Starting phenix.real_space_refine on Mon Nov 18 11:11:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9es7_19938/11_2024/9es7_19938.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9es7_19938/11_2024/9es7_19938.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9es7_19938/11_2024/9es7_19938.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9es7_19938/11_2024/9es7_19938.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9es7_19938/11_2024/9es7_19938.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9es7_19938/11_2024/9es7_19938.cif" } resolution = 1.94 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 12 7.16 5 Mg 2 5.21 5 S 72 5.16 5 C 10676 2.51 5 N 2506 2.21 5 O 3145 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 16413 Number of models: 1 Model: "" Number of chains: 46 Chain: "A" Number of atoms: 1697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1697 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 203} Chain: "B" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1226 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 141} Chain: "C" Number of atoms: 2168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2168 Classifications: {'peptide': 279} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 255} Chain breaks: 1 Chain: "D" Number of atoms: 1260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1260 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 152} Chain breaks: 1 Chain: "E" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 244 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Chain: "F" Number of atoms: 277 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 37, 269 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Conformer: "B" Number of residues, atoms: 37, 269 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} bond proxies already assigned to first conformer: 260 Chain: "G" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 270 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "H" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 223 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "I" Number of atoms: 1697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1697 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 203} Chain: "J" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1226 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 141} Chain: "K" Number of atoms: 2168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2168 Classifications: {'peptide': 279} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 255} Chain breaks: 1 Chain: "L" Number of atoms: 1260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1260 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 152} Chain breaks: 1 Chain: "M" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 244 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Chain: "N" Number of atoms: 277 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 37, 269 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Conformer: "B" Number of residues, atoms: 37, 269 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} bond proxies already assigned to first conformer: 260 Chain: "O" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 270 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "P" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 223 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "Q" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 219 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 1, 'TRANS': 24} Chain: "R" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 219 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 1, 'TRANS': 24} Chain: "A" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 218 Unusual residues: {'HEC': 1, 'HEM': 2, 'LMG': 1, 'UMQ': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 65 Unusual residues: {'CLA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'FES': 1, 'SQD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'UMQ': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 218 Unusual residues: {'HEC': 1, 'HEM': 2, 'LMG': 1, 'UMQ': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "J" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 65 Unusual residues: {'CLA': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'FES': 1, 'SQD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'UMQ': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "C" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Classifications: {'water': 57} Link IDs: {None: 56} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Chain: "J" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "K" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Classifications: {'water': 57} Link IDs: {None: 56} Chain: "L" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "O" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "P" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5795 SG CYS D 107 45.641 79.400 43.001 1.00 53.58 S ATOM 5931 SG CYS D 125 43.335 76.459 42.143 1.00 54.32 S ATOM 13160 SG CYS L 107 88.518 28.958 43.002 1.00 53.58 S ATOM 13296 SG CYS L 125 90.823 31.899 42.144 1.00 54.32 S Time building chain proxies: 12.70, per 1000 atoms: 0.77 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: 4.94 Conformation dependent library (CDL) restraints added in 2.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES D 202 " pdb="FE1 FES D 202 " - pdb=" ND1 HIS D 128 " pdb="FE1 FES D 202 " - pdb=" ND1 HIS D 109 " pdb="FE2 FES D 202 " - pdb=" SG CYS D 107 " pdb="FE2 FES D 202 " - pdb=" SG CYS D 125 " pdb=" FES L 202 " pdb="FE1 FES L 202 " - pdb=" ND1 HIS L 128 " pdb="FE1 FES L 202 " - pdb=" ND1 HIS L 109 " pdb="FE2 FES L 202 " - pdb=" SG CYS L 125 " pdb="FE2 FES L 202 " - pdb=" SG CYS L 107 " Number of angles added : 6 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3572 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 14 sheets defined 53.4% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'A' and resid 2 through 13 removed outlier: 4.016A pdb=" N ARG A 11 " --> pdb=" O TRP A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 22 Processing helix chain 'A' and resid 31 through 34 Processing helix chain 'A' and resid 35 through 55 Processing helix chain 'A' and resid 64 through 75 Processing helix chain 'A' and resid 78 through 107 removed outlier: 3.700A pdb=" N SER A 91 " --> pdb=" O ARG A 87 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 136 removed outlier: 3.514A pdb=" N TRP A 118 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 154 removed outlier: 3.536A pdb=" N VAL A 154 " --> pdb=" O ILE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 158 Processing helix chain 'A' and resid 161 through 171 Processing helix chain 'A' and resid 176 through 189 Processing helix chain 'A' and resid 189 through 210 Processing helix chain 'B' and resid 11 through 20 removed outlier: 3.608A pdb=" N LYS B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 58 Processing helix chain 'B' and resid 78 through 80 No H-bonds generated for 'chain 'B' and resid 78 through 80' Processing helix chain 'B' and resid 81 through 91 removed outlier: 3.560A pdb=" N ILE B 87 " --> pdb=" O PRO B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 110 removed outlier: 3.905A pdb=" N VAL B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) Proline residue: B 105 - end of helix removed outlier: 3.890A pdb=" N THR B 110 " --> pdb=" O ALA B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 115 Processing helix chain 'B' and resid 122 through 125 Processing helix chain 'B' and resid 126 through 147 Processing helix chain 'B' and resid 148 through 149 No H-bonds generated for 'chain 'B' and resid 148 through 149' Processing helix chain 'B' and resid 150 through 154 Processing helix chain 'C' and resid 2 through 9 Processing helix chain 'C' and resid 19 through 24 Processing helix chain 'C' and resid 85 through 89 Processing helix chain 'C' and resid 90 through 98 removed outlier: 3.616A pdb=" N GLY C 98 " --> pdb=" O LYS C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 283 removed outlier: 3.791A pdb=" N LYS C 277 " --> pdb=" O LYS C 273 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL C 278 " --> pdb=" O GLN C 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 40 removed outlier: 3.898A pdb=" N LEU D 28 " --> pdb=" O GLY D 24 " (cutoff:3.500A) Proline residue: D 29 - end of helix Proline residue: D 36 - end of helix Processing helix chain 'D' and resid 64 through 72 removed outlier: 3.526A pdb=" N LEU D 69 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYS D 70 " --> pdb=" O ALA D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'E' and resid 2 through 28 Processing helix chain 'F' and resid 2 through 37 Processing helix chain 'G' and resid 3 through 33 removed outlier: 3.513A pdb=" N ILE G 14 " --> pdb=" O VAL G 10 " (cutoff:3.500A) Proline residue: G 15 - end of helix Processing helix chain 'H' and resid 2 through 27 removed outlier: 3.716A pdb=" N LEU H 19 " --> pdb=" O PHE H 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 13 removed outlier: 4.016A pdb=" N ARG I 11 " --> pdb=" O TRP I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 22 Processing helix chain 