Starting phenix.real_space_refine on Thu Feb 15 00:52:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f95_4196/02_2024/6f95_4196_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f95_4196/02_2024/6f95_4196.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f95_4196/02_2024/6f95_4196.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f95_4196/02_2024/6f95_4196.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f95_4196/02_2024/6f95_4196_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f95_4196/02_2024/6f95_4196_updated.pdb" } resolution = 3.44 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= 0.010 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 P 10 5.49 5 Mg 5 5.21 5 S 65 5.16 5 C 6750 2.51 5 N 1690 2.21 5 O 2115 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10635 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2099 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 5, 'TRANS': 261} Chain: "B" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2099 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 5, 'TRANS': 261} Chain: "C" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2099 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 5, 'TRANS': 261} Chain: "D" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2099 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 5, 'TRANS': 261} Chain: "E" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2099 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 5, 'TRANS': 261} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.18, per 1000 atoms: 0.58 Number of scatterers: 10635 At special positions: 0 Unit cell: (94.16, 92.02, 175.48, 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) S 65 16.00 P 10 15.00 Mg 5 11.99 O 2115 8.00 N 1690 7.00 C 6750 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.04 Conformation dependent library (CDL) restraints added in 1.9 seconds 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2430 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 20 sheets defined 22.1% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'A' and resid 59 through 65 removed outlier: 4.026A pdb=" N LYS A 62 " --> pdb=" O GLU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 71 No H-bonds generated for 'chain 'A' and resid 69 through 71' Processing helix chain 'A' and resid 85 through 96 Processing helix chain 'A' and resid 118 through 120 No H-bonds generated for 'chain 'A' and resid 118 through 120' Processing helix chain 'A' and resid 153 through 158 removed outlier: 3.825A pdb=" N ASN A 157 " --> pdb=" O GLY A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 211 removed outlier: 3.829A pdb=" N LYS A 206 " --> pdb=" O MET A 202 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N THR A 207 " --> pdb=" O ASP A 203 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS A 210 " --> pdb=" O LYS A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 235 removed outlier: 4.122A pdb=" N GLU A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N CYS A 234 " --> pdb=" O GLU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 263 removed outlier: 3.685A pdb=" N VAL A 257 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ASN A 258 " --> pdb=" O TYR A 255 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL A 260 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLY A 261 " --> pdb=" O ASN A 258 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 262 " --> pdb=" O SER A 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 65 removed outlier: 4.026A pdb=" N LYS B 62 " --> pdb=" O GLU B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 71 No H-bonds generated for 'chain 'B' and resid 69 through 71' Processing helix chain 'B' and resid 85 through 96 Processing helix chain 'B' and resid 118 through 120 No H-bonds generated for 'chain 'B' and resid 118 through 120' Processing helix chain 'B' and resid 153 through 158 removed outlier: 3.826A pdb=" N ASN B 157 " --> pdb=" O GLY B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 211 removed outlier: 3.830A pdb=" N LYS B 206 " --> pdb=" O MET B 202 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N THR B 207 " --> pdb=" O ASP B 203 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS B 210 " --> pdb=" O LYS B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 235 removed outlier: 4.122A pdb=" N GLU B 233 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 263 removed outlier: 3.687A pdb=" N VAL B 257 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ASN B 258 " --> pdb=" O TYR B 255 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL B 260 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLY B 261 " --> pdb=" O ASN B 258 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 262 " --> pdb=" O SER B 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 65 removed outlier: 4.026A pdb=" N LYS C 62 " --> pdb=" O GLU C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 71 No H-bonds generated for 'chain 'C' and resid 69 through 71' Processing helix chain 'C' and resid 85 through 96 Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 153 through 158 removed outlier: 3.826A pdb=" N ASN C 157 " --> pdb=" O GLY C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 211 removed outlier: 3.829A pdb=" N LYS C 206 " --> pdb=" O MET C 202 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR C 207 " --> pdb=" O ASP C 203 