Starting phenix.real_space_refine on Thu Sep 18 11:08:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9es7_19938/09_2025/9es7_19938.cif Found real_map, /net/cci-nas-00/data/ceres_data/9es7_19938/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9es7_19938/09_2025/9es7_19938.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9es7_19938/09_2025/9es7_19938.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9es7_19938/09_2025/9es7_19938.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9es7_19938/09_2025/9es7_19938.map" } resolution = 1.94 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.66, per 1000 atoms: 0.22 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: 1.47 Conformation dependent library (CDL) restraints added in 594.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.39 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: 1.83 Time building geometry restraints manager: 1.72 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'L' } 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 'H' selection = chain 'P' } ncs_group { reference = chain 'Q' selection = chain 'R' } 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: 8.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.690 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.840 ------------------------------------------------------------------------------- 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 : 1.78 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (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 ARG 0.003 0.000 ARG I 182 TYR 0.012 0.001 TYR A 136 PHE 0.011 0.001 PHE D 40 TRP 0.007 0.001 TRP I 146 HIS 0.005 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00280 (16540) covalent geometry : angle 0.51412 (22624) SS BOND : bond 0.00415 ( 2) SS BOND : angle 1.73049 ( 4) hydrogen bonds : bond 0.30072 ( 845) hydrogen bonds : angle 5.91992 ( 2407) metal coordination : bond 0.01407 ( 8) metal coordination : angle 9.07644 ( 6) 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 : 0.546 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 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: 0.7496 time to fit residues: 214.4024 Evaluate side-chains 234 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 230 time to evaluate : 0.625 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.5980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.0370 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- 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 L 135 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.100950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.060673 restraints weight = 35065.079| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 2.12 r_work: 0.2647 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2549 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2539 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2539 r_free = 0.2539 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2539 r_free = 0.2539 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2539 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9099 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.183 16564 Z= 0.183 Angle : 0.687 9.835 22634 Z= 0.336 Chirality : 0.046 0.180 2530 Planarity : 0.005 0.054 2778 Dihedral : 12.578 92.344 2666 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 1.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.85 % Allowed : 5.79 % Favored : 93.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.03 (0.19), residues: 1908 helix: 2.64 (0.17), residues: 970 sheet: 0.39 (0.36), residues: 200 loop : -0.12 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 30 TYR 0.014 0.001 TYR A 136 PHE 0.015 0.002 PHE A 52 TRP 0.012 0.001 TRP I 146 HIS 0.004 0.001 HIS L 72 Details of bonding type rmsd covalent geometry : bond 0.00344 (16540) covalent geometry : angle 0.68309 (22624) SS BOND : bond 0.00373 ( 2) SS BOND : angle 1.39385 ( 4) hydrogen bonds : bond 0.10533 ( 845) hydrogen bonds : angle 4.33431 ( 2407) metal coordination : bond 0.01079 ( 8) metal coordination : angle 4.55450 ( 6) Misc. bond : bond 0.09391 ( 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 264 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 250 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 LYS cc_start: 0.8335 (mttt) cc_final: 0.7658 (tttt) REVERT: A 167 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8540 (tp30) REVERT: B 29 GLU cc_start: 0.8914 (tt0) cc_final: 0.8578 (tt0) REVERT: C 32 ASP cc_start: 0.8554 (t70) cc_final: 0.8207 (t70) REVERT: D 76 ASP cc_start: 0.8543 (t70) cc_final: 0.8182 (t70) REVERT: I 3 LYS cc_start: 0.8449 (mttt) cc_final: 0.7751 (tttt) REVERT: I 167 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8547 (tp30) REVERT: J 29 GLU cc_start: 0.8915 (tt0) cc_final: 0.8579 (tt0) REVERT: K 32 ASP cc_start: 0.8542 (t70) cc_final: 0.8191 (t70) REVERT: K 283 MET cc_start: 0.8394 (mmm) cc_final: 0.8179 (mmm) REVERT: L 76 ASP cc_start: 0.8529 (t70) cc_final: 0.8185 (t70) outliers start: 14 outliers final: 12 residues processed: 254 average time/residue: 0.6990 time to fit residues: 192.9562 Evaluate side-chains 242 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 230 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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 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 101 optimal weight: 0.3980 chunk 111 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 137 optimal weight: 0.0670 chunk 51 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 119 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 = 0.3567 r_free = 0.3567 target = 0.102534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.063247 restraints weight = 25459.740| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 1.86 r_work: 0.2691 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2618 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2618 r_free = 0.2618 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 = 0.2618 r_free = 0.2618 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2618 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9017 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.143 16564 Z= 0.156 Angle : 0.629 10.565 22634 Z= 0.298 Chirality : 0.044 0.170 2530 Planarity : 0.005 0.056 2778 Dihedral : 11.985 89.109 2666 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.34 % Allowed : 6.39 % Favored : 92.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.15 (0.19), residues: 1908 helix: 2.82 (0.17), residues: 972 sheet: 0.19 (0.35), residues: 214 loop : -0.12 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O 30 TYR 0.008 0.001 TYR A 136 PHE 0.013 0.001 PHE E 2 TRP 0.013 0.001 TRP I 146 HIS 0.005 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00295 (16540) covalent geometry : angle 0.62612 (22624) SS BOND : bond 0.00285 ( 2) SS BOND : angle 1.15803 ( 4) hydrogen bonds : bond 0.09067 ( 845) hydrogen bonds : angle 3.99114 ( 2407) metal coordination : bond 0.00910 ( 8) metal coordination : angle 3.94411 ( 6) Misc. bond : bond 0.07300 ( 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 254 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 232 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 LYS cc_start: 0.8287 (mttt) cc_final: 0.7606 (tttt) REVERT: B 29 GLU cc_start: 0.8877 (tt0) cc_final: 0.8560 (tt0) REVERT: B 119 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.7505 (pptt) REVERT: C 32 ASP cc_start: 0.8480 (t70) cc_final: 0.8069 (t70) REVERT: D 76 ASP cc_start: 0.8469 (t70) cc_final: 0.8075 (t70) REVERT: G 31 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.6787 (tpp-160) REVERT: I 3 LYS cc_start: 0.8361 (mttt) cc_final: 0.7633 (tmtt) REVERT: J 29 GLU cc_start: 0.8881 (tt0) cc_final: 0.8566 (tt0) REVERT: J 119 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.7479 (pptt) REVERT: K 32 ASP cc_start: 0.8467 (t70) cc_final: 0.8052 (t70) REVERT: K 284 ASN cc_start: 0.8360 (p0) cc_final: 0.8141 (p0) REVERT: L 76 ASP cc_start: 0.8463 (t70) cc_final: 0.8069 (t70) REVERT: O 31 ARG cc_start: 0.6983 (OUTLIER) cc_final: 0.6730 (tpp-160) outliers start: 22 outliers final: 10 residues processed: 237 average time/residue: 0.7563 time to fit residues: 195.3347 Evaluate side-chains 232 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 218 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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 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 L residue 34 LEU 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 71 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 142 optimal weight: 0.5980 chunk 112 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 121 optimal weight: 0.0870 chunk 118 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 