Starting phenix.real_space_refine on Sat Jun 14 14:59:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9es7_19938/06_2025/9es7_19938.cif Found real_map, /net/cci-nas-00/data/ceres_data/9es7_19938/06_2025/9es7_19938.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9es7_19938/06_2025/9es7_19938.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9es7_19938/06_2025/9es7_19938.map" model { file = "/net/cci-nas-00/data/ceres_data/9es7_19938/06_2025/9es7_19938.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9es7_19938/06_2025/9es7_19938.cif" } resolution = 1.94 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= 0.000 sd= 0.005 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: 6 Type Number sf(0) Gaussians Fe 12 7.16 5 Mg 2 5.21 5 S 72 5.16 5 C 10676 2.51 5 N 2506 2.21 5 O 3145 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16413 Number of models: 1 Model: "" Number of chains: 46 Chain: "A" Number of atoms: 1697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1697 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 203} Chain: "B" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1226 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 141} Chain: "C" Number of atoms: 2168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2168 Classifications: {'peptide': 279} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 255} Chain breaks: 1 Chain: "D" Number of atoms: 1260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1260 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 152} Chain breaks: 1 Chain: "E" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 244 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Chain: "F" Number of atoms: 277 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 37, 269 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Conformer: "B" Number of residues, atoms: 37, 269 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} bond proxies already assigned to first conformer: 260 Chain: "G" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 270 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "H" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 223 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "I" Number of atoms: 1697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1697 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 203} Chain: "J" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1226 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 141} Chain: "K" Number of atoms: 2168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2168 Classifications: {'peptide': 279} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 255} Chain breaks: 1 Chain: "L" Number of atoms: 1260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1260 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 152} Chain breaks: 1 Chain: "M" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 244 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Chain: "N" Number of atoms: 277 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 37, 269 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Conformer: "B" Number of residues, atoms: 37, 269 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} bond proxies already assigned to first conformer: 260 Chain: "O" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 270 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "P" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 223 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "Q" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 219 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 1, 'TRANS': 24} Chain: "R" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 219 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 1, 'TRANS': 24} Chain: "A" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 218 Unusual residues: {'HEC': 1, 'HEM': 2, 'LMG': 1, 'UMQ': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 65 Unusual residues: {'CLA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'FES': 1, 'SQD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'UMQ': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 218 Unusual residues: {'HEC': 1, 'HEM': 2, 'LMG': 1, 'UMQ': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "J" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 65 Unusual residues: {'CLA': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'FES': 1, 'SQD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'UMQ': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "C" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Classifications: {'water': 57} Link IDs: {None: 56} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Chain: "J" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "K" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Classifications: {'water': 57} Link IDs: {None: 56} Chain: "L" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "O" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "P" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5795 SG CYS D 107 45.641 79.400 43.001 1.00 53.58 S ATOM 5931 SG CYS D 125 43.335 76.459 42.143 1.00 54.32 S ATOM 13160 SG CYS L 107 88.518 28.958 43.002 1.00 53.58 S ATOM 13296 SG CYS L 125 90.823 31.899 42.144 1.00 54.32 S Time building chain proxies: 13.03, per 1000 atoms: 0.79 Number of scatterers: 16413 At special positions: 0 Unit cell: (135.02, 109.22, 121.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 12 26.01 S 72 16.00 Mg 2 11.99 O 3145 8.00 N 2506 7.00 C 10676 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS D 112 " - pdb=" SG CYS D 127 " distance=2.04 Simple disulfide: pdb=" SG CYS L 112 " - pdb=" SG CYS L 127 " distance=2.04 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=14, symmetry=0 Number of additional bonds: simple=14, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.42 Conformation dependent library (CDL) restraints added in 2.