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 235 removed outlier: 4.121A pdb=" N GLU C 233 " --> pdb=" O GLU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 263 removed outlier: 3.685A pdb=" N VAL C 257 " --> pdb=" O SER C 254 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ASN C 258 " --> pdb=" O TYR C 255 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL C 260 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLY C 261 " --> pdb=" O ASN C 258 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU C 262 " --> pdb=" O SER C 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 65 removed outlier: 4.025A pdb=" N LYS D 62 " --> pdb=" O GLU D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 71 No H-bonds generated for 'chain 'D' and resid 69 through 71' Processing helix chain 'D' and resid 85 through 96 Processing helix chain 'D' and resid 118 through 120 No H-bonds generated for 'chain 'D' and resid 118 through 120' Processing helix chain 'D' and resid 153 through 158 removed outlier: 3.826A pdb=" N ASN D 157 " --> pdb=" O GLY D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 211 removed outlier: 3.829A pdb=" N LYS D 206 " --> pdb=" O MET D 202 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N THR D 207 " --> pdb=" O ASP D 203 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS D 210 " --> pdb=" O LYS D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 235 removed outlier: 4.121A pdb=" N GLU D 233 " --> pdb=" O GLU D 229 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS D 234 " --> pdb=" O GLU D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 263 removed outlier: 3.686A pdb=" N VAL D 257 " --> pdb=" O SER D 254 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ASN D 258 " --> pdb=" O TYR D 255 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL D 260 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLY D 261 " --> pdb=" O ASN D 258 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU D 262 " --> pdb=" O SER D 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 65 removed outlier: 4.026A pdb=" N LYS E 62 " --> pdb=" O GLU E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 71 No H-bonds generated for 'chain 'E' and resid 69 through 71' Processing helix chain 'E' and resid 85 through 96 Processing helix chain 'E' and resid 118 through 120 No H-bonds generated for 'chain 'E' and resid 118 through 120' Processing helix chain 'E' and resid 153 through 158 removed outlier: 3.826A pdb=" N ASN E 157 " --> pdb=" O GLY E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 211 removed outlier: 3.829A pdb=" N LYS E 206 " --> pdb=" O MET E 202 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N THR E 207 " --> pdb=" O ASP E 203 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS E 210 " --> pdb=" O LYS E 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 235 removed outlier: 4.122A pdb=" N GLU E 233 " --> pdb=" O GLU E 229 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N CYS E 234 " --> pdb=" O GLU E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 263 removed outlier: 3.687A pdb=" N VAL E 257 " --> pdb=" O SER E 254 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ASN E 258 " --> pdb=" O TYR E 255 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL E 260 " --> pdb=" O VAL E 257 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLY E 261 " --> pdb=" O ASN E 258 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU E 262 " --> pdb=" O SER E 259 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 25 through 30 removed outlier: 3.848A pdb=" N THR A 109 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ILE A 9 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N THR A 142 " --> pdb=" O PHE A 104 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU A 106 " --> pdb=" O THR A 142 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N HIS A 144 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 12.110A pdb=" N LEU A 108 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 9.146A pdb=" N ILE A 146 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 10.868A pdb=" N CYS A 110 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N MET A 148 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 45 through 48 Processing sheet with id= C, first strand: chain 'A' and resid 130 through 134 Processing sheet with id= D, first strand: chain 'A' and resid 220 through 225 Processing sheet with id= E, first strand: chain 'B' and resid 25 through 30 removed outlier: 3.848A pdb=" N THR B 109 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ILE B 9 " --> pdb=" O THR B 109 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N THR B 142 " --> pdb=" O PHE B 104 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU B 106 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N HIS B 144 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 12.108A pdb=" N LEU B 108 " --> pdb=" O HIS B 144 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N ILE B 146 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 10.868A pdb=" N CYS B 110 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N MET B 148 " --> pdb=" O CYS B 110 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 45 through 48 Processing sheet with id= G, first strand: chain 'B' and resid 130 through 134 Processing sheet with id= H, first strand: chain 'B' and resid 220 through 225 Processing sheet with id= I, first