'I' and resid 31 through 34 Processing helix chain 'I' and resid 35 through 55 Processing helix chain 'I' and resid 64 through 75 Processing helix chain 'I' and resid 78 through 107 removed outlier: 3.700A pdb=" N SER I 91 " --> pdb=" O ARG I 87 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL I 94 " --> pdb=" O ALA I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 136 removed outlier: 3.514A pdb=" N TRP I 118 " --> pdb=" O ARG I 114 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY I 132 " --> pdb=" O THR I 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 154 removed outlier: 3.535A pdb=" N VAL I 154 " --> pdb=" O ILE I 150 " (cutoff:3.500A) Processing helix chain 'I' and resid 155 through 158 Processing helix chain 'I' and resid 161 through 171 Processing helix chain 'I' and resid 176 through 189 Processing helix chain 'I' and resid 189 through 210 Processing helix chain 'J' and resid 11 through 20 removed outlier: 3.608A pdb=" N LYS J 20 " --> pdb=" O ALA J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 39 through 58 Processing helix chain 'J' and resid 78 through 80 No H-bonds generated for 'chain 'J' and resid 78 through 80' Processing helix chain 'J' and resid 81 through 91 removed outlier: 3.560A pdb=" N ILE J 87 " --> pdb=" O PRO J 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 110 removed outlier: 3.905A pdb=" N VAL J 104 " --> pdb=" O LEU J 100 " (cutoff:3.500A) Proline residue: J 105 - end of helix removed outlier: 3.890A pdb=" N THR J 110 " --> pdb=" O ALA J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 110 through 115 Processing helix chain 'J' and resid 122 through 125 Processing helix chain 'J' and resid 126 through 147 Processing helix chain 'J' and resid 148 through 149 No H-bonds generated for 'chain 'J' and resid 148 through 149' Processing helix chain 'J' and resid 150 through 154 Processing helix chain 'K' and resid 2 through 9 Processing helix chain 'K' and resid 19 through 24 Processing helix chain 'K' and resid 85 through 89 Processing helix chain 'K' and resid 90 through 98 removed outlier: 3.616A pdb=" N GLY K 98 " --> pdb=" O LYS K 94 " (cutoff:3.500A) Processing helix chain 'K' and resid 247 through 283 removed outlier: 3.792A pdb=" N LYS K 277 " --> pdb=" O LYS K 273 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL K 278 " --> pdb=" O GLN K 274 " (cutoff:3.500A) Processing helix chain 'L' and resid 11 through 40 removed outlier: 3.898A pdb=" N LEU L 28 " --> pdb=" O GLY L 24 " (cutoff:3.500A) Proline residue: L 29 - end of helix Proline residue: L 36 - end of helix Processing helix chain 'L' and resid 64 through 72 removed outlier: 3.526A pdb=" N LEU L 69 " --> pdb=" O ALA L 65 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYS L 70 " --> pdb=" O ALA L 66 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 85 No H-bonds generated for 'chain 'L' and resid 83 through 85' Processing helix chain 'M' and resid 2 through 28 Processing helix chain 'N' and resid 2 through 37 Processing helix chain 'O' and resid 3 through 33 removed outlier: 3.518A pdb=" N ILE O 14 " --> pdb=" O VAL O 10 " (cutoff:3.500A) Proline residue: O 15 - end of helix Processing helix chain 'P' and resid 2 through 27 removed outlier: 3.716A pdb=" N LEU P 19 " --> pdb=" O PHE P 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 33 through 43 Processing helix chain 'Q' and resid 52 through 57 Processing helix chain 'R' and resid 33 through 43 Processing helix chain 'R' and resid 52 through 57 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA2, first strand: chain 'C' and resid 32 through 34 removed outlier: 3.668A pdb=" N GLU C 82 " --> pdb=" O LEU C 131 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 38 through 39 removed outlier: 6.200A pdb=" N VAL C 71 " --> pdb=" O PRO C 117 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 59 through 60 Processing sheet with id=AA5, first strand: chain 'C' and resid 178 through 184 removed outlier: 6.927A pdb=" N ASN C 193 " --> pdb=" O LYS C 180 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE C 182 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLU C 191 " --> pdb=" O ILE C 182 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 53 through 54 removed outlier: 7.062A pdb=" N PHE D 101 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N VAL D 91 " --> pdb=" O PHE D 101 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE D 103 " --> pdb=" O TYR D 89 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR D 78 " --> pdb=" O LEU D 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 116 through 117 removed outlier: 6.634A