc_start: 0.8428 (tt) cc_final: 0.7926 (tt) REVERT: L 335 ILE cc_start: 0.9129 (tp) cc_final: 0.8910 (tt) REVERT: D 49 GLU cc_start: 0.6835 (tm-30) cc_final: 0.6216 (tm-30) REVERT: D 150 ARG cc_start: 0.6547 (mtm180) cc_final: 0.6005 (mpp80) REVERT: B 89 LYS cc_start: 0.8675 (mptt) cc_final: 0.8460 (mmtm) REVERT: B 147 TYR cc_start: 0.7030 (m-10) cc_final: 0.6700 (m-10) outliers start: 1 outliers final: 0 residues processed: 464 average time/residue: 0.2998 time to fit residues: 214.4412 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 : 2.396 ------------------------------------------------------------------------------- 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: 3.9990 chunk 199 optimal weight: 6.9990 chunk 202 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 chunk 6 optimal weight: 10.0000 chunk 127 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 19 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 241 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 204 HIS D 204 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.143154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.135886 restraints weight = 29104.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.118728 restraints weight = 75891.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.115540 restraints weight = 74298.674| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3112 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3112 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 20714 Z= 0.232 Angle : 0.701 8.230 28128 Z= 0.345 Chirality : 0.044 0.204 3204 Planarity : 0.004 0.044 3518 Dihedral : 5.400 123.665 2794 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: 1.05 (0.18), residues: 2432 helix: 1.67 (0.14), residues: 1440 sheet: 0.61 (0.34), residues: 262 loop : -1.24 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 10 HIS 0.013 0.001 HIS C 65 PHE 0.014 0.001 PHE B 136 TYR 0.018 0.002 TYR K 343 ARG 0.012 0.001 ARG G 166 Details of bonding type rmsd hydrogen bonds : bond 0.04404 ( 1232) hydrogen bonds : angle 4.47034 ( 3579) SS BOND : bond 0.00261 ( 6) SS BOND : angle 1.29520 ( 12) covalent geometry : bond 0.00548 (20708) covalent geometry : angle 0.70107 (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 452 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 452 time to evaluate : 2.548 Fit side-chains REVERT: A 114 GLU cc_start: 0.5793 (mm-30) cc_final: 0.5582 (mm-30) REVERT: C 49 GLU cc_start: 0.6750 (tm-30) cc_final: 0.5614 (tm-30) REVERT: F 343 TYR cc_start: 0.8717 (t80) cc_final: 0.8450 (t80) REVERT: G 369 HIS cc_start: 0.7544 (t-90) cc_final: 0.7111 (t-90) REVERT: H 80 GLN cc_start: 0.7978 (tm-30) cc_final: 0.7713 (tm-30) REVERT: H 138 CYS cc_start: 0.8456 (m) cc_final: 0.8231 (t) REVERT: J 15 GLN cc_start: 0.8564 (pt0) cc_final: 0.8313 (pt0) REVERT: J 343 TYR cc_start: 0.8662 (t80) cc_final: 0.8397 (t80) REVERT: K 361 LEU cc_start: 0.8594 (tt) cc_final: 0.8131 (tt) REVERT: L 335 ILE cc_start: 0.9131 (tp) cc_final: 0.8894 (tt) REVERT: D 49 GLU cc_start: 0.7078 (tm-30) cc_final: 0.6393 (tm-30) REVERT: B 86 GLU cc_start: 0.7967 (pm20) cc_final: 0.7418 (pm20) outliers start: 0 outliers final: 0 residues processed: 452 average time/residue: 0.2988 time to fit residues: 208.0582 Evaluate side-chains 364 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 364 time to evaluate : 2.237 ------------------------------------------------------------------------------- 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: 9.9990 chunk 135 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 225 optimal weight: 9.9990 chunk 118 optimal weight: 2.9990 chunk 241 optimal weight: 0.0060 chunk 26 optimal weight: 10.0000 chunk 114 optimal weight: 0.5980 chunk 239 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 overall best weight: 1.9202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 204 HIS C 221 HIS D 204 HIS D 221 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.143372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.135621 restraints weight = 29255.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.134887 restraints weight = 71844.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.122172 restraints weight = 69962.172| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3234 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3234 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 20714 Z= 0.227 Angle : 0.716 21.997 28128 Z= 0.348 Chirality : 0.044 0.246 3204 Planarity : 0.004 0.044 3518 Dihedral : 5.444 123.059 2794 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % 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: 0.97 (0.18), residues: 2432 helix: 1.61 (0.14), residues: 1430 sheet: 0.43 (0.34), residues: 262 loop : -1.19 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 10 HIS 0.009 0.001 HIS D 65 PHE 0.015 0.001 PHE B 136 TYR 0.018 0.002 TYR F 343 ARG 0.011 0.000 ARG G 166 Details of bonding type rmsd hydrogen bonds : bond 0.04398 ( 1232) hydrogen bonds : angle 4.49037 ( 3579) SS BOND : bond 0.00316 ( 6) SS BOND : angle 1.31662 ( 12) covalent geometry : bond 0.00534 (20708) covalent geometry : angle 0.71518 (28116) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6232.95 seconds wall clock time: 110 minutes 10.11 seconds (6610.11 seconds total)