strand: chain 'C' and resid 25 through 30 removed outlier: 3.847A pdb=" N THR C 109 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ILE C 9 " --> pdb=" O THR C 109 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N THR C 142 " --> pdb=" O PHE C 104 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU C 106 " --> pdb=" O THR C 142 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N HIS C 144 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 12.108A pdb=" N LEU C 108 " --> pdb=" O HIS C 144 " (cutoff:3.500A) removed outlier: 9.146A pdb=" N ILE C 146 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 10.868A pdb=" N CYS C 110 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 8.891A pdb=" N MET C 148 " --> pdb=" O CYS C 110 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 45 through 48 Processing sheet with id= K, first strand: chain 'C' and resid 130 through 134 Processing sheet with id= L, first strand: chain 'C' and resid 220 through 225 Processing sheet with id= M, first strand: chain 'D' and resid 25 through 30 removed outlier: 3.849A pdb=" N THR D 109 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ILE D 9 " --> pdb=" O THR D 109 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N THR D 142 " --> pdb=" O PHE D 104 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N LEU D 106 " --> pdb=" O THR D 142 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N HIS D 144 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 12.109A pdb=" N LEU D 108 " --> pdb=" O HIS D 144 " (cutoff:3.500A) removed outlier: 9.146A pdb=" N ILE D 146 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 10.868A pdb=" N CYS D 110 " --> pdb=" O ILE D 146 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N MET D 148 " --> pdb=" O CYS D 110 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 45 through 48 Processing sheet with id= O, first strand: chain 'D' and resid 130 through 134 Processing sheet with id= P, first strand: chain 'D' and resid 220 through 225 Processing sheet with id= Q, first strand: chain 'E' and resid 25 through 30 removed outlier: 3.849A pdb=" N THR E 109 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ILE E 9 " --> pdb=" O THR E 109 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N THR E 142 " --> pdb=" O PHE E 104 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU E 106 " --> pdb=" O THR E 142 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N HIS E 144 " --> pdb=" O LEU E 106 " (cutoff:3.500A) removed outlier: 12.109A pdb=" N LEU E 108 " --> pdb=" O HIS E 144 " (cutoff:3.500A) removed outlier: 9.145A pdb=" N ILE E 146 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 10.868A pdb=" N CYS E 110 " --> pdb=" O ILE E 146 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N MET E 148 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 45 through 48 Processing sheet with id= S, first strand: chain 'E' and resid 130 through 134 Processing sheet with id= T, first strand: chain 'E' and resid 220 through 225 272 hydrogen bonds defined for protein. 636 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: 2.58 Time building geometry restraints manager: 4.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3333 1.34 - 1.46: 2319 1.46 - 1.57: 5078 1.57 - 1.69: 15 1.69 - 1.81: 105 Bond restraints: 10850 Sorted by residual: bond pdb=" CB ARG A 87 " pdb=" CG ARG A 87 " ideal model delta sigma weight residual 1.520 1.478 0.042 3.00e-02 1.11e+03 1.98e+00 bond pdb=" CB ARG B 87 " pdb=" CG ARG B 87 " ideal model delta sigma weight residual 1.520 1.478 0.042 3.00e-02 1.11e+03 1.95e+00 bond pdb=" CB ARG C 87 " pdb=" CG ARG C 87 " ideal model delta sigma weight residual 1.520 1.478 0.042 3.00e-02 1.11e+03 1.93e+00 bond pdb=" CB ARG E 87 " pdb=" CG ARG E 87 " ideal model delta sigma weight residual 1.520 1.479 0.041 3.00e-02 1.11e+03 1.88e+00 bond pdb=" CB ARG D 87 " pdb=" CG ARG D 87 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.81e+00 ... (remaining 10845 not shown) Histogram of bond angle deviations from ideal: 100.35 - 107.46: 333 107.46 - 114.56: 6146 114.56 - 121.67: 5680 121.67 - 128.77: 2476 128.77 - 135.88: 40 Bond angle restraints: 14675 Sorted by residual: angle pdb=" C ARG B 78 " pdb=" N LYS B 79 " pdb=" CA LYS B 79 " ideal model delta sigma weight residual 121.05 125.51 -4.46 1.43e+00 4.89e-01 9.71e+00 angle pdb=" C ARG A 78 " pdb=" N LYS A 79 " pdb=" CA LYS A 79 " ideal model delta sigma weight residual 121.05 125.49 -4.44 1.43e+00 4.89e-01 9.63e+00 angle pdb=" C ARG E 78 " pdb=" N LYS E 79 " pdb=" CA LYS E 79 " ideal model delta sigma weight residual 121.05 125.47 -4.42 1.43e+00 4.89e-01 9.54e+00 angle pdb=" C ARG D 78 " pdb=" N LYS D 79 " pdb=" CA LYS D 79 " ideal model delta sigma weight residual 121.05 125.46 -4.41 1.43e+00 4.89e-01 9.51e+00 angle pdb=" C ARG C 78 " pdb=" N LYS C 79 " pdb=" CA LYS C 79 " ideal model delta sigma weight residual 121.05 125.43 -4.38 1.43e+00 4.89e-01 9.40e+00 ... (remaining 14670 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.37: 6304 29.37 - 58.74: 51 58.74 - 88.11: 0 88.11 - 117.48: 5 117.48 - 146.84: 10 Dihedral angle restraints: 6370 sinusoidal: 2510 harmonic: 3860 Sorted by residual: dihedral pdb=" O1B ADP E 302 " pdb=" O3A ADP E 302 " pdb=" PB ADP E 302 " pdb=" PA ADP E 302 " ideal model delta sinusoidal sigma weight residual 300.00 153.15 146.84 1 2.00e+01 2.50e-03 4.41e+01 dihedral pdb=" O1B ADP C 302 " pdb=" O3A