pdb=" N GLN D 131 " --> pdb=" O VAL D 139 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 25 through 26 Processing sheet with id=AA9, first strand: chain 'K' and resid 32 through 34 removed outlier: 3.668A pdb=" N GLU K 82 " --> pdb=" O LEU K 131 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 38 through 39 removed outlier: 6.200A pdb=" N VAL K 71 " --> pdb=" O PRO K 117 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 59 through 60 Processing sheet with id=AB3, first strand: chain 'K' and resid 178 through 184 removed outlier: 6.927A pdb=" N ASN K 193 " --> pdb=" O LYS K 180 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE K 182 " --> pdb=" O GLU K 191 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLU K 191 " --> pdb=" O ILE K 182 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 53 through 54 removed outlier: 7.063A pdb=" N PHE L 101 " --> pdb=" O VAL L 91 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N VAL L 91 " --> pdb=" O PHE L 101 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE L 103 " --> pdb=" O TYR L 89 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR L 78 " --> pdb=" O LEU L 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 116 through 117 removed outlier: 6.634A pdb=" N GLN L 131 " --> pdb=" O VAL L 139 " (cutoff:3.500A) 845 hydrogen bonds defined for protein. 2407 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.81 Time building geometry restraints manager: 5.21 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: 0.00 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' and (resid 1 through 6 or resid 8 through 37)) selection = (chain 'N' and (resid 1 through 6 or resid 8 through 37)) } 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: 9.450 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 43.640 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.560 ------------------------------------------------------------------------------- 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 : 0.003 0.048 16540 Z= 0.178 Angle : 0.514 12.952 22624 Z= 0.236 Chirality : 0.042 0.131 2530 Planarity : 0.004 0.046 2778 Dihedral : 12.591 126.626 6166 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.37 % Allowed : 1.34 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.19), residues: 1908 helix: 2.16 (0.17), residues: 956 sheet: 0.32 (0.35), residues: 214 loop : 0.00 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 146 HIS 0.005 0.001 HIS A 202 PHE 0.011 0.001 PHE D 40 TYR 0.012 0.001 TYR A 136 ARG 0.003 0.000 ARG I 182 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 258 time to evaluate : 1.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 LYS cc_start: 0.8452 (mttt) cc_final: 0.8101 (tttt) REVERT: A 9 GLU cc_start: 0.8520 (tp30) cc_final: 0.8270 (tp30) REVERT: B 29 GLU cc_start: 0.8730 (tt0) cc_final: 0.8383 (tt0) REVERT: C 32 ASP cc_start: 0.8531 (t70) cc_final: 0.8289 (t70) REVERT: D 76 ASP cc_start: 0.8784 (t70) cc_final: 0.8583 (t70) REVERT: F 5 GLU cc_start: 0.8845 (tp30) cc_final: 0.8404 (tp30) REVERT: I 3 LYS cc_start: 0.8455 (mttt) cc_final: 0.8087 (tttt) REVERT: I 9 GLU cc_start: 0.8490 (tp30) cc_final: 0.8242 (tp30) REVERT: J 29 GLU cc_start: 0.8730 (tt0) cc_final: 0.8383 (tt0) REVERT: K 32 ASP cc_start: 0.8536 (t70) cc_final: 0.8288 (t70) REVERT: K 227 LEU cc_start: 0.8506 (mp) cc_final: 0.8301 (mp) REVERT: K 284 ASN cc_start: 0.8388 (p0) cc_final: 0.8188 (p0) REVERT: L 76 ASP cc_start: 0.8783 (t70) cc_final: 0.8581 (t70) REVERT: N 5 GLU cc_start: 0.8775 (tp30) cc_final: 0.8328 (tp30) REVERT: P 1 MET cc_start: 0.7286 (ptt) cc_final: 0.6795 (ptp) outliers start: 6 outliers final: 4 residues processed: 264 average time/residue: 1.6988 time to fit residues: 486.9585 Evaluate side-chains 235 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 231 time to evaluate : 2.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain K residue 154 ARG Chi-restraints excluded: chain L residue 34 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.7980 chunk 139 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 chunk 144 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 chunk 167 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 103 GLN D 135 GLN J 10 ASN K 56 GLN K 103 GLN L 135 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16540 Z= 0.217 Angle : 0.668 9.275 22624 Z= 0.328 Chirality : 0.046 0.178 2530 Planarity : 0.005 0.054 2778 Dihedral : 12.643 95.500 2666 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.85 % Allowed : 5.91 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.19), residues: 1908 helix: 2.61 (0.17), residues: 