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES D 202 " pdb="FE1 FES D 202 " - pdb=" ND1 HIS D 128 " pdb="FE1 FES D 202 " - pdb=" ND1 HIS D 109 " pdb="FE2 FES D 202 " - pdb=" SG CYS D 107 " pdb="FE2 FES D 202 " - pdb=" SG CYS D 125 " pdb=" FES L 202 " pdb="FE1 FES L 202 " - pdb=" ND1 HIS L 128 " pdb="FE1 FES L 202 " - pdb=" ND1 HIS L 109 " pdb="FE2 FES L 202 " - pdb=" SG CYS L 125 " pdb="FE2 FES L 202 " - pdb=" SG CYS L 107 " Number of angles added : 6 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3572 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 14 sheets defined 53.4% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 2 through 13 removed outlier: 4.016A pdb=" N ARG A 11 " --> pdb=" O TRP A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 22 Processing helix chain 'A' and resid 31 through 34 Processing helix chain 'A' and resid 35 through 55 Processing helix chain 'A' and resid 64 through 75 Processing helix chain 'A' and resid 78 through 107 removed outlier: 3.700A pdb=" N SER A 91 " --> pdb=" O ARG A 87 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 136 removed outlier: 3.514A pdb=" N TRP A 118 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 154 removed outlier: 3.536A pdb=" N VAL A 154 " --> pdb=" O ILE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 158 Processing helix chain 'A' and resid 161 through 171 Processing helix chain 'A' and resid 176 through 189 Processing helix chain 'A' and resid 189 through 210 Processing helix chain 'B' and resid 11 through 20 removed outlier: 3.608A pdb=" N LYS B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 58 Processing helix chain 'B' and resid 78 through 80 No H-bonds generated for 'chain 'B' and resid 78 through 80' Processing helix chain 'B' and resid 81 through 91 removed outlier: 3.560A pdb=" N ILE B 87 " --> pdb=" O PRO B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 110 removed outlier: 3.905A pdb=" N VAL B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) Proline residue: B 105 - end of helix removed outlier: 3.890A pdb=" N THR B 110 " --> pdb=" O ALA B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 115 Processing helix chain 'B' and resid 122 through 125 Processing helix chain 'B' and resid 126 through 147 Processing helix chain 'B' and resid 148 through 149 No H-bonds generated for 'chain 'B' and resid 148 through 149' Processing helix chain 'B' and resid 150 through 154 Processing helix chain 'C' and resid 2 through 9 Processing helix chain 'C' and resid 19 through 24 Processing helix chain 'C' and resid 85 through 89 Processing helix chain 'C' and resid 90 through 98 removed outlier: 3.616A pdb=" N GLY C 98 " --> pdb=" O LYS C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 283 removed outlier: 3.791A pdb=" N LYS C 277 " --> pdb=" O LYS C 273 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL C 278 " --> pdb=" O GLN C 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 40 removed outlier: 3.898A pdb=" N LEU D 28 " --> pdb=" O GLY D 24 " (cutoff:3.500A) Proline residue: D 29 - end of helix Proline residue: D 36 - end of helix Processing helix chain 'D' and resid 64 through 72 removed outlier: 3.526A pdb=" N LEU D 69 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYS D 70 " --> pdb=" O ALA D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'E' and resid 2 through 28 Processing helix chain 'F' and resid 2 through 37 Processing helix chain 'G' and resid 3 through 33 removed outlier: 3.513A pdb=" N ILE G 14 " --> pdb=" O VAL G 10 " (cutoff:3.500A) Proline residue: G 15 - end of helix Processing helix chain 'H' and resid 2 through 27 removed outlier: 3.716A pdb=" N LEU H 19 " --> pdb=" O PHE H 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 13 removed outlier: 4.016A pdb=" N ARG I 11 " --> pdb=" O TRP I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 22 Processing helix chain 'I' and resid 31 through 34 Processing helix chain 'I' and resid 35 through 55 Processing helix chain 'I' and resid 64 through 75 Processing helix chain 'I' and resid 78 through 107 removed outlier: 3.700A pdb=" N SER I 91 " --> pdb=" O ARG I 87 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL I 94 " --> pdb=" O ALA I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 136 removed outlier: 3.514A pdb=" N TRP I 118 " --> pdb=" O ARG I 114 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY I 132 " --> pdb=" O THR I 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 154 removed outlier: 3.535A pdb=" N VAL I 154 " --> pdb=" O ILE I 150 " (cutoff:3.500A) Processing helix chain 'I' and resid 155 through 158 Processing helix chain 'I' and resid 161 through 171 Processing helix chain 'I' and resid 176 through 189 Processing helix chain 'I' and resid 189 through 210 Processing helix chain 'J' and resid 11 through 20 removed outlier: 3.608A pdb=" N LYS J 20 " --> pdb=" O ALA J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 39 through 58 Processing helix chain 'J' and resid 78 through 80 No H-bonds generated for 'chain 'J' and resid 78 through 80' Processing helix chain 'J' and resid 81 through 91 removed outlier: 3.560A pdb=" N ILE J 87 " --> pdb=" O PRO J 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 110 removed outlier: 3.905A pdb=" N VAL J 104 " --> pdb=" O LEU J 100 " (cutoff:3.500A) Proline residue: J 105 - end of helix removed outlier: 3.890A pdb=" N THR J 110 " --> pdb=" O ALA J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 110 through 115 Processing helix chain 'J' and resid 122 through 125 Processing helix chain 'J' and resid 126 through 147 Processing helix chain 'J' and resid 148 through 149 No H-bonds generated for 'chain 'J' and resid 148 through 149' Processing helix chain 'J' and resid 150 through 154 Processing helix chain 'K' and resid 2 through 9 Processing helix chain 'K' and resid 19 through 24 Processing helix chain 'K' and resid 85 through 89 Processing helix chain 'K' and resid 90 through 98 removed outlier: 3.616A pdb=" N GLY K 98 " --> pdb=" O LYS K 94 " (cutoff:3.500A) Processing helix chain 'K' and resid 247 through 283 removed outlier: 3.792A pdb=" N LYS K 277 " --> pdb=" O LYS K 273 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL K 278 " --> pdb=" O GLN K 274 " (cutoff:3.500A) Processing helix chain 'L' and resid 11 through 40 removed outlier: 3.898A pdb=" N LEU L 28 " --> pdb=" O GLY L 24 " (cutoff:3.500A) Proline residue: L 29 - end of helix Proline residue: L 36 - end of helix Processing helix chain 'L' and resid 64 through 72 removed outlier: 3.526A pdb=" N LEU L 69 " --> pdb=" O ALA L 65 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYS L 70 " --> pdb=" O ALA L 66 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 85 No H-bonds generated for 'chain 'L' and resid 83 through 85' Processing helix chain 'M' and resid 2 through 28 Processing helix chain 'N' and resid 2 through 37 Processing helix chain 'O' and resid 3 through 33 removed outlier: 3.518A pdb=" N ILE O 14 " --> pdb=" O VAL O 10 " (cutoff:3.500A) Proline residue: O 15 - end of helix Processing helix chain 'P' and resid 2 through 27 removed outlier: 3.716A pdb=" N LEU P 19 " --> pdb=" O PHE P 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 33 through 43 Processing helix chain 'Q' and resid 52 through 57 Processing helix chain 'R' and resid 33 through 43 Processing helix chain 'R' and resid 52 through 57 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA2, first strand: chain 'C' and resid 32 through 34 removed outlier: 3.668A pdb=" N GLU C 82 " --> pdb=" O LEU C 131 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 38 through 39 removed outlier: 