ADP C 302 " pdb=" PB ADP C 302 " pdb=" PA ADP C 302 " ideal model delta sinusoidal sigma weight residual 300.00 153.21 146.79 1 2.00e+01 2.50e-03 4.41e+01 dihedral pdb=" O1B ADP A 302 " pdb=" O3A ADP A 302 " pdb=" PB ADP A 302 " pdb=" PA ADP A 302 " ideal model delta sinusoidal sigma weight residual 300.00 153.21 146.78 1 2.00e+01 2.50e-03 4.41e+01 ... (remaining 6367 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 991 0.044 - 0.089: 436 0.089 - 0.133: 154 0.133 - 0.177: 24 0.177 - 0.222: 5 Chirality restraints: 1610 Sorted by residual: chirality pdb=" CB VAL C 26 " pdb=" CA VAL C 26 " pdb=" CG1 VAL C 26 " pdb=" CG2 VAL C 26 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CB VAL B 26 " pdb=" CA VAL B 26 " pdb=" CG1 VAL B 26 " pdb=" CG2 VAL B 26 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CB VAL E 26 " pdb=" CA VAL E 26 " pdb=" CG1 VAL E 26 " pdb=" CG2 VAL E 26 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1607 not shown) Planarity restraints: 1850 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 252 " 0.035 5.00e-02 4.00e+02 5.25e-02 4.41e+00 pdb=" N PRO B 253 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 253 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 253 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS E 252 " -0.035 5.00e-02 4.00e+02 5.24e-02 4.40e+00 pdb=" N PRO E 253 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO E 253 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 253 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 252 " 0.035 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO D 253 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO D 253 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 253 " 0.029 5.00e-02 4.00e+02 ... (remaining 1847 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1840 2.76 - 3.29: 9044 3.29 - 3.83: 17087 3.83 - 4.36: 20663 4.36 - 4.90: 35639 Nonbonded interactions: 84273 Sorted by model distance: nonbonded pdb=" NZ LYS E 15 " pdb=" O3B ADP E 302 " model vdw 2.224 2.520 nonbonded pdb=" OE2 GLU C 131 " pdb=" OG SER C 138 " model vdw 2.296 2.440 nonbonded pdb=" OE2 GLU D 131 " pdb=" OG SER D 138 " model vdw 2.297 2.440 nonbonded pdb=" OE2 GLU E 131 " pdb=" OG SER E 138 " model vdw 2.297 2.440 nonbonded pdb=" OE2 GLU A 131 " pdb=" OG SER A 138 " model vdw 2.298 2.440 ... (remaining 84268 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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=1.00 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: 2.090 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: 9.770 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 30.230 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.060 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 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 : 0.007 0.044 10850 Z= 0.477 Angle : 0.894 7.509 14675 Z= 0.459 Chirality : 0.055 0.222 1610 Planarity : 0.005 0.053 1850 Dihedral : 12.029 146.845 3940 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 0.44 % Allowed : 0.44 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.24 (0.19), residues: 1325 helix: -4.70 (0.08), residues: 300 sheet: -1.66 (0.28), residues: 340 loop : -2.49 (0.20), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS D 81 PHE 0.028 0.003 PHE C 126 TYR 0.032 0.003 TYR A 56 ARG 0.006 0.001 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 338 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 THR cc_start: 0.9292 (p) cc_final: 0.8134 (p) REVERT: A 62 LYS cc_start: 0.8850 (pttt) cc_final: 0.8548 (ptmm) REVERT: A 82 MET cc_start: 0.6346 (mmm) cc_final: 0.5678 (pmm) REVERT: A 97 LYS cc_start: 0.8550 (mmmm) cc_final: 0.8300 (ttmm) REVERT: A 161 SER cc_start: 0.8889 (t) cc_final: 0.8675 (p) REVERT: A 258 ASN cc_start: 0.8859 (m-40) cc_final: 0.8530 (m-40) REVERT: B 45 MET cc_start: 0.8875 (ptp) cc_final: 0.8587 (ptp) REVERT: B 82 MET cc_start: 0.6037 (mmm) cc_final: 0.5784 (pmm) REVERT: B 142 THR cc_start: 0.7956 (m) cc_final: 0.7551 (p) REVERT: B 248 LEU cc_start: 0.8679 (mt) cc_final: 0.8022 (mp) REVERT: C 85 GLN cc_start: 0.8387 (mt0) cc_final: 0.8110 (mt0) REVERT: C 202 MET cc_start: 0.8008 (tpp) cc_final: 0.7431 (tpp) REVERT: C 254 SER cc_start: 0.8679 (m) cc_final: 0.8344 (t) REVERT: D 20 ASP cc_start: 0.6746 (p0) cc_final: 0.6475 (p0) REVERT: D 72 MET cc_start: 0.7858 (ptp) cc_final: 0.7469 (ptp) REVERT: D 82 MET cc_start: 0.6458 (mmm) cc_final: 0.6242 (pmm) REVERT: D 186 LYS cc_start: 0.8054 (ttmt) cc_final: 0.7816 (ttmm) REVERT: D 188 ASP cc_start: 0.6909 (m-30) cc_final: 0.6428 (t0) REVERT: D 256 TYR cc_start: 0.8210 (m-80) cc_final: 0.7955 (m-80) REVERT: E 6 VAL cc_start: 0.9552 (OUTLIER) cc_final: 0.9305 (m) REVERT: E 112 TYR cc_start: 0.8702 (t80) cc_final: 0.8146 (t80) REVERT: E 214 ASN cc_start: 0.8743 (p0) cc_final: 0.8527 (p0) REVERT: E 233 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7156 (mt-10) REVERT: E 254 SER cc_start: 0.8843 (m) cc_final: 0.8531 (p) outliers start: 5 outliers final: 1 residues processed: 343 average time/residue: 0.2431 time to fit residues: 115.2142 Evaluate side-chains 174 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 172 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain E residue 6 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 118 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN A 125 HIS A 144 HIS ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 