2 optimal weight: 0.0040 overall best weight: 0.4770 ------------------------------------------------------------------------------- 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 = 0.3583 r_free = 0.3583 target = 0.103637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.063693 restraints weight = 34252.555| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 2.12 r_work: 0.2699 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2628 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2628 r_free = 0.2628 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 = 0.2628 r_free = 0.2628 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2628 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9005 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.131 16564 Z= 0.145 Angle : 0.614 9.934 22634 Z= 0.288 Chirality : 0.043 0.173 2530 Planarity : 0.004 0.054 2778 Dihedral : 11.246 88.807 2666 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.40 % Allowed : 7.43 % Favored : 91.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.29 (0.19), residues: 1908 helix: 2.89 (0.17), residues: 972 sheet: 0.67 (0.36), residues: 200 loop : -0.13 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 30 TYR 0.008 0.001 TYR O 29 PHE 0.011 0.001 PHE I 52 TRP 0.012 0.001 TRP A 146 HIS 0.004 0.001 HIS I 202 Details of bonding type rmsd covalent geometry : bond 0.00275 (16540) covalent geometry : angle 0.61052 (22624) SS BOND : bond 0.00269 ( 2) SS BOND : angle 1.10277 ( 4) hydrogen bonds : bond 0.08155 ( 845) hydrogen bonds : angle 3.82693 ( 2407) metal coordination : bond 0.00797 ( 8) metal coordination : angle 3.86699 ( 6) Misc. bond : bond 0.07136 ( 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 255 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 232 time to evaluate : 0.570 Fit side-chains revert: symmetry clash REVERT: A 3 LYS cc_start: 0.8278 (mttt) cc_final: 0.7573 (tttt) REVERT: B 29 GLU cc_start: 0.8922 (tt0) cc_final: 0.8605 (tt0) REVERT: B 119 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.7524 (pptt) REVERT: C 32 ASP cc_start: 0.8547 (t70) cc_final: 0.8160 (t70) REVERT: C 190 TYR cc_start: 0.8106 (m-80) cc_final: 0.7603 (m-10) REVERT: D 76 ASP cc_start: 0.8478 (t70) cc_final: 0.8077 (t70) REVERT: G 31 ARG cc_start: 0.6891 (OUTLIER) cc_final: 0.6629 (tpp-160) REVERT: I 3 LYS cc_start: 0.8350 (mttt) cc_final: 0.7641 (tttt) REVERT: J 29 GLU cc_start: 0.8926 (tt0) cc_final: 0.8610 (tt0) REVERT: J 119 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.7496 (pptt) REVERT: K 32 ASP cc_start: 0.8536 (t70) cc_final: 0.8149 (t70) REVERT: K 190 TYR cc_start: 0.8126 (m-80) cc_final: 0.7639 (m-10) REVERT: K 209 ARG cc_start: 0.8119 (ttt180) cc_final: 0.7908 (ttp80) REVERT: K 283 MET cc_start: 0.7893 (mmm) cc_final: 0.7675 (mmm) REVERT: L 76 ASP cc_start: 0.8477 (t70) cc_final: 0.8079 (t70) REVERT: O 31 ARG cc_start: 0.6965 (OUTLIER) cc_final: 0.6681 (tpp-160) outliers start: 23 outliers final: 14 residues processed: 239 average time/residue: 0.7360 time to fit residues: 191.6990 Evaluate side-chains 245 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 227 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 B residue 151 ILE 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 G residue 3 GLU Chi-restraints excluded: chain G residue 31 ARG 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 J residue 151 ILE 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 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 38 optimal weight: 0.7980 chunk 183 optimal weight: 8.9990 chunk 30 optimal weight: 0.5980 chunk 2 optimal weight: 0.0980 chunk 51 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 121 optimal weight: 0.9980 chunk 92 optimal weight: 0.0010 chunk 113 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 overall best weight: 0.4386 ------------------------------------------------------------------------------- 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 = 0.3591 r_free = 0.3591 target = 0.104088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.064648 restraints weight = 29942.727| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 2.01 r_work: 0.2724 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2653 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2653 r_free = 0.2653 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2653 r_free = 0.2653 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2653 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8990 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.119 16564 Z= 0.140 Angle : 0.586 9.986 22634 Z= 0.278 Chirality : 0.044 0.173 2530 Planarity : 0.004 0.056 2778 Dihedral : 10.929 88.984 2666 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.58 % Allowed : 7.37 % Favored : 91.