970 sheet: 0.36 (0.36), residues: 200 loop : -0.12 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 146 HIS 0.005 0.002 HIS L 72 PHE 0.014 0.002 PHE C 128 TYR 0.013 0.001 TYR A 136 ARG 0.005 0.000 ARG G 30 *********************** 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 265 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 251 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 LYS cc_start: 0.8164 (mttt) cc_final: 0.7673 (tttt) REVERT: B 29 GLU cc_start: 0.8826 (tt0) cc_final: 0.8587 (tt0) REVERT: C 32 ASP cc_start: 0.8658 (t70) cc_final: 0.8387 (t70) REVERT: D 76 ASP cc_start: 0.8816 (t70) cc_final: 0.8610 (t70) REVERT: I 3 LYS cc_start: 0.8257 (mttt) cc_final: 0.7734 (tttt) REVERT: J 29 GLU cc_start: 0.8824 (tt0) cc_final: 0.8587 (tt0) REVERT: K 32 ASP cc_start: 0.8656 (t70) cc_final: 0.8381 (t70) REVERT: K 283 MET cc_start: 0.8390 (mmm) cc_final: 0.8184 (mmm) REVERT: K 284 ASN cc_start: 0.8482 (p0) cc_final: 0.8197 (p0) REVERT: L 76 ASP cc_start: 0.8815 (t70) cc_final: 0.8614 (t70) outliers start: 14 outliers final: 12 residues processed: 255 average time/residue: 1.6324 time to fit residues: 455.0834 Evaluate side-chains 241 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 229 time to evaluate : 1.868 ------------------------------------------------------------------------------- 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 92 optimal weight: 0.0670 chunk 51 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 113 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 167 optimal weight: 6.9990 chunk 180 optimal weight: 9.9990 chunk 149 optimal weight: 3.9990 chunk 165 optimal weight: 7.9990 chunk 57 optimal weight: 7.9990 chunk 134 optimal weight: 2.9990 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 10 ASN J 10 ASN K 103 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8989 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16540 Z= 0.249 Angle : 0.695 10.603 22624 Z= 0.338 Chirality : 0.046 0.185 2530 Planarity : 0.005 0.057 2778 Dihedral : 12.554 89.847 2666 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.28 % Allowed : 6.76 % Favored : 91.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.19), residues: 1908 helix: 2.62 (0.16), residues: 972 sheet: 0.11 (0.35), residues: 214 loop : -0.28 (0.21), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 146 HIS 0.008 0.002 HIS I 202 PHE 0.019 0.002 PHE L 40 TYR 0.014 0.001 TYR I 136 ARG 0.005 0.000 ARG G 30 *********************** 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 246 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 225 time to evaluate : 1.808 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 LYS cc_start: 0.8180 (mttt) cc_final: 0.7662 (tttt) REVERT: B 119 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8045 (pptt) REVERT: C 32 ASP cc_start: 0.8644 (t70) cc_final: 0.8338 (t70) REVERT: D 76 ASP cc_start: 0.8810 (t70) cc_final: 0.8609 (t70) REVERT: I 3 LYS cc_start: 0.8237 (mttt) cc_final: 0.7664 (tmtt) REVERT: J 119 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8035 (pptt) REVERT: K 32 ASP cc_start: 0.8633 (t70) cc_final: 0.8337 (t70) outliers start: 21 outliers final: 12 residues processed: 231 average time/residue: 1.6092 time to fit residues: 406.0430 Evaluate side-chains 233 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 219 time to evaluate : 1.827 ------------------------------------------------------------------------------- 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 D residue 34 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain K residue 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 6.9990 chunk 125 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 112 optimal weight: 0.2980 chunk 167 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 159 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 103 GLN C 193 ASN J 10 ASN K 56 GLN K 193 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16540 Z= 0.207 Angle : 0.647 10.761 22624 Z= 0.311 Chirality : 0.045 0.167 2530 Planarity : 0.005 0.055 2778 Dihedral : 12.092 88.776 2666 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.58 % Allowed : 7.00 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.19), residues: 1908 helix: 2.70 (0.16), residues: 972 sheet: 0.21 (0.35), residues: 214 loop : -0.25 (0.21), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 146 HIS 0.006 0.001 HIS A 202 PHE 0.014 0.002 PHE C 128 TYR 0.011 0.001 TYR I 136 ARG 0.003 0.000 ARG O 30 *********************** 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 251 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 225 time to evaluate : 2.