ASN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 11 ASN C 76 ASN C 125 HIS D 11 ASN D 125 HIS E 11 ASN E 85 GLN E 125 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10850 Z= 0.256 Angle : 0.646 7.729 14675 Z= 0.314 Chirality : 0.046 0.139 1610 Planarity : 0.005 0.044 1850 Dihedral : 11.945 118.373 1517 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 3.23 % Allowed : 8.65 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.12 (0.21), residues: 1325 helix: -3.59 (0.20), residues: 255 sheet: -1.63 (0.25), residues: 385 loop : -1.61 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 190 PHE 0.011 0.001 PHE B 126 TYR 0.017 0.002 TYR E 56 ARG 0.009 0.001 ARG D 130 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 186 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.6921 (mmm) cc_final: 0.5832 (pmm) REVERT: B 82 MET cc_start: 0.6111 (mmm) cc_final: 0.5852 (pmm) REVERT: B 142 THR cc_start: 0.8145 (m) cc_final: 0.7752 (p) REVERT: B 206 LYS cc_start: 0.8461 (mttt) cc_final: 0.8111 (mtmm) REVERT: B 248 LEU cc_start: 0.8461 (mt) cc_final: 0.7927 (mt) REVERT: C 115 MET cc_start: 0.7057 (mmt) cc_final: 0.6851 (tpp) REVERT: C 202 MET cc_start: 0.8221 (tpp) cc_final: 0.7861 (tpp) REVERT: C 254 SER cc_start: 0.8537 (m) cc_final: 0.8207 (t) REVERT: D 85 GLN cc_start: 0.8173 (mt0) cc_final: 0.7958 (mt0) REVERT: D 186 LYS cc_start: 0.8541 (ttmt) cc_final: 0.8316 (ttmm) REVERT: D 256 TYR cc_start: 0.8487 (m-80) cc_final: 0.8190 (m-80) outliers start: 37 outliers final: 28 residues processed: 217 average time/residue: 0.2363 time to fit residues: 71.9495 Evaluate side-chains 170 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 142 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 144 HIS Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 216 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 0.0060 chunk 36 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 117 optimal weight: 0.4980 chunk 40 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS B 76 ASN B 190 HIS B 193 ASN C 190 HIS E 85 GLN E 124 GLN E 163 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10850 Z= 0.168 Angle : 0.584 7.262 14675 Z= 0.277 Chirality : 0.044 0.133 1610 Planarity : 0.004 0.035 1850 Dihedral : 10.922 113.919 1516 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 4.80 % Allowed : 10.31 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.61 (0.21), residues: 1325 helix: -2.90 (0.24), residues: 260 sheet: -1.23 (0.25), residues: 385 loop : -1.45 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 81 PHE 0.011 0.001 PHE D 126 TYR 0.019 0.001 TYR E 266 ARG 0.006 0.001 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 167 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLU cc_start: 0.3397 (OUTLIER) cc_final: 0.1884 (mt-10) REVERT: A 68 ARG cc_start: 0.8620 (ptt90) cc_final: 0.8419 (ptt90) REVERT: A 82 MET cc_start: 0.6765 (mmm) cc_final: 0.5849 (pmm) REVERT: B 82 MET cc_start: 0.6379 (mmm) cc_final: 0.5915 (pmm) REVERT: B 130 ARG cc_start: 0.7294 (mmt-90) cc_final: 0.7084 (mtp85) REVERT: B 206 LYS cc_start: 0.8438 (mttt) cc_final: 0.8213 (mtmm) REVERT: C 82 MET cc_start: 0.6887 (pmm) cc_final: 0.4884 (ptm) REVERT: C 202 MET cc_start: 0.8318 (tpp) cc_final: 0.8028 (tpp) REVERT: C 254 SER cc_start: 0.8351 (m) cc_final: 0.8009 (t) REVERT: D 82 MET cc_start: 0.6121 (pmm) cc_final: 0.4736 (ptt) REVERT: D 106 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8922 (mp) REVERT: D 186 LYS cc_start: 0.8638 (ttmt) cc_final: 0.8417 (tptt) REVERT: D 256 TYR cc_start: 0.8559 (m-80) cc_final: 0.8312 (m-80) outliers start: 55 outliers final: 37 residues processed: 206 average time/residue: 0.2286 time to fit residues: 66.7093 Evaluate side-chains 183 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 144 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 144 HIS Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 265 LYS Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 23 GLN Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 144 HIS Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 251 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 13 optimal weight: 0.2980 chunk 56 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 118 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS B 190 HIS D 190 HIS E 124 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10850 Z= 0.193 Angle : 0.574 7.201 14675 Z= 0.273 Chirality : 0.045 0.139 1610 Planarity : 0.003 0.036 1850 Dihedral : 10.632 115.259 1516 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 4.63 % Allowed : 12.14 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.27 (0.22), residues: 1325 helix: -2.48 (0.26), residues: 265 sheet: -0.80 (0.24), residues: 425 loop : -1.45 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS B 190 PHE 0.010 0.001 PHE D 126 TYR 0.015 0.001 TYR E 56 ARG 0.006 0.001 ARG D 130 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 148 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLU cc_start: 0.3313 (OUTLIER) cc_final: 0.1114 (pt0) REVERT: A 162 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8343 (mt) REVERT: B 82 MET cc_start: 0.6456 (mmm) cc_final: 0.5931 (pmm) REVERT: B 87 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7756 (mtm-85) REVERT: B 130 ARG cc_start: 0.7416 (mmt-90) cc_final: 0.7149 (mtp85) REVERT: B 202 MET cc_start: 0.7612 (tpp) cc_final: 0.7312 (tpp) REVERT: B 248 LEU cc_start: 0.8560 (mt) cc_final: 0.7685 (mp) REVERT: C 82 MET cc_start: 0.7037 (pmm) cc_final: 0.6405 (ptt) REVERT: C 202 MET cc_start: 0.8283 (tpp) cc_final: 0.7942 (tpp) REVERT: C 254 SER cc_start: 0.8330 (m) cc_final: 0.7966 (t) REVERT: D 46 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7427 (mt-10) REVERT: D 82 MET cc_start: 0.6385 (pmm) cc_final: 0.6069 (pmm) REVERT: D 106 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8863 (mp) REVERT: D 147 VAL cc_start: 0.8603 (t) cc_final: 0.8385 (m) REVERT: D 186 LYS cc_start: 0.8660 (ttmt) cc_final: 0.8421 (tppt) REVERT: D 256 TYR cc_start: 0.8709 (m-80) cc_final: 0.8464 (m-80) REVERT: E 47 ARG cc_start: 0.8463 (ttt180) cc_final: 0.8191 (ttt-90) outliers start: 53 outliers final: 42 residues processed: 184 average time/residue: 0.2924 time to fit residues: 73.8470 Evaluate side-chains 181 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 135 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 265 LYS Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 23 GLN Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 144 HIS Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 160 ASP Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 251 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 93 optimal weight: 0.0170 chunk 51 optimal weight: 0.0270 chunk 107 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 chunk 0 optimal weight: 0.6980 chunk 64 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS B 190 HIS C 190 HIS D 190 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10850 Z= 0.130 Angle : 0.543 7.167 14675 Z= 0.254 Chirality : 0.044 0.126 1610 Planarity : 0.003 0.033 1850 Dihedral : 9.815 105.790 1516 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.93 % Allowed : 13.19 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.22), residues: 1325 helix: -2.22 (0.27), residues: 265 sheet: -0.58 (0.25), residues: 425 loop : -1.37 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 190 PHE 0.010 0.001 PHE C 158 TYR 0.013 0.001 TYR E 56 ARG 0.007 0.000 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 153 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLU cc_start: 0.3545 (OUTLIER) cc_final: 0.1577 (mp0) REVERT: A 82 MET cc_start: 0.7030 (mmt) cc_final: 0.6719 (mmm) REVERT: B 82 MET cc_start: 0.6468 (mmm) cc_final: 0.5841 (pmm) REVERT: C 82 MET cc_start: 0.6945 (pmm) cc_final: 0.6642 (ptt) REVERT: C 87 ARG cc_start: 0.8540 (mtm180) cc_final: 0.8328 (mtm180) REVERT: C 202 MET cc_start: 0.8345 (tpp) cc_final: 0.8023 (tpp) REVERT: C 254 SER cc_start: 0.8230 (m) cc_final: 0.7888 (t) REVERT: D 82 MET cc_start: 0.6432 (pmm) cc_final: 0.6115 (pmm) REVERT: D 186 LYS cc_start: 0.8650 (ttmt) cc_final: 0.8428 (tppt) REVERT: E 47 ARG cc_start: 0.8427 (ttt180) cc_final: 0.7985 (ttt-90) REVERT: E 56 TYR cc_start: 0.8416 (m-80) cc_final: 0.8212 (m-80) outliers start: 45 outliers final: 34 residues processed: 182 average time/residue: 0.2503 time to fit residues: 64.6963 Evaluate side-chains 167 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 132 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 265 LYS Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 216 ASP Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 23 GLN Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 144 HIS Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain E residue 212 CYS Chi-restraints excluded: chain E residue 216 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 2.9990 chunk 113 optimal weight: 0.0570 chunk 24 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS B 85 GLN B 144 HIS B 190 HIS C 23 GLN C 190 HIS E 85 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 10850 Z= 0.408 Angle : 0.672 7.096 14675 Z= 0.328 Chirality : 0.048 0.143 1610 Planarity : 0.004 0.041 1850 Dihedral : 11.026 120.715 1516 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 5.68 % Allowed : 13.19 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.98 (0.23), residues: 1325 helix: -2.20 (0.28), residues: 255 sheet: -0.63 (0.25), residues: 425 loop : -1.31 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS B 190 PHE 0.019 0.002 PHE D 158 TYR 0.021 0.002 TYR B 56 ARG 0.008 0.001 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 125 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLU cc_start: 0.3875 (OUTLIER) cc_final: 0.2411 (mt-10) REVERT: A 87 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.7596 (mtm-85) REVERT: A 144 HIS cc_start: 0.7027 (OUTLIER) cc_final: 0.6251 (p90) REVERT: B 82 MET cc_start: 0.7073 (mmm) cc_final: 0.6347 (ptt) REVERT: C 202 MET cc_start: 0.8197 (tpp) cc_final: 0.7533 (tpt) REVERT: C 254 SER cc_start: 0.8379 (m) cc_final: 0.8140 (p) REVERT: D 82 MET cc_start: 0.6460 (pmm) cc_final: 0.5228 (ptt) REVERT: D 85 GLN cc_start: 0.8589 (mt0) cc_final: 0.7832 (mp10) outliers start: 65 outliers final: 50 residues processed: 176 average time/residue: 0.2247 time to fit residues: 56.3012 Evaluate side-chains 167 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 114 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 144 HIS Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 265 LYS Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 216 ASP Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 23 GLN Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 135 GLU Chi-restraints excluded: chain E residue 144 HIS Chi-restraints excluded: chain E residue 160 