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.36 (0.19), residues: 1908 helix: 2.91 (0.17), residues: 982 sheet: 0.73 (0.36), residues: 200 loop : -0.09 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 30 TYR 0.008 0.001 TYR O 29 PHE 0.011 0.001 PHE K 267 TRP 0.011 0.001 TRP A 146 HIS 0.004 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00270 (16540) covalent geometry : angle 0.58250 (22624) SS BOND : bond 0.00254 ( 2) SS BOND : angle 1.04132 ( 4) hydrogen bonds : bond 0.07772 ( 845) hydrogen bonds : angle 3.74675 ( 2407) metal coordination : bond 0.00721 ( 8) metal coordination : angle 3.67266 ( 6) Misc. bond : bond 0.06772 ( 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 255 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 229 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 LYS cc_start: 0.8253 (mttt) cc_final: 0.7567 (tmtt) REVERT: B 29 GLU cc_start: 0.8877 (tt0) cc_final: 0.8588 (tt0) REVERT: B 119 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.7549 (pptt) REVERT: C 32 ASP cc_start: 0.8538 (t70) cc_final: 0.8167 (t70) REVERT: C 190 TYR cc_start: 0.7991 (m-80) cc_final: 0.7656 (m-10) REVERT: D 76 ASP cc_start: 0.8494 (t70) cc_final: 0.8086 (t70) REVERT: G 31 ARG cc_start: 0.6896 (OUTLIER) cc_final: 0.6667 (tpp-160) REVERT: I 3 LYS cc_start: 0.8335 (mttt) cc_final: 0.7620 (tttt) REVERT: J 29 GLU cc_start: 0.8878 (tt0) cc_final: 0.8591 (tt0) REVERT: J 119 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.7538 (pptt) REVERT: K 32 ASP cc_start: 0.8526 (t70) cc_final: 0.8157 (t70) REVERT: K 190 TYR cc_start: 0.8007 (m-80) cc_final: 0.7675 (m-10) REVERT: L 76 ASP cc_start: 0.8489 (t70) cc_final: 0.8081 (t70) REVERT: O 31 ARG cc_start: 0.6903 (OUTLIER) cc_final: 0.6687 (tpp-160) outliers start: 26 outliers final: 14 residues processed: 241 average time/residue: 0.7635 time to fit residues: 200.6205 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 : 0.690 ------------------------------------------------------------------------------- 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 154 ARG 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 G residue 31 ARG 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 154 ARG 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 Chi-restraints excluded: chain O residue 31 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 136 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 161 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 170 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3541 r_free = 0.3541 target = 0.100900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.061080 restraints weight = 24917.114| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 1.85 r_work: 0.2635 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2533 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2568 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2568 r_free = 0.2568 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 = 0.2568 r_free = 0.2568 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2568 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9043 moved from start: 0.1958 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= 0.180 Angle : 0.663 10.455 22634 Z= 0.319 Chirality : 0.046 0.158 2530 Planarity : 0.005 0.055 2778 Dihedral : 11.075 89.794 2666 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.16 (0.19), residues: 1908 helix: 2.71 (0.16), residues: 982 sheet: 0.69 (0.37), residues: 200 loop : -0.14 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 30 TYR 0.011 0.001 TYR A 136 PHE 0.019 0.002 PHE D 40 TRP 0.012 0.001 TRP A 146 HIS 0.008 0.002 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00370 (16540) covalent geometry : angle 0.65826 (22624) SS BOND : bond 0.00483 ( 2) SS BOND : angle 1.73638 ( 4) hydrogen bonds : bond 0.09833 ( 845) hydrogen bonds : angle 3.96651 ( 2407) metal coordination : bond 0.01049 ( 8) metal coordination : angle 4.47692 ( 6) Misc. bond : bond 0.08207 ( 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 