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 LYS cc_start: 0.8151 (mttt) cc_final: 0.7648 (tttt) REVERT: B 119 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8048 (pptt) REVERT: C 32 ASP cc_start: 0.8653 (t70) cc_final: 0.8362 (t70) REVERT: I 3 LYS cc_start: 0.8217 (mttt) cc_final: 0.7646 (tmtt) REVERT: J 119 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8047 (pptt) REVERT: K 32 ASP cc_start: 0.8648 (t70) cc_final: 0.8351 (t70) outliers start: 26 outliers final: 14 residues processed: 235 average time/residue: 1.5875 time to fit residues: 408.0993 Evaluate side-chains 236 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 220 time to evaluate : 2.010 ------------------------------------------------------------------------------- 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 G residue 3 GLU Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain K residue 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 O residue 3 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 2 optimal weight: 0.0060 chunk 132 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 151 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 159 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16540 Z= 0.228 Angle : 0.673 10.549 22624 Z= 0.323 Chirality : 0.046 0.172 2530 Planarity : 0.005 0.056 2778 Dihedral : 11.590 89.304 2666 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.34 % Allowed : 7.43 % Favored : 91.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.19), residues: 1908 helix: 2.65 (0.16), residues: 970 sheet: 0.23 (0.35), residues: 214 loop : -0.22 (0.21), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 146 HIS 0.007 0.002 HIS I 202 PHE 0.017 0.002 PHE D 40 TYR 0.012 0.001 TYR I 136 ARG 0.003 0.000 ARG G 31 *********************** 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 245 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 223 time to evaluate : 1.923 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 LYS cc_start: 0.8169 (mttt) cc_final: 0.7648 (tttt) REVERT: B 119 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8041 (pptt) REVERT: C 32 ASP cc_start: 0.8658 (t70) cc_final: 0.8359 (t70) REVERT: C 190 TYR cc_start: 0.8326 (m-80) cc_final: 0.7662 (m-10) REVERT: I 3 LYS cc_start: 0.8219 (mttt) cc_final: 0.7696 (tttt) REVERT: J 119 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8037 (pptt) REVERT: K 32 ASP cc_start: 0.8649 (t70) cc_final: 0.8350 (t70) outliers start: 22 outliers final: 14 residues processed: 233 average time/residue: 1.5996 time to fit residues: 407.2795 Evaluate side-chains 234 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 218 time to evaluate : 1.849 ------------------------------------------------------------------------------- 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 G residue 3 GLU Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain K residue 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 O residue 3 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 0.6980 chunk 160 optimal weight: 5.9990 chunk 35 optimal weight: 0.0170 chunk 104 optimal weight: 0.0870 chunk 43 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 93 optimal weight: 0.1980 overall best weight: 0.3196 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16540 Z= 0.171 Angle : 0.579 9.452 22624 Z= 0.278 Chirality : 0.043 0.163 2530 Planarity : 0.004 0.055 2778 Dihedral : 10.793 87.842 2666 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.97 % Allowed : 7.92 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.19), residues: 1908 helix: 2.99 (0.17), residues: 968 sheet: 0.78 (0.36), residues: 208 loop : -0.12 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 146 HIS 0.003 0.001 HIS D 151 PHE 0.010 0.001 PHE E 2 TYR 0.007 0.001 TYR O 29 ARG 0.002 0.000 ARG G 31 *********************** 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: 16 poor density : 230 time to evaluate : 1.740 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 LYS cc_start: 0.8134 (mttt) cc_final: 0.7598 (tmtt) REVERT: B 119 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.7980 (pptt) REVERT: C 32 ASP cc_start: 0.8658 (t70) cc_final: 0.8371 (t70) REVERT: C 190 TYR cc_start: 0.8200 (m-80) cc_final: 0.7612 (m-10) REVERT: C 283 MET cc_start: 0.8071 (mmm) cc_final: 0.7861 (mmm) REVERT: I 3 LYS cc_start: 0.8207 (mttt) cc_final: 0.7635 (tttt) REVERT: J 119 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.7975 (pptt) REVERT: K 32 ASP cc_start: 0.8655 (t70) cc_final: 0.8371 (t70) REVERT: K 283 MET cc_start: 0.8097 (mmm) cc_final: 