6.200A pdb=" N VAL C 71 " --> pdb=" O PRO C 117 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 59 through 60 Processing sheet with id=AA5, first strand: chain 'C' and resid 178 through 184 removed outlier: 6.927A pdb=" N ASN C 193 " --> pdb=" O LYS C 180 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE C 182 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLU C 191 " --> pdb=" O ILE C 182 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 53 through 54 removed outlier: 7.062A pdb=" N PHE D 101 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N VAL D 91 " --> pdb=" O PHE D 101 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE D 103 " --> pdb=" O TYR D 89 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR D 78 " --> pdb=" O LEU D 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 116 through 117 removed outlier: 6.634A pdb=" N GLN D 131 " --> pdb=" O VAL D 139 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 25 through 26 Processing sheet with id=AA9, first strand: chain 'K' and resid 32 through 34 removed outlier: 3.668A pdb=" N GLU K 82 " --> pdb=" O LEU K 131 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 38 through 39 removed outlier: 6.200A pdb=" N VAL K 71 " --> pdb=" O PRO K 117 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 59 through 60 Processing sheet with id=AB3, first strand: chain 'K' and resid 178 through 184 removed outlier: 6.927A pdb=" N ASN K 193 " --> pdb=" O LYS K 180 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE K 182 " --> pdb=" O GLU K 191 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLU K 191 " --> pdb=" O ILE K 182 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 53 through 54 removed outlier: 7.063A pdb=" N PHE L 101 " --> pdb=" O VAL L 91 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N VAL L 91 " --> pdb=" O PHE L 101 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE L 103 " --> pdb=" O TYR L 89 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR L 78 " --> pdb=" O LEU L 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 116 through 117 removed outlier: 6.634A pdb=" N GLN L 131 " --> pdb=" O VAL L 139 " (cutoff:3.500A) 845 hydrogen bonds defined for protein. 2407 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: 4.87 Time building geometry restraints manager: 5.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.39: 6298 1.39 - 1.59: 10080 1.59 - 1.80: 46 1.80 - 2.00: 68 2.00 - 2.20: 48 Bond restraints: 16540 Sorted by residual: bond pdb=" CA ASP H 2 " pdb=" CB ASP H 2 " ideal model delta sigma weight residual 1.526 1.483 0.043 1.26e-02 6.30e+03 1.19e+01 bond pdb=" CA ASP P 2 " pdb=" CB ASP P 2 " ideal model delta sigma weight residual 1.526 1.483 0.043 1.26e-02 6.30e+03 1.14e+01 bond pdb=" N GLY J 2 " pdb=" CA GLY J 2 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.10e+00 bond pdb=" N GLY B 2 " pdb=" CA GLY B 2 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.10e+00 bond pdb=" CB ASP P 2 " pdb=" CG ASP P 2 " ideal model delta sigma weight residual 1.516 1.468 0.048 2.50e-02 1.60e+03 3.65e+00 ... (remaining 16535 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 22447 2.59 - 5.18: 167 5.18 - 7.77: 6 7.77 - 10.36: 2 10.36 - 12.95: 2 Bond angle restraints: 22624 Sorted by residual: angle pdb=" C3C HEC I 303 " pdb=" CAC HEC I 303 " pdb=" CBC HEC I 303 " ideal model delta sigma weight residual 109.00 121.95 -12.95 3.00e+00 1.11e-01 1.86e+01 angle pdb=" C3C HEC A 303 " pdb=" CAC HEC A 303 " pdb=" CBC HEC A 303 " ideal model delta sigma weight residual 109.00 121.92 -12.92 3.00e+00 1.11e-01 1.85e+01 angle pdb=" N ASP P 2 " pdb=" CA ASP P 2 " pdb=" CB ASP P 2 " ideal model delta sigma weight residual 109.94 103.12 6.82 1.60e+00 3.91e-01 1.82e+01 angle pdb=" N ASP H 2 " pdb=" CA ASP H 2 " pdb=" CB ASP H 2 " ideal model delta sigma weight residual 109.94 103.13 6.81 1.60e+00 3.91e-01 1.81e+01 angle pdb=" CA VAL D 139 " pdb=" C VAL D 139 " pdb=" N ARG D 140 " ideal model delta sigma weight residual 116.60 120.12 -3.52 1.45e+00 4.76e-01 5.89e+00 ... (remaining 22619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.33: 9444 25.33 - 50.65: 236 50.65 - 75.98: 42 75.98 - 101.30: 14 101.30 - 126.63: 8 Dihedral angle restraints: 9744 sinusoidal: 4176 harmonic: 5568 Sorted by residual: dihedral pdb=" C2B HEC I 303 " pdb=" C3B HEC I 303 " pdb=" CAB HEC I 303 " pdb=" CBB HEC I 303 " ideal model delta sinusoidal sigma weight residual -120.00 -71.08 -48.92 2 1.00e+01 1.00e-02 2.73e+01 dihedral pdb=" C2B HEC A 303 " pdb=" C3B HEC A 303 " pdb=" CAB HEC A 303 " pdb=" CBB HEC A 303 " ideal model delta sinusoidal sigma weight residual -120.00 -71.13 -48.87 2 1.00e+01 1.00e-02 2.72e+01 dihedral pdb=" C2C HEC I 303 " pdb=" C3C HEC I 303 " pdb=" CAC HEC I 303 " pdb=" CBC HEC I 303 " ideal model delta sinusoidal sigma weight residual -120.00 -161.26 41.26 2 1.00e+01 1.00e-02 2.09e+01 ... (remaining 9741 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1477 0.026 - 0.052: 589 0.052 - 0.078: 258 0.078 - 0.105: 106 0.105 - 0.131: 100 Chirality restraints: 2530 Sorted by residual: chirality pdb=" CA ILE I 158 " pdb=" N ILE I 158 " pdb=" C ILE I 158 " pdb=" CB ILE I 158 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.27e-01 chirality pdb=" CA ILE G 2 " pdb=" N ILE G 2 " pdb=" C ILE G 2 " pdb=" CB ILE G 2 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 chirality pdb=" CA ILE B 75 " pdb=" N ILE B 75 " pdb=" C ILE B 75 " pdb=" CB ILE B 75 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 2527 not shown) Planarity restraints: 2778 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 210 " 0.030 5.00e-02 4.00e+02 4.57e-02 3.35e+00 pdb=" N PRO C 211 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 211 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 211 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY K 210 " -0.030 5.00e-02 4.00e+02 4.57e-02 3.34e+00 pdb=" N PRO K 211 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO K 211 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO K 211 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 223 " 0.007 2.00e-02 2.50e+03 1.38e-02 1.91e+00 pdb=" C LEU C 223 " -0.024 2.00e-02 2.50e+03 pdb=" O LEU C 223 " 0.009 2.00e-02 2.50e+03 pdb=" N ASP C 224 " 0.008 2.00e-02 2.50e+03 ... (remaining 2775 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 72 2.55 - 3.14: 12651 3.14 - 3.73: 23617 3.73 - 4.31: 35228 4.31 - 4.90: 57247 Nonbonded interactions: 128815 Sorted by model distance: nonbonded pdb=" O1A HEC A 303 " pdb=" O HOH A 401 " model vdw 1.967 3.040 nonbonded pdb=" O1A HEC I 303 " pdb=" O HOH I 401 " model vdw 1.968 3.040 nonbonded pdb=" OE2 GLU J 29 " pdb=" O HOH J 301 " model vdw 2.056 3.040 nonbonded pdb=" OE2 GLU B 29 " pdb=" O HOH B 301 " model vdw 2.056 3.040 nonbonded