ASP Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain E residue 212 CYS Chi-restraints excluded: chain E residue 216 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 105 optimal weight: 0.4980 chunk 70 optimal weight: 2.9990 chunk 125 optimal weight: 0.4980 chunk 78 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 57 optimal weight: 0.0770 chunk 77 optimal weight: 0.7980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS A 199 ASN B 85 GLN B 144 HIS C 190 HIS E 85 GLN E 124 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.4862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10850 Z= 0.141 Angle : 0.556 11.459 14675 Z= 0.260 Chirality : 0.044 0.129 1610 Planarity : 0.003 0.032 1850 Dihedral : 9.848 112.476 1516 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 4.28 % Allowed : 14.32 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.70 (0.23), residues: 1325 helix: -1.78 (0.29), residues: 265 sheet: -0.34 (0.25), residues: 425 loop : -1.31 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 144 PHE 0.010 0.001 PHE D 139 TYR 0.014 0.001 TYR B 56 ARG 0.005 0.000 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 140 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLU cc_start: 0.3289 (OUTLIER) cc_final: 0.2008 (mt-10) REVERT: A 82 MET cc_start: 0.7226 (mmt) cc_final: 0.5299 (ptp) REVERT: A 87 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.7387 (mtm-85) REVERT: B 82 MET cc_start: 0.7031 (mmm) cc_final: 0.6059 (ptt) REVERT: B 251 ASP cc_start: 0.7251 (t70) cc_final: 0.6972 (t70) REVERT: C 124 GLN cc_start: 0.7201 (tm-30) cc_final: 0.6673 (tm-30) REVERT: C 202 MET cc_start: 0.8130 (tpp) cc_final: 0.7424 (tpt) REVERT: D 82 MET cc_start: 0.6520 (pmm) cc_final: 0.5912 (pmm) REVERT: D 85 GLN cc_start: 0.8544 (mt0) cc_final: 0.7912 (mp10) REVERT: D 95 ILE cc_start: 0.9229 (mt) cc_final: 0.9022 (mp) REVERT: D 106 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8875 (mp) REVERT: D 148 MET cc_start: 0.7089 (OUTLIER) cc_final: 0.6470 (mtp) REVERT: D 256 TYR cc_start: 0.8832 (m-80) cc_final: 0.8604 (m-80) REVERT: E 47 ARG cc_start: 0.8513 (ttt180) cc_final: 0.8158 (ttt-90) outliers start: 49 outliers final: 40 residues processed: 172 average time/residue: 0.2335 time to fit residues: 56.9807 Evaluate side-chains 173 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 129 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 265 LYS Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 81 HIS Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 216 ASP Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 23 GLN Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain E residue 212 CYS Chi-restraints excluded: chain E residue 216 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 85 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 11 optimal weight: 0.0570 chunk 98 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 overall best weight: 0.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS B 23 GLN B 144 HIS C 190 HIS E 85 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.4923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10850 Z= 0.186 Angle : 0.566 9.757 14675 Z= 0.265 Chirality : 0.044 0.130 1610 Planarity : 0.003 0.033 1850 Dihedral : 9.704 115.460 1516 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 4.37 % Allowed : 14.41 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.59 (0.23), residues: 1325 helix: -1.65 (0.29), residues: 265 sheet: -0.26 (0.25), residues: 425 loop : -1.26 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 81 PHE 0.010 0.001 PHE D 139 TYR 0.018 0.001 TYR E 56 ARG 0.006 0.000 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 131 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLU cc_start: 0.2953 (OUTLIER) cc_final: 0.0951 (mp0) REVERT: A 87 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.7407 (mtm-85) REVERT: B 82 MET cc_start: 0.6904 (mmm) cc_final: 0.6200 (ptt) REVERT: B 251 ASP cc_start: 0.7270 (t70) cc_final: 0.6993 (t70) REVERT: C 124 GLN cc_start: 0.7204 (tm-30) cc_final: 0.6681 (tm-30) REVERT: D 82 MET cc_start: 0.6561 (pmm) cc_final: 0.5504 (ptt) REVERT: D 85 GLN cc_start: 0.8565 (mt0) cc_final: 0.7934 (mp10) REVERT: D 95 ILE cc_start: 0.9244 (mt) cc_final: 0.9023 (mp) REVERT: D 148 MET cc_start: 0.7109 (OUTLIER) cc_final: 0.6287 (mtp) REVERT: E 56 TYR cc_start: 0.8447 (m-80) cc_final: 0.8238 (m-80) outliers start: 50 outliers final: 41 residues processed: 163 average time/residue: 0.2326 time to fit residues: 54.0256 Evaluate side-chains 171 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 127 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 265 LYS Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 216 ASP Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 23 GLN Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 144 HIS Chi-restraints excluded: chain E residue 160 ASP Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain E residue 212 CYS Chi-restraints excluded: chain E residue 216 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 7.9990 chunk 116 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 110 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS B 125 HIS B 190 HIS E 85 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.5034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10850 Z= 0.245 Angle : 0.594 8.854 14675 Z= 0.280 Chirality : 0.045 0.136 1610 Planarity : 0.003 