0.7884 (mmm) outliers start: 16 outliers final: 12 residues processed: 236 average time/residue: 1.5544 time to fit residues: 401.1289 Evaluate side-chains 236 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 222 time to evaluate : 1.876 ------------------------------------------------------------------------------- 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 3 GLU Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain K residue 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 177 optimal weight: 0.5980 chunk 110 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16540 Z= 0.198 Angle : 0.622 10.620 22624 Z= 0.299 Chirality : 0.044 0.167 2530 Planarity : 0.005 0.055 2778 Dihedral : 10.836 89.229 2666 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.28 % Allowed : 8.04 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.19), residues: 1908 helix: 2.81 (0.16), residues: 982 sheet: 0.71 (0.36), residues: 200 loop : -0.14 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 146 HIS 0.006 0.001 HIS A 202 PHE 0.014 0.001 PHE D 40 TYR 0.008 0.001 TYR O 29 ARG 0.002 0.000 ARG B 126 *********************** 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 245 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 224 time to evaluate : 1.815 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 LYS cc_start: 0.8163 (mttt) cc_final: 0.7635 (tmtt) REVERT: B 119 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8019 (pptt) REVERT: C 32 ASP cc_start: 0.8664 (t70) cc_final: 0.8381 (t70) REVERT: C 190 TYR cc_start: 0.8207 (m-80) cc_final: 0.7696 (m-10) REVERT: I 3 LYS cc_start: 0.8229 (mttt) cc_final: 0.7662 (tttt) REVERT: J 119 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8012 (pptt) REVERT: K 32 ASP cc_start: 0.8663 (t70) cc_final: 0.8385 (t70) outliers start: 21 outliers final: 15 residues processed: 232 average time/residue: 1.5996 time to fit residues: 404.9788 Evaluate side-chains 237 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 220 time to evaluate : 1.873 ------------------------------------------------------------------------------- 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 G residue 3 GLU Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain K residue 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 105 optimal weight: 0.0970 chunk 53 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 120 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 161 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16540 Z= 0.222 Angle : 0.651 10.319 22624 Z= 0.315 Chirality : 0.045 0.167 2530 Planarity : 0.005 0.056 2778 Dihedral : 10.890 89.363 2666 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.28 % Allowed : 7.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.19), residues: 1908 helix: 2.70 (0.16), residues: 982 sheet: 0.69 (0.36), residues: 200 loop : -0.17 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 146 HIS 0.007 0.001 HIS A 202 PHE 0.017 0.002 PHE D 40 TYR 0.009 0.001 TYR I 136 ARG 0.002 0.000 ARG A 114 *********************** 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: 21 poor density : 225 time to evaluate : 1.837 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 LYS cc_start: 0.8159 (mttt) cc_final: 0.7649 (tmtt) REVERT: B 119 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8038 (pptt) REVERT: C 32 ASP cc_start: 0.8658 (t70) cc_final: 0.8371 (t70) REVERT: I 3 LYS cc_start: 0.8238 (mttt) cc_final: 0.7669 (tttt) REVERT: J 119 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8036 (pptt) REVERT: K 32 ASP cc_start: 0.8653 (t70) cc_final: 0.8369 (t70) outliers start: 21 outliers final: 15 residues processed: 233 average time/residue: 1.6442 time to fit residues: 418.8113 Evaluate side-chains 235 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 218 time to evaluate : 1.987 ------------------------------------------------------------------------------- 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 H residue 1 MET 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 165 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 129 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 164 optimal weight: 0.7980 chunk 108 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16540 Z= 0.214 Angle : 0.649 10.188 22624 Z= 0.313 Chirality : 0.045 0.173 2530 Planarity : 0.005 0.054 2778 Dihedral : 10.846 88.866 2666 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.10 % Allowed : 8.