pdb=" O5 LMG A 305 " pdb=" O9 LMG A 305 " model vdw 2.093 3.040 ... (remaining 128810 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: 0.08 Found NCS groups: ncs_group { reference = chain 'H' selection = chain 'P' } ncs_group { reference = chain 'C' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'L' } ncs_group { reference = chain 'B' selection = chain 'J' } ncs_group { reference = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'M' } ncs_group { reference = chain 'F' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'O' } ncs_group { reference = chain 'A' selection = chain 'I' } 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=0.48 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.540 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: 0.700 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 46.550 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9021 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 : 0.010 0.739 16564 Z= 0.269 Angle : 0.535 14.464 22634 Z= 0.236 Chirality : 0.042 0.131 2530 Planarity : 0.004 0.046 2778 Dihedral : 12.591 126.626 6166 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.37 % Allowed : 1.34 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 1.66 (0.19), residues: 1908 helix: 2.16 (0.17), residues: 956 sheet: 0.32 (0.35), residues: 214 loop : 0.00 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 146 HIS 0.005 0.001 HIS A 202 PHE 0.011 0.001 PHE D 40 TYR 0.012 0.001 TYR A 136 ARG 0.003 0.000 ARG I 182 Details of bonding type rmsd hydrogen bonds : bond 0.30072 ( 845) hydrogen bonds : angle 5.91992 ( 2407) metal coordination : bond 0.01407 ( 8) metal coordination : angle 9.07644 ( 6) SS BOND : bond 0.00415 ( 2) SS BOND : angle 1.73049 ( 4) covalent geometry : bond 0.00280 (16540) covalent geometry : angle 0.51412 (22624) Misc. bond : bond 0.33982 ( 14) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 258 time to evaluate : 1.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 LYS cc_start: 0.8452 (mttt) cc_final: 0.8101 (tttt) REVERT: A 9 GLU cc_start: 0.8520 (tp30) cc_final: 0.8270 (tp30) REVERT: B 29 GLU cc_start: 0.8730 (tt0) cc_final: 0.8383 (tt0) REVERT: C 32 ASP cc_start: 0.8531 (t70) cc_final: 0.8289 (t70) REVERT: D 76 ASP cc_start: 0.8784 (t70) cc_final: 0.8583 (t70) REVERT: F 5 GLU cc_start: 0.8845 (tp30) cc_final: 0.8404 (tp30) REVERT: I 3 LYS cc_start: 0.8455 (mttt) cc_final: 0.8087 (tttt) REVERT: I 9 GLU cc_start: 0.8490 (tp30) cc_final: 0.8242 (tp30) REVERT: J 29 GLU cc_start: 0.8730 (tt0) cc_final: 0.8383 (tt0) REVERT: K 32 ASP cc_start: 0.8536 (t70) cc_final: 0.8288 (t70) REVERT: K 227 LEU cc_start: 0.8506 (mp) cc_final: 0.8301 (mp) REVERT: K 284 ASN cc_start: 0.8388 (p0) cc_final: 0.8188 (p0) REVERT: L 76 ASP cc_start: 0.8783 (t70) cc_final: 0.8581 (t70) REVERT: N 5 GLU cc_start: 0.8775 (tp30) cc_final: 0.8328 (tp30) REVERT: P 1 MET cc_start: 0.7286 (ptt) cc_final: 0.6795 (ptp) outliers start: 6 outliers final: 4 residues processed: 264 average time/residue: 1.6581 time to fit residues: 474.9979 Evaluate side-chains 235 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 231 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain K residue 154 ARG Chi-restraints excluded: chain L residue 34 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.7980 chunk 139 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 chunk 167 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 10 ASN C 56 GLN D 135 GLN J 10 ASN K 56 GLN K 103 GLN L 135 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.100759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.060099 restraints weight = 40115.746| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 2.25 r_work: 0.2633 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2536 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2525 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2525 r_free = 0.2525 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2525 r_free = 0.2525 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2525 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9106 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.191 16564 Z= 0.181 Angle : 0.691 10.186 22634 Z= 0.337 Chirality : 0.046 0.179 2530 Planarity : 0.005 0.054 2778 Dihedral : 12.649 94.627 2666 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 1.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.91 % Allowed : 5.79 % Favored : 93.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 2.01 (0.19), residues: 1908 helix: 2.62 (0.17), residues: 970 sheet: 0.38 (0.36), residues: 200 loop : -0.13 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 146 HIS 0.005 0.002 HIS L 72 PHE 0.015 0.002 PHE A 52 TYR 0.014 0.001 TYR A 136 ARG 0.005 0.000 ARG O 30 Details of bonding type rmsd hydrogen bonds : bond 0.10696 ( 845) hydrogen bonds : angle 4.34529 ( 2407) metal coordination : bond 0.01127 ( 8) metal coordination : angle 4.59282 ( 6) SS BOND : bond 0.00389 ( 2) SS BOND : angle 1.44384 ( 4) covalent geometry : bond 0.00343 (16540) covalent geometry : angle 0.68695 (22624) Misc. bond : bond 0.09670 ( 14) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 248 time to evaluate : 1.714 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 LYS cc_start: 0.8346 (mttt) cc_final: 0.7669 (tttt) REVERT: A 167 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8546 (tp30) REVERT: B 29 GLU cc_start: 0.8921 (tt0) cc_final: 0.8599 (tt0) REVERT: C 32 ASP cc_start: 0.8547 (t70) cc_final: 0.8173 (t70) REVERT: D 76 ASP cc_start: 0.8544 (t70) cc_final: 0.8184 (t70) REVERT: I 3 LYS cc_start: 0.8459 (mttt) cc_final: 0.7765 (tttt) REVERT: I 167 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8559 (tp30) REVERT: J 29 GLU cc_start: 0.8922 (tt0) cc_final: 0.8602 (tt0) REVERT: J 119 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.7545 (pptt) REVERT: K 32 ASP cc_start: 0.8539 (t70) cc_final: 0.8162 (t70) REVERT: K 227 LEU cc_start: 0.8538 (mp) cc_final: 0.8335 (mp) REVERT: K 283 MET cc_start: 0.8374 (mmm) cc_final: 0.8154 (mmm) REVERT: L 76 ASP cc_start: 0.8530 (t70) cc_final: 0.8188 (t70) outliers start: 15 outliers final: 12 residues processed: 252 average time/residue: 1.4953 time to fit residues: 412.2101 Evaluate side-chains 243 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 230 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain J residue 151 ILE Chi-restraints excluded: chain K residue 154 ARG Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain M residue 25 LEU Chi-restraints excluded: chain O residue 3 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 154 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 74 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 64 optimal weight: 0.7980 chunk 2 optimal weight: 0.0050 chunk 17 optimal weight: 0.5980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 10 ASN J 10 ASN K 103 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.102165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.062321 restraints weight = 29566.576| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 2.01 r_work: 0.2667 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2568 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2595 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2595 r_free = 0.2595 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2595 r_free = 0.2595 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2595 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9027 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.151 16564 Z= 0.158 Angle : 0.632 10.135 22634 Z= 0.301 Chirality : 0.044 0.160 2530 Planarity : 0.005 0.056 2778 Dihedral : 12.141 88.990 2666 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.28 % Allowed : 6.52 % Favored : 92.