0.034 1850 Dihedral : 9.724 125.520 1516 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 4.72 % Allowed : 14.24 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.57 (0.23), residues: 1325 helix: -1.60 (0.29), residues: 265 sheet: -0.28 (0.25), residues: 425 loop : -1.23 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 81 PHE 0.011 0.001 PHE D 158 TYR 0.019 0.001 TYR C 56 ARG 0.009 0.001 ARG D 130 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 126 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLU cc_start: 0.3323 (OUTLIER) cc_final: 0.1944 (mt-10) REVERT: A 87 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.7533 (mtm-85) REVERT: B 82 MET cc_start: 0.7243 (mmm) cc_final: 0.6305 (ptt) REVERT: B 251 ASP cc_start: 0.7221 (t70) cc_final: 0.6900 (t70) REVERT: C 124 GLN cc_start: 0.7197 (tm-30) cc_final: 0.6691 (tm-30) REVERT: C 202 MET cc_start: 0.8196 (tpt) cc_final: 0.7823 (tpp) REVERT: D 82 MET cc_start: 0.6607 (pmm) cc_final: 0.5915 (ptp) REVERT: D 85 GLN cc_start: 0.8555 (mt0) cc_final: 0.7932 (mp10) REVERT: D 95 ILE cc_start: 0.9265 (mt) cc_final: 0.9058 (mp) REVERT: D 148 MET cc_start: 0.7103 (OUTLIER) cc_final: 0.6345 (mtp) outliers start: 54 outliers final: 45 residues processed: 164 average time/residue: 0.2203 time to fit residues: 51.4017 Evaluate side-chains 171 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 123 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 265 LYS Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 216 ASP Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 144 HIS Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 23 GLN Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 135 GLU Chi-restraints excluded: chain E residue 144 HIS Chi-restraints excluded: chain E residue 160 ASP Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain E residue 212 CYS Chi-restraints excluded: chain E residue 216 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 1.9990 chunk 58 optimal weight: 0.2980 chunk 85 optimal weight: 4.9990 chunk 129 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 10 optimal weight: 0.4980 chunk 79 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 109 optimal weight: 7.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS B 23 GLN E 85 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.5132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10850 Z= 0.155 Angle : 0.559 8.399 14675 Z= 0.262 Chirality : 0.044 0.129 1610 Planarity : 0.003 0.032 1850 Dihedral : 9.023 117.050 1516 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 4.10 % Allowed : 14.32 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.23), residues: 1325 helix: -1.41 (0.30), residues: 265 sheet: -0.28 (0.25), residues: 445 loop : -1.21 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 190 PHE 0.009 0.001 PHE D 139 TYR 0.022 0.001 TYR E 56 ARG 0.005 0.000 ARG A 130 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 135 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLU cc_start: 0.2951 (OUTLIER) cc_final: 0.1836 (mt-10) REVERT: A 87 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.7419 (mtm-85) REVERT: B 82 MET cc_start: 0.7289 (mmm) cc_final: 0.6407 (ptt) REVERT: C 124 GLN cc_start: 0.7204 (tm-30) cc_final: 0.6702 (tm-30) REVERT: C 202 MET cc_start: 0.8152 (tpt) cc_final: 0.7829 (tpp) REVERT: D 82 MET cc_start: 0.6765 (pmm) cc_final: 0.5708 (ptt) REVERT: D 85 GLN cc_start: 0.8541 (mt0) cc_final: 0.7926 (mp10) REVERT: D 95 ILE cc_start: 0.9245 (mt) cc_final: 0.9043 (mp) REVERT: D 148 MET cc_start: 0.7088 (OUTLIER) cc_final: 0.6297 (mtp) outliers start: 47 outliers final: 42 residues processed: 166 average time/residue: 0.2221 time to fit residues: 52.7485 Evaluate side-chains 168 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 123 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 265 LYS Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 216 ASP Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 144 HIS Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 23 GLN Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 135 GLU Chi-restraints excluded: chain E residue 144 HIS Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain E residue 212 CYS Chi-restraints excluded: chain E residue 216 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 15 optimal weight: 0.0870 chunk 28 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 HIS B 23 GLN B 190 HIS D 124 GLN E 85 GLN E 124 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.107007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.088424 restraints weight = 18285.471| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.38 r_work: 0.2976 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.5176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10850 Z= 0.258 Angle : 0.603 8.170 14675 Z= 0.286 Chirality : 0.046 0.131 1610 Planarity : 0.003 0.035 1850 Dihedral : 9.157 113.401 1516 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 4.72 % Allowed : 14.24 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.23), residues: 1325 helix: -1.38 (0.30), residues: 255 sheet: -0.29 (0.25), residues: 425 loop : -1.13 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 81 PHE 0.012 0.001 PHE C 64 TYR 0.017 0.001 TYR D 256 ARG 0.010 0.001 ARG D 130 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2423.67 seconds wall clock time: 45 minutes 11.21 seconds (2711.21 seconds total)