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.19), residues: 1908 helix: 2.68 (0.16), residues: 982 sheet: 0.66 (0.36), residues: 200 loop : -0.17 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 146 HIS 0.006 0.001 HIS I 202 PHE 0.016 0.002 PHE D 40 TYR 0.022 0.001 TYR K 190 ARG 0.002 0.000 ARG A 114 *********************** 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 244 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 226 time to evaluate : 1.818 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 LYS cc_start: 0.8148 (mttt) cc_final: 0.7635 (tmtt) REVERT: B 119 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8052 (pptt) REVERT: C 32 ASP cc_start: 0.8663 (t70) cc_final: 0.8372 (t70) REVERT: I 3 LYS cc_start: 0.8236 (mttt) cc_final: 0.7662 (tttt) REVERT: J 119 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8047 (pptt) REVERT: K 32 ASP cc_start: 0.8658 (t70) cc_final: 0.8369 (t70) outliers start: 18 outliers final: 13 residues processed: 232 average time/residue: 1.6146 time to fit residues: 408.8194 Evaluate side-chains 237 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 222 time to evaluate : 1.646 ------------------------------------------------------------------------------- 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 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 O residue 3 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 121 optimal weight: 0.0020 chunk 183 optimal weight: 0.9990 chunk 168 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 15 optimal weight: 0.0770 chunk 112 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 chunk 115 optimal weight: 0.9980 overall best weight: 0.4746 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16540 Z= 0.184 Angle : 0.603 9.933 22624 Z= 0.291 Chirality : 0.044 0.167 2530 Planarity : 0.004 0.056 2778 Dihedral : 10.588 88.062 2666 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.97 % Allowed : 8.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.19), residues: 1908 helix: 2.87 (0.16), residues: 970 sheet: 0.44 (0.36), residues: 214 loop : -0.14 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 146 HIS 0.004 0.001 HIS I 202 PHE 0.011 0.001 PHE I 52 TYR 0.020 0.001 TYR K 190 ARG 0.002 0.000 ARG O 30 ********************** 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 242 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 226 time to evaluate : 1.883 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 LYS cc_start: 0.8127 (mttt) cc_final: 0.7603 (tmtt) REVERT: B 119 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8023 (pptt) REVERT: C 32 ASP cc_start: 0.8655 (t70) cc_final: 0.8379 (t70) REVERT: I 3 LYS cc_start: 0.8219 (mttt) cc_final: 0.7622 (tttt) REVERT: J 119 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8017 (pptt) REVERT: K 32 ASP cc_start: 0.8651 (t70) cc_final: 0.8381 (t70) outliers start: 16 outliers final: 14 residues processed: 232 average time/residue: 1.5895 time to fit residues: 402.7841 Evaluate side-chains 235 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 219 time to evaluate : 1.704 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.0670 chunk 44 optimal weight: 0.1980 chunk 134 optimal weight: 0.0570 chunk 21 optimal weight: 6.9990 chunk 40 optimal weight: 0.6980 chunk 146 optimal weight: 6.9990 chunk 61 optimal weight: 0.6980 chunk 150 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 overall best weight: 0.3436 ------------------------------------------------------------------------------- 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 = 0.3609 r_free = 0.3609 target = 0.105218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.065139 restraints weight = 40696.683| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 2.31 r_work: 0.2730 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2661 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2661 r_free = 0.2661 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2661 r_free = 0.2661 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2661 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16540 Z= 0.173 Angle : 0.594 10.670 22624 Z= 0.282 Chirality : 0.043 0.175 2530 Planarity : 0.004 0.053 2778 Dihedral : 10.367 88.497 2666 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.97 % Allowed : 8.83 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.19), residues: 1908 helix: 2.96 (0.17), residues: 972 sheet: 0.58 (0.36), residues: 214 loop : -0.07 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 146 HIS 0.003 0.001 HIS L 151 PHE 0.010 0.001 PHE K 267 TYR 0.026 0.001 TYR K 190 ARG 0.002 0.000 ARG O 30 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8515.14 seconds wall clock time: 152 minutes 37.72 seconds (9157.72 seconds total)