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 2.11 (0.19), residues: 1908 helix: 2.79 (0.17), residues: 972 sheet: 0.15 (0.35), residues: 214 loop : -0.14 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 146 HIS 0.005 0.001 HIS I 202 PHE 0.013 0.001 PHE E 2 TYR 0.009 0.001 TYR A 136 ARG 0.004 0.000 ARG G 30 Details of bonding type rmsd hydrogen bonds : bond 0.09264 ( 845) hydrogen bonds : angle 4.02862 ( 2407) metal coordination : bond 0.00930 ( 8) metal coordination : angle 4.03371 ( 6) SS BOND : bond 0.00300 ( 2) SS BOND : angle 1.20340 ( 4) covalent geometry : bond 0.00298 (16540) covalent geometry : angle 0.62868 (22624) Misc. bond : bond 0.07491 ( 14) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 229 time to evaluate : 1.771 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 LYS cc_start: 0.8295 (mttt) cc_final: 0.7606 (tttt) REVERT: B 29 GLU cc_start: 0.8901 (tt0) cc_final: 0.8527 (tt0) REVERT: B 119 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.7507 (pptt) REVERT: C 32 ASP cc_start: 0.8513 (t70) cc_final: 0.8093 (t70) REVERT: C 121 GLN cc_start: 0.8830 (tp40) cc_final: 0.8556 (mm-40) REVERT: D 76 ASP cc_start: 0.8475 (t70) cc_final: 0.8080 (t70) REVERT: G 31 ARG cc_start: 0.7049 (OUTLIER) cc_final: 0.6814 (tpp-160) REVERT: I 3 LYS cc_start: 0.8352 (mttt) cc_final: 0.7635 (tmtt) REVERT: J 29 GLU cc_start: 0.8899 (tt0) cc_final: 0.8527 (tt0) REVERT: K 32 ASP cc_start: 0.8499 (t70) cc_final: 0.8085 (t70) REVERT: K 227 LEU cc_start: 0.8546 (mp) cc_final: 0.8331 (mp) REVERT: K 284 ASN cc_start: 0.8377 (p0) cc_final: 0.8148 (p0) REVERT: L 76 ASP cc_start: 0.8464 (t70) cc_final: 0.8068 (t70) REVERT: O 31 ARG cc_start: 0.7066 (OUTLIER) cc_final: 0.6819 (tpp-160) outliers start: 21 outliers final: 12 residues processed: 234 average time/residue: 1.5438 time to fit residues: 395.3449 Evaluate side-chains 237 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 222 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 31 ARG Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain K residue 154 ARG Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 62 ASP Chi-restraints excluded: chain M residue 25 LEU Chi-restraints excluded: chain O residue 3 GLU Chi-restraints excluded: chain O residue 31 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 110 optimal weight: 0.5980 chunk 51 optimal weight: 6.9990 chunk 28 optimal weight: 0.2980 chunk 173 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 chunk 142 optimal weight: 0.0870 chunk 5 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 10 ASN C 56 GLN C 193 ASN J 10 ASN K 56 GLN K 193 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.102898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.063344 restraints weight = 28194.123| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 1.95 r_work: 0.2692 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2620 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2620 r_free = 0.2620 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2620 r_free = 0.2620 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2620 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9013 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.141 16564 Z= 0.150 Angle : 0.622 10.979 22634 Z= 0.293 Chirality : 0.044 0.165 2530 Planarity : 0.004 0.054 2778 Dihedral : 11.694 88.839 2666 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.34 % Allowed : 7.31 % Favored : 91.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 2.22 (0.19), residues: 1908 helix: 2.85 (0.17), residues: 972 sheet: 0.63 (0.36), residues: 200 loop : -0.18 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 146 HIS 0.005 0.001 HIS I 202 PHE 0.012 0.001 PHE A 52 TYR 0.008 0.001 TYR O 29 ARG 0.003 0.000 ARG O 30 Details of bonding type rmsd hydrogen bonds : bond 0.08593 ( 845) hydrogen bonds : angle 3.90312 ( 2407) metal coordination : bond 0.00836 ( 8) metal coordination : angle 3.93647 ( 6) SS BOND : bond 0.00289 ( 2) SS BOND : angle 1.13682 ( 4) covalent geometry : bond 0.00283 (16540) covalent geometry : angle 0.61894 (22624) Misc. bond : bond 0.07368 ( 14) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 232 time to evaluate : 1.915 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 LYS cc_start: 0.8259 (mttt) cc_final: 0.7582 (tttt) REVERT: B 29 GLU cc_start: 0.8891 (tt0) cc_final: 0.8568 (tt0) REVERT: B 119 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.7525 (pptt) REVERT: C 32 ASP cc_start: 0.8491 (t70) cc_final: 0.8089 (t70) REVERT: D 76 ASP cc_start: 0.8471 (t70) cc_final: 0.8053 (t70) REVERT: G 31 ARG cc_start: 0.6916 (OUTLIER) cc_final: 0.6705 (tpp-160) REVERT: H 2 ASP cc_start: 0.7025 (t0) cc_final: 0.6824 (t0) REVERT: I 3 LYS cc_start: 0.8338 (mttt) cc_final: 0.7631 (tttt) REVERT: J 29 GLU cc_start: 0.8892 (tt0) cc_final: 0.8571 (tt0) REVERT: J 119 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.7491 (pptt) REVERT: K 32 ASP cc_start: 0.8484 (t70) cc_final: 0.8101 (t70) REVERT: K 227 LEU cc_start: 0.8532 (mp) cc_final: 0.8321 (mp) REVERT: K 283 MET cc_start: 0.7922 (mmm) cc_final: 0.7689 (mmm) REVERT: L 76 ASP cc_start: 0.8470 (t70) cc_final: 0.8055 (t70) REVERT: O 31 ARG cc_start: 0.6925 (OUTLIER) cc_final: 0.6673 (tpp-160) REVERT: P 2 ASP cc_start: 0.7035 (t0) cc_final: 0.6820 (t0) outliers start: 22 outliers final: 14 residues processed: 238 average time/residue: 1.5231 time to fit residues: 396.5449 Evaluate side-chains 238 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 220 time to evaluate : 1.