Starting phenix.real_space_refine on Wed Feb 21 22:15:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbp_13298/02_2024/7pbp_13298_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbp_13298/02_2024/7pbp_13298.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbp_13298/02_2024/7pbp_13298.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbp_13298/02_2024/7pbp_13298.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbp_13298/02_2024/7pbp_13298_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbp_13298/02_2024/7pbp_13298_neut_trim_updated.pdb" } resolution = 3.2 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 45 5.49 5 Mg 3 5.21 5 S 101 5.16 5 C 10134 2.51 5 N 2757 2.21 5 O 3219 1.98 5 H 15818 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 111": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 32077 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "B" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "C" Number of atoms: 4895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 4895 Classifications: {'peptide': 309} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 294} Chain breaks: 1 Chain: "D" Number of atoms: 4934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 4934 Classifications: {'peptide': 313} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 298} Chain: "E" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "F" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "G" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 718 Classifications: {'peptide': 48} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "H" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 760 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "U" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 479 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "V" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 474 Classifications: {'DNA': 15} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 14} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.80, per 1000 atoms: 0.43 Number of scatterers: 32077 At special positions: 0 Unit cell: (125.35, 137.34, 106.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 101 16.00 P 45 15.00 Mg 3 11.99 O 3219 8.00 N 2757 7.00 C 10134 6.00 H 15818 1.00 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: 23.64 Conformation dependent library (CDL) restraints added in 3.1 seconds 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3624 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 108 helices and 18 sheets defined 51.0% alpha, 10.4% beta 12 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 17.09 Creating SS restraints... Processing helix chain 'A' and resid 32 through 48 removed outlier: 3.554A pdb=" N GLN A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE A 40 " --> pdb=" O ASP A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 76 Processing helix chain 'A' and resid 85 through 87 No H-bonds generated for 'chain 'A' and resid 85 through 87' Processing helix chain 'A' and resid 91 through 100 Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 117 through 129 removed outlier: 4.472A pdb=" N VAL A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU A 123 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N TYR A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N SER A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 166 through 171 removed outlier: 3.827A pdb=" N ARG A 171 " --> pdb=" O PRO A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 196 removed outlier: 3.740A pdb=" N GLU A 188 " --> pdb=" O PRO A 184 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE A 196 " --> pdb=" O ARG A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 211 Processing helix chain 'A' and resid 217 through 233 Processing helix chain 'A' and resid 241 through 250 removed outlier: 3.645A pdb=" N ASP A 245 " --> pdb=" O ASP A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 273 Processing helix chain 'A' and resid 280 through 287 Processing helix chain 'A' and resid 291 through 297 Processing helix chain 'A' and resid 299 through 304 Processing helix chain 'A' and resid 319 through 325 Processing helix chain 'B' and resid 32 through 47 Processing helix chain 'B' and resid 65 through 76 removed outlier: 3.641A pdb=" N PHE B 70 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 97 Processing helix chain 'B' and resid 112 through 114 No H-bonds generated for 'chain 'B' and resid 112 through 114' Processing helix chain 'B' and resid 117 through 129 removed outlier: 4.684A pdb=" N VAL B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU B 123 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TYR B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N SER B 125