246 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 224 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 LYS cc_start: 0.8284 (mttt) cc_final: 0.7601 (tttt) REVERT: B 119 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.7599 (pptt) REVERT: C 32 ASP cc_start: 0.8513 (t70) cc_final: 0.8126 (t70) REVERT: C 190 TYR cc_start: 0.8053 (m-80) cc_final: 0.7789 (m-10) REVERT: D 76 ASP cc_start: 0.8533 (t70) cc_final: 0.8106 (t70) REVERT: G 31 ARG cc_start: 0.7032 (OUTLIER) cc_final: 0.6745 (tpp-160) REVERT: I 3 LYS cc_start: 0.8353 (mttt) cc_final: 0.7686 (tttt) REVERT: J 119 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.7581 (pptt) REVERT: K 32 ASP cc_start: 0.8506 (t70) cc_final: 0.8122 (t70) REVERT: K 190 TYR cc_start: 0.8049 (m-80) cc_final: 0.7788 (m-10) REVERT: L 76 ASP cc_start: 0.8524 (t70) cc_final: 0.8097 (t70) REVERT: O 31 ARG cc_start: 0.7036 (OUTLIER) cc_final: 0.6795 (tpp-160) outliers start: 22 outliers final: 14 residues processed: 232 average time/residue: 0.7838 time to fit residues: 197.8446 Evaluate side-chains 236 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 218 time to evaluate : 0.797 ------------------------------------------------------------------------------- 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 154 ARG 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 G residue 31 ARG 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 154 ARG 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 Chi-restraints excluded: chain O residue 31 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 137 optimal weight: 0.7980 chunk 135 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 183 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.101184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.060423 restraints weight = 35819.507| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 2.17 r_work: 0.2661 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2565 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2556 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2556 r_free = 0.2556 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2556 r_free = 0.2556 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2556 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9115 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.126 16564 Z= 0.168 Angle : 0.645 10.093 22634 Z= 0.311 Chirality : 0.045 0.171 2530 Planarity : 0.005 0.056 2778 Dihedral : 10.948 88.876 2666 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.16 % Allowed : 8.28 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.16 (0.19), residues: 1908 helix: 2.70 (0.16), residues: 980 sheet: 0.66 (0.37), residues: 200 loop : -0.11 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG O 30 TYR 0.010 0.001 TYR A 136 PHE 0.016 0.002 PHE D 40 TRP 0.012 0.001 TRP I 146 HIS 0.007 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00334 (16540) covalent geometry : angle 0.64118 (22624) SS BOND : bond 0.00409 ( 2) SS BOND : angle 1.50835 ( 4) hydrogen bonds : bond 0.09529 ( 845) hydrogen bonds : angle 3.94777 ( 2407) metal coordination : bond 0.00983 ( 8) metal coordination : angle 4.03576 ( 6) Misc. bond : bond 0.07552 ( 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 241 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 222 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: A 3 LYS cc_start: 0.8346 (mttt) cc_final: 0.7663 (tmtt) REVERT: B 119 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.7728 (pptt) REVERT: C 32 ASP cc_start: 0.8589 (t70) cc_final: 0.8207 (t70) REVERT: C 190 TYR cc_start: 0.8090 (m-80) cc_final: 0.7783 (m-10) REVERT: D 76 ASP cc_start: 0.8590 (t70) cc_final: 0.8192 (t70) REVERT: G 31 ARG cc_start: 0.7132 (OUTLIER) cc_final: 0.6865 (tpp-160) REVERT: I 3 LYS cc_start: 0.8421 (mttt) cc_final: 0.7723 (tttt) REVERT: J 119 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.7709 (pptt) REVERT: K 32 ASP cc_start: 0.8583 (t70) cc_final: 0.8206 (t70) REVERT: K 190 TYR cc_start: 0.8096 (m-80) cc_final: 0.7873 (m-10) REVERT: L 76 ASP cc_start: 0.8584 (t70) cc_final: 0.8186 (t70) REVERT: O 31 ARG cc_start: 0.7131 (OUTLIER) cc_final: 0.6863 (tpp-160) outliers start: 19 outliers final: 14 residues processed: 229 average time/residue: 0.7225 time to fit residues: 180.3028 Evaluate side-chains 234 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 216 time to evaluate : 0.458 ------------------------------------------------------------------------------- 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 154 ARG 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 G residue 31 ARG 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 154 ARG 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 Chi-restraints excluded: chain O residue 31 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 125 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 171 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 144 optimal weight: 6.9990 chunk 151 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.3515 r_free = 0.3515 target = 0.099163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.057952 restraints weight = 35615.430| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 2.18 r_work: 0.2604 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2506 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2506 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2496 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2496 r_free = 0.2496 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2496 r_free = 0.2496 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2496 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9154 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.210 16564 Z= 0.206 Angle : 0.716 10.417 22634 Z= 0.349 Chirality : 0.047 0.172 2530 Planarity : 0.005 0.055 2778 Dihedral : 11.218 89.956 2666 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.22 % Allowed : 8.04 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.89 (0.19), residues: 1908 helix: 2.51 (0.16), residues: 980 sheet: 0.28 (0.36), residues: 214 loop : -0.21 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 114 TYR 0.013 0.001 TYR A 136 PHE 0.021 0.002 PHE D 40 TRP 0.013 0.001 TRP A 146 HIS 0.009 0.002 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00428 (16540) covalent geometry : angle 0.71164 (22624) SS BOND : bond 0.00605 ( 2) SS BOND : angle 2.07398 ( 4) hydrogen bonds : bond 0.11207 ( 845) hydrogen bonds : angle 4.15979 ( 2407) metal coordination : bond 0.01239 ( 8) metal coordination : angle 4.49357 ( 6) Misc. bond : bond 0.10190 ( 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 246 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 226 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 LYS cc_start: 0.8356 (mttt) cc_final: 0.7687 (tttt) REVERT: B 119 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.7823 (pptt) REVERT: C 32 ASP cc_start: 0.8598 (t70) cc_final: 0.8220 (t70) REVERT: C 190 TYR cc_start: 0.8121 (m-80) cc_final: 0.7736 (m-10) REVERT: D 76 ASP cc_start: 0.8605 (t70) cc_final: 0.8185 (t70) REVERT: F 5 GLU cc_start: 0.8300 (mm-30) cc_final: 0.8073 (mm-30) REVERT: G 31 ARG cc_start: 0.7316 (OUTLIER) cc_final: 0.6951 (tpp-160) REVERT: I 3 LYS cc_start: 0.8434 (mttt) cc_final: 0.7770 (tttt) REVERT: J 119 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.7805 (pptt) REVERT: K 32 ASP cc_start: 0.8595 (t70) cc_final: 0.8205 (t70) REVERT: K 190 TYR cc_start: 0.8112 (m-80) cc_final: 0.7813 (m-10) REVERT: K 283 MET cc_start: 0.8282 (mmm) cc_final: 0.8062 (mmm) REVERT: L 76 ASP cc_start: 0.8600 (t70) cc_final: 0.8181 (t70) REVERT: N 5 GLU cc_start: 0.8298 (mm-30) cc_final: 0.8070 (mm-30) REVERT: O 31 ARG cc_start: 0.7308 (OUTLIER) cc_final: 0.6953 (tpp-160) outliers start: 20 outliers final: 14 residues processed: 232 average time/residue: 0.8049 time to fit residues: 202.7647 Evaluate side-chains 241 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 223 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 154 ARG 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 G residue 31 ARG 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 154 ARG 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 Chi-restraints excluded: chain O residue 31 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 84 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 132 optimal weight: 0.3980 chunk 108 optimal weight: 6.9990 chunk 172 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 75 optimal weight: 0.0370 chunk 77 optimal weight: 2.9990 overall best weight: 0.8864 ------------------------------------------------------------------------------- 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 = 0.3535 r_free = 0.3535 target = 0.100454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.059241 