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 31 ARG Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain K residue 154 ARG Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 62 ASP Chi-restraints excluded: chain M residue 25 LEU Chi-restraints excluded: chain O residue 3 GLU Chi-restraints excluded: chain O residue 31 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 136 optimal weight: 0.0010 chunk 117 optimal weight: 0.2980 chunk 22 optimal weight: 0.7980 chunk 15 optimal weight: 0.0070 chunk 89 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 105 optimal weight: 0.0470 overall best weight: 0.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 10 ASN J 10 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.106651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.067438 restraints weight = 36824.623| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 2.21 r_work: 0.2789 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2720 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2720 r_free = 0.2720 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2720 r_free = 0.2720 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2720 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.116 16564 Z= 0.129 Angle : 0.570 9.330 22634 Z= 0.268 Chirality : 0.043 0.160 2530 Planarity : 0.004 0.055 2778 Dihedral : 10.828 88.578 2666 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.34 % Allowed : 7.80 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 2.44 (0.19), residues: 1908 helix: 2.99 (0.17), residues: 972 sheet: 0.78 (0.36), residues: 208 loop : -0.04 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 146 HIS 0.003 0.001 HIS D 151 PHE 0.008 0.001 PHE A 52 TYR 0.007 0.001 TYR O 29 ARG 0.002 0.000 ARG O 30 Details of bonding type rmsd hydrogen bonds : bond 0.06635 ( 845) hydrogen bonds : angle 3.65225 ( 2407) metal coordination : bond 0.00553 ( 8) metal coordination : angle 3.42382 ( 6) SS BOND : bond 0.00156 ( 2) SS BOND : angle 0.67737 ( 4) covalent geometry : bond 0.00251 (16540) covalent geometry : angle 0.56771 (22624) Misc. bond : bond 0.06515 ( 14) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 238 time to evaluate : 1.840 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 LYS cc_start: 0.8236 (mttt) cc_final: 0.7537 (tmtt) REVERT: B 29 GLU cc_start: 0.8903 (tt0) cc_final: 0.8598 (tt0) REVERT: B 119 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.7495 (pptt) REVERT: C 32 ASP cc_start: 0.8545 (t70) cc_final: 0.8176 (t70) REVERT: D 76 ASP cc_start: 0.8472 (t70) cc_final: 0.8063 (t70) REVERT: I 3 LYS cc_start: 0.8321 (mttt) cc_final: 0.7599 (tttt) REVERT: J 29 GLU cc_start: 0.8899 (tt0) cc_final: 0.8595 (tt0) REVERT: J 119 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.7479 (pptt) REVERT: K 32 ASP cc_start: 0.8526 (t70) cc_final: 0.8171 (t70) REVERT: K 190 TYR cc_start: 0.8033 (m-80) cc_final: 0.7522 (m-10) REVERT: L 76 ASP cc_start: 0.8464 (t70) cc_final: 0.8080 (t70) REVERT: N 29 ARG cc_start: 0.8343 (tpm170) cc_final: 0.8142 (tpp-160) outliers start: 22 outliers final: 5 residues processed: 246 average time/residue: 1.4863 time to fit residues: 400.5380 Evaluate side-chains 232 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 225 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain L residue 34 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 160 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 37 optimal weight: 0.0670 chunk 175 optimal weight: 1.9990 chunk 119 optimal weight: 0.4980 chunk 145 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 143 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.7122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 10 ASN C 56 GLN J 10 ASN K 56 GLN K 225 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.102153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.061232 restraints weight = 40290.006| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 2.29 r_work: 0.2680 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2575 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2575 r_free = 0.2575 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2575 r_free = 0.2575 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2575 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9101 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.135 16564 Z= 0.159 Angle : 0.631 10.863 22634 Z= 0.300 Chirality : 0.044 0.174 2530 Planarity : 0.005 0.054 2778 Dihedral : 10.858 89.671 2658 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.40 % Allowed : 8.28 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 2.29 (0.19), residues: 1908 helix: 2.83 (0.17), residues: 982 sheet: 0.72 (0.36), residues: 200 loop : -0.10 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 146 HIS 0.007 0.001 HIS I 202 PHE 0.014 0.002 PHE D 40 TYR 0.009 0.001 TYR A 136 ARG 0.003 0.000 ARG O 30 Details of bonding type rmsd hydrogen bonds : bond 0.08975 ( 845) hydrogen bonds : angle 3.85713 ( 2407) metal coordination : bond 0.00915 ( 8) metal coordination : angle 4.24452 ( 6) SS BOND : bond 0.00377 ( 2) SS BOND : angle 1.41131 ( 4) covalent geometry : bond 0.00309 (16540) covalent geometry : angle 0.62670 (22624) Misc. bond : bond 0.07460 ( 14) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 227 time to evaluate : 1.836 Fit side-chains revert: symmetry clash REVERT: A 3 LYS cc_start: 0.8322 (mttt) cc_final: 0.7650 (tttt) REVERT: B 29 GLU cc_start: 0.8935 (tt0) cc_final: 0.8656 (tt0) REVERT: B 119 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.7656 (pptt) REVERT: C 32 ASP cc_start: 0.8602 (t70) cc_final: 0.8263 (t70) REVERT: C 283 MET cc_start: 0.8001 (mmm) cc_final: 0.7778 (mmm) REVERT: D 76 ASP cc_start: 0.8555 (t70) cc_final: 0.8164 (t70) REVERT: I 3 LYS cc_start: 0.8395 (mttt) cc_final: 0.7688 (tttt) REVERT: J 29 GLU cc_start: 0.8935 (tt0) cc_final: 0.8658 (tt0) REVERT: J 119 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.7606 (pptt) REVERT: K 32 ASP cc_start: 0.8592 (t70) cc_final: 0.8257 (t70) REVERT: K 190 TYR cc_start: 0.8049 (m-80) cc_final: 0.7477 (m-10) REVERT: L 76 ASP cc_start: 0.8544 (t70) cc_final: 0.8157 (t70) outliers start: 23 outliers final: 12 residues processed: 237 average time/residue: 1.5263 time to fit residues: 395.3356 Evaluate side-chains 233 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 219 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain M residue 25 LEU Chi-restraints excluded: chain M residue 28 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 10 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 30 optimal weight: 0.0670 chunk 174 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 17 optimal weight: 0.0980 chunk 89 optimal weight: 3.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 10 ASN J 10 ASN K 225 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.101133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.060873 restraints weight = 29079.638| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 1.98 r_work: 0.2674 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2575 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2566 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2566 r_free = 0.2566 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2566 r_free = 0.2566 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2566 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9111 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.131 16564 Z= 0.174 Angle : 0.657 10.223 22634 Z= 0.316 Chirality : 0.045 0.169 2530 Planarity : 0.005 0.055 2778 Dihedral : 10.868 89.536 2658 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.34 % Allowed : 8.22 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 2.12 (0.19), residues: 1908 helix: 2.71 (0.16), residues: 982 sheet: 0.35 (0.36), residues: 214 loop : -0.11 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 146 HIS 0.008 0.001 HIS I 202 PHE 0.018 0.002 PHE D 40 TYR 0.011 0.001 TYR A 136 ARG 0.002 0.000 ARG A 114 Details of bonding type rmsd hydrogen bonds : bond 0.09620 ( 845) hydrogen bonds : angle 3.93930 ( 2407) metal coordination : bond 0.01019 ( 8) metal coordination : angle 4.32146 ( 6) SS BOND : bond 0.00453 ( 2) SS BOND : angle 1.61397 ( 4) covalent geometry : bond 0.00351 (16540) covalent geometry : angle 0.65261 (22624) Misc. bond : bond 0.07832 ( 14) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 221 time to evaluate : 2.047 Fit side-chains revert: symmetry clash REVERT: A 3 LYS cc_start: 0.8341 (mttt) cc_final: 0.7658 (tmtt) REVERT: B 29 GLU cc_start: 0.8879 (tt0) cc_final: 0.8597 (tt0) REVERT: B 119 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.7692 (pptt) REVERT: C 32 ASP cc_start: 0.8552 (t70) cc_final: 0.8192 (t70) REVERT: D 76 ASP cc_start: 0.8574 (t70) cc_final: 0.8162 (t70) REVERT: I 3 LYS cc_start: 0.8403 (mttt) cc_final: 0.7717 (tttt) REVERT: J 29 GLU cc_start: 0.8872 (tt0) cc_final: 0.8591 (tt0) REVERT: J 119 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.7660 (pptt) REVERT: K 32 ASP cc_start: 0.8542 (t70) cc_final: 0.8187 (t70) REVERT: K 190 TYR cc_start: 0.8082 (m-80) cc_final: 0.7578 (m-10) REVERT: L 76 ASP cc_start: 0.8562 (t70) cc_final: 0.8159 (t70) outliers start: 22 outliers final: 10 residues processed: 230 average time/residue: 1.7962 time to fit residues: 451.8315 Evaluate side-chains 229 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 217 time to evaluate : 2.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain M residue 28 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 166 optimal weight: 6.9990 chunk 180 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 164 optimal weight: 10.0000 chunk 40 optimal weight: 0.5980 chunk 149 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 152 optimal weight: 0.9990 chunk 177 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 10 ASN C 56 GLN J 10 ASN K 56 GLN K 225 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.099476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.057915 restraints weight = 40226.892| |-----------------------------------------------------------------------------| r_work (start): 0.2719 rms_B_bonded: 2.31 r_work: 0.2603 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2505 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2495 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2495 r_free = 0.2495 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2495 r_free = 0.2495 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2495 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9153 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.193 16564 Z= 0.200 Angle : 0.706 10.251 22634 Z= 0.344 Chirality : 0.047 0.162 2530 Planarity : 0.005 0.054 2778 Dihedral : 11.079 89.854 2658 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.97 % Allowed : 8.83 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 1.92 (0.19), residues: 1908 helix: 2.54 (0.16), residues: 980 sheet: 0.25 (0.35), residues: 214 loop : -0.19 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 146 HIS 0.009 0.002 HIS I 202 PHE 0.021 0.002 PHE D 40 TYR 0.014 0.002 TYR I 136 ARG 0.003 0.000 ARG I 114 Details of bonding type rmsd hydrogen bonds : bond 0.10953 ( 845) hydrogen bonds : angle 4.12419 ( 2407) metal coordination : bond 0.01193 ( 8) metal coordination : angle 4.53373 ( 6) SS BOND : bond 0.00577 ( 2) SS BOND : angle 1.97142 ( 4) covalent geometry : bond 0.00414 (16540) covalent geometry : angle 0.70161 (22624) Misc. bond : bond 0.09763 ( 14) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 227 time to evaluate : 2.684 Fit side-chains revert: symmetry clash REVERT: A 3 LYS cc_start: 0.8356 (mttt) cc_final: 0.7681 (tttt) REVERT: B 119 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.7810 (pptt) REVERT: C 32 ASP cc_start: 0.8614 (t70) cc_final: 0.8225 (t70) REVERT: D 76 ASP cc_start: 0.8615 (t70) cc_final: 0.8191 (t70) REVERT: F 5 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7996 (mm-30) REVERT: I 3 LYS cc_start: 0.8431 (mttt) cc_final: 0.7764 (tttt) REVERT: J 119 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.7755 (pptt) REVERT: K 32 ASP cc_start: 0.8610 (t70) cc_final: 0.8243 (t70) REVERT: L 76 ASP cc_start: 0.8602 (t70) cc_final: 0.8179 (t70) REVERT: N 5 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7987 (mm-30) outliers start: 16 outliers final: 12 residues processed: 236 average time/residue: 2.0483 time to fit residues: 526.0216 Evaluate side-chains 237 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 223 time to evaluate : 2.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain M residue 25 LEU Chi-restraints excluded: chain M residue 28 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 79 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 100 optimal weight: 0.0980 chunk 87 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 176 optimal weight: 1.9990 chunk 147 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 21 optimal weight: 7.