restraints weight = 40419.250| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 2.30 r_work: 0.2633 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2536 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2527 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2527 r_free = 0.2527 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2527 r_free = 0.2527 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2527 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9133 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.126 16564 Z= 0.176 Angle : 0.661 10.123 22634 Z= 0.320 Chirality : 0.046 0.190 2530 Planarity : 0.005 0.056 2778 Dihedral : 11.028 88.764 2666 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.10 % Allowed : 8.40 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.02 (0.19), residues: 1908 helix: 2.62 (0.16), residues: 980 sheet: 0.63 (0.36), residues: 202 loop : -0.24 (0.21), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 103 TYR 0.011 0.001 TYR I 136 PHE 0.017 0.002 PHE L 40 TRP 0.014 0.001 TRP A 146 HIS 0.007 0.002 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00348 (16540) covalent geometry : angle 0.65715 (22624) SS BOND : bond 0.00468 ( 2) SS BOND : angle 1.56333 ( 4) hydrogen bonds : bond 0.09963 ( 845) hydrogen bonds : angle 4.02159 ( 2407) metal coordination : bond 0.01049 ( 8) metal coordination : angle 4.15956 ( 6) Misc. bond : bond 0.07701 ( 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 241 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 223 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 3 LYS cc_start: 0.8345 (mttt) cc_final: 0.7667 (tmtt) REVERT: B 119 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.7814 (pptt) REVERT: C 32 ASP cc_start: 0.8621 (t70) cc_final: 0.8215 (t70) REVERT: C 190 TYR cc_start: 0.8061 (m-80) cc_final: 0.7682 (m-10) REVERT: D 76 ASP cc_start: 0.8584 (t70) cc_final: 0.8152 (t70) REVERT: F 5 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7909 (mm-30) REVERT: G 31 ARG cc_start: 0.7210 (OUTLIER) cc_final: 0.6888 (tpp-160) REVERT: I 3 LYS cc_start: 0.8438 (mttt) cc_final: 0.7725 (tttt) REVERT: J 119 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.7790 (pptt) REVERT: K 32 ASP cc_start: 0.8618 (t70) cc_final: 0.8217 (t70) REVERT: K 190 TYR cc_start: 0.8052 (m-80) cc_final: 0.7751 (m-10) REVERT: L 76 ASP cc_start: 0.8579 (t70) cc_final: 0.8150 (t70) REVERT: N 5 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7907 (mm-30) REVERT: O 31 ARG cc_start: 0.7216 (OUTLIER) cc_final: 0.6927 (tpp-160) outliers start: 18 outliers final: 16 residues processed: 229 average time/residue: 0.7758 time to fit residues: 192.9760 Evaluate side-chains 239 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 219 time to evaluate : 0.635 ------------------------------------------------------------------------------- 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 154 ARG 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 G residue 3 GLU Chi-restraints excluded: chain G residue 31 ARG 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 154 ARG 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 Chi-restraints excluded: chain O residue 3 GLU Chi-restraints excluded: chain O residue 31 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 93 optimal weight: 0.5980 chunk 55 optimal weight: 7.9990 chunk 176 optimal weight: 0.6980 chunk 148 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 180 optimal weight: 8.9990 chunk 122 optimal weight: 0.5980 chunk 126 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 chunk 105 optimal weight: 0.0270 chunk 155 optimal weight: 0.5980 overall best weight: 0.5038 ------------------------------------------------------------------------------- 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 = 0.3574 r_free = 0.3574 target = 0.102986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.062834 restraints weight = 35807.696| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 2.16 r_work: 0.2681 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2583 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2609 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2609 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9018 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.117 16564 Z= 0.149 Angle : 0.616 9.687 22634 Z= 0.296 Chirality : 0.044 0.176 