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 10 ASN J 10 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.101030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.060445 restraints weight = 33427.820| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 2.11 r_work: 0.2665 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2567 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2557 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2557 r_free = 0.2557 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2557 r_free = 0.2557 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2557 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9116 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.131 16564 Z= 0.168 Angle : 0.656 10.077 22634 Z= 0.316 Chirality : 0.045 0.182 2530 Planarity : 0.005 0.055 2778 Dihedral : 10.872 88.418 2658 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.85 % Allowed : 8.95 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 2.00 (0.19), residues: 1908 helix: 2.64 (0.16), residues: 980 sheet: 0.25 (0.35), residues: 214 loop : -0.20 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 146 HIS 0.006 0.001 HIS I 202 PHE 0.014 0.001 PHE D 40 TYR 0.010 0.001 TYR A 136 ARG 0.002 0.000 ARG M 29 Details of bonding type rmsd hydrogen bonds : bond 0.09553 ( 845) hydrogen bonds : angle 3.97605 ( 2407) metal coordination : bond 0.00950 ( 8) metal coordination : angle 3.85050 ( 6) SS BOND : bond 0.00370 ( 2) SS BOND : angle 1.34413 ( 4) covalent geometry : bond 0.00325 (16540) covalent geometry : angle 0.65295 (22624) Misc. bond : bond 0.07631 ( 14) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 223 time to evaluate : 2.111 Fit side-chains revert: symmetry clash REVERT: A 3 LYS cc_start: 0.8331 (mttt) cc_final: 0.7655 (tmtt) REVERT: B 119 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.7785 (pptt) REVERT: C 32 ASP cc_start: 0.8583 (t70) cc_final: 0.8196 (t70) REVERT: D 76 ASP cc_start: 0.8602 (t70) cc_final: 0.8175 (t70) REVERT: F 5 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7887 (mm-30) REVERT: I 3 LYS cc_start: 0.8411 (mttt) cc_final: 0.7718 (tttt) REVERT: J 119 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.7734 (pptt) REVERT: K 32 ASP cc_start: 0.8576 (t70) cc_final: 0.8194 (t70) REVERT: L 76 ASP cc_start: 0.8591 (t70) cc_final: 0.8166 (t70) REVERT: N 5 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7872 (mm-30) outliers start: 14 outliers final: 12 residues processed: 228 average time/residue: 1.6058 time to fit residues: 399.6437 Evaluate side-chains 236 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 222 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain O residue 3 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 123 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 181 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 122 optimal weight: 0.0070 chunk 136 optimal weight: 1.9990 chunk 48 optimal weight: 0.2980 chunk 93 optimal weight: 0.3980 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 10 ASN C 56 GLN J 10 ASN K 56 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.103017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.063490 restraints weight = 28275.860| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 1.95 r_work: 0.2697 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2626 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2626 r_free = 0.2626 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2626 r_free = 0.2626 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2626 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9011 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.115 16564 Z= 0.150 Angle : 0.621 9.947 22634 Z= 0.298 Chirality : 0.044 0.181 2530 Planarity : 0.004 0.057 2778 Dihedral : 10.565 87.876 2658 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.85 % Allowed : 8.95 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 2.14 (0.19), residues: 1908 helix: 2.82 (0.17), residues: 970 sheet: 0.33 (0.36), residues: 214 loop : -0.19 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 146 HIS 0.004 0.001 HIS I 202 PHE 0.011 0.001 PHE D 40 TYR 0.007 0.001 TYR Q 49 ARG 0.002 0.000 ARG G 30 Details of bonding type rmsd hydrogen bonds : bond 0.08245 ( 845) hydrogen bonds : angle 3.81334 ( 2407) metal coordination : bond 0.00762 ( 8) metal coordination : angle 3.60529 ( 6) SS BOND : bond 0.00275 ( 2) SS BOND : angle 1.02821 ( 4) covalent geometry : bond 0.00290 (16540) covalent geometry : angle 0.61801 (22624) Misc. bond : bond 0.06796 ( 14) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 223 time to evaluate : 1.886 Fit side-chains revert: symmetry clash REVERT: A 3 LYS cc_start: 0.8247 (mttt) cc_final: 0.7569 (tmtt) REVERT: B 119 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.7691 (pptt) REVERT: C 32 ASP cc_start: 0.8540 (t70) cc_final: 0.8140 (t70) REVERT: D 76 ASP cc_start: 0.8524 (t70) cc_final: 0.8092 (t70) REVERT: I 3 LYS cc_start: 0.8345 (mttt) cc_final: 0.7631 (tttt) REVERT: J 119 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.7643 (pptt) REVERT: K 32 ASP cc_start: 0.8533 (t70) cc_final: 0.8136 (t70) REVERT: L 76 ASP cc_start: 0.8521 (t70) cc_final: 0.8099 (t70) outliers start: 14 outliers final: 10 residues processed: 228 average time/residue: 1.6071 time to fit residues: 405.2219 Evaluate side-chains 228 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 216 time to evaluate : 1.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain M residue 28 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 154 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 47 optimal weight: 0.0470 chunk 156 optimal weight: 0.0980 chunk 53 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 166 optimal weight: 0.0670 chunk 143 optimal weight: 6.9990 chunk 122 optimal weight: 0.0870 chunk 3 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 overall best weight: 0.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 10 ASN J 10 ASN K 225 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.108066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.069577 restraints weight = 32670.417| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.08 r_work: 0.2871 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2759 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2759 r_free = 0.2759 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2759 r_free = 0.2759 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2759 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.121 16564 Z= 0.125 Angle : 0.576 11.041 22634 Z= 0.272 Chirality : 0.043 0.195 2530 Planarity : 0.004 0.051 2778 Dihedral : 10.064 88.328 2658 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.91 % Allowed : 9.26 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 2.46 (0.20), residues: 1908 helix: 3.05 (0.17), residues: 970 sheet: 0.63 (0.35), residues: 224 loop : -0.04 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 146 HIS 0.003 0.001 HIS I 202 PHE 0.008 0.001 PHE J 124 TYR 0.019 0.001 TYR K 190 ARG 0.002 0.000 ARG C 154 Details of bonding type rmsd hydrogen bonds : bond 0.05948 ( 845) hydrogen bonds : angle 3.53757 ( 2407) metal coordination : bond 0.00533 ( 8) metal coordination : angle 3.45507 ( 6) SS BOND : bond 0.00150 ( 2) SS BOND : angle 0.64124 ( 4) covalent geometry : bond 0.00259 (16540) covalent geometry : angle 0.57361 (22624) Misc. bond : bond 0.05991 ( 14) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28379.06 seconds wall clock time: 486 minutes 56.75 seconds (29216.75 seconds total)