2530 Planarity : 0.004 0.055 2778 Dihedral : 10.662 87.739 2666 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.16 % Allowed : 8.28 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.23 (0.19), residues: 1908 helix: 2.85 (0.17), residues: 970 sheet: 0.66 (0.37), residues: 200 loop : -0.17 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG O 30 TYR 0.007 0.001 TYR O 29 PHE 0.012 0.001 PHE L 40 TRP 0.015 0.001 TRP I 146 HIS 0.005 0.001 HIS I 202 Details of bonding type rmsd covalent geometry : bond 0.00290 (16540) covalent geometry : angle 0.61302 (22624) SS BOND : bond 0.00312 ( 2) SS BOND : angle 1.03930 ( 4) hydrogen bonds : bond 0.08230 ( 845) hydrogen bonds : angle 3.80791 ( 2407) metal coordination : bond 0.00810 ( 8) metal coordination : angle 3.61247 ( 6) Misc. bond : bond 0.06663 ( 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 244 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 225 time to evaluate : 0.509 Fit side-chains revert: symmetry clash REVERT: A 3 LYS cc_start: 0.8233 (mttt) cc_final: 0.7525 (tmtt) REVERT: B 119 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.7711 (pptt) REVERT: C 32 ASP cc_start: 0.8571 (t70) cc_final: 0.8158 (t70) REVERT: C 190 TYR cc_start: 0.7983 (m-80) cc_final: 0.7713 (m-10) REVERT: D 76 ASP cc_start: 0.8526 (t70) cc_final: 0.8118 (t70) REVERT: G 31 ARG cc_start: 0.6951 (OUTLIER) cc_final: 0.6661 (tpp-160) REVERT: I 3 LYS cc_start: 0.8364 (mttt) cc_final: 0.7625 (tttt) REVERT: J 119 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.7692 (pptt) REVERT: K 32 ASP cc_start: 0.8564 (t70) cc_final: 0.8160 (t70) REVERT: K 190 TYR cc_start: 0.7968 (m-80) cc_final: 0.7676 (m-10) REVERT: K 222 LYS cc_start: 0.8755 (mptt) cc_final: 0.8553 (mppt) REVERT: L 76 ASP cc_start: 0.8521 (t70) cc_final: 0.8119 (t70) REVERT: O 31 ARG cc_start: 0.6956 (OUTLIER) cc_final: 0.6666 (tpp-160) outliers start: 19 outliers final: 11 residues processed: 231 average time/residue: 0.7263 time to fit residues: 182.7192 Evaluate side-chains 231 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 216 time to evaluate : 0.677 ------------------------------------------------------------------------------- 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 154 ARG Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain G residue 31 ARG 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 154 ARG 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 31 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 81 optimal weight: 0.9980 chunk 138 optimal weight: 0.0030 chunk 104 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 114 optimal weight: 0.3980 chunk 106 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- 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 = 0.3565 r_free = 0.3565 target = 0.102409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.061648 restraints weight = 40372.352| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 2.30 r_work: 0.2651 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2554 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2581 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2581 r_free = 0.2581 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2581 r_free = 0.2581 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2581 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9031 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.120 16564 Z= 0.155 Angle : 0.632 11.710 22634 Z= 0.301 Chirality : 0.044 0.192 2530 Planarity : 0.005 0.056 2778 Dihedral : 10.647 88.559 2666 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.91 % Allowed : 8.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.21 (0.19), residues: 1908 helix: 2.75 (0.16), residues: 982 sheet: 0.71 (0.37), residues: 200 loop : -0.11 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG O 30 TYR 0.008 0.001 TYR O 29 PHE 0.013 0.001 PHE L 40 TRP 0.014 0.001 TRP A 146 HIS 0.005 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00304 (16540) covalent geometry : angle 0.62843 (22624) SS BOND : bond 0.00335 ( 2) SS BOND : angle 1.23816 ( 4) hydrogen bonds : bond 0.08646 ( 845) hydrogen bonds : angle 3.82774 ( 2407) metal coordination : bond 0.00798 ( 8) metal coordination : angle 3.96997 ( 6) Misc. bond : bond 0.06977 ( 14) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14147.10 seconds wall clock time: 239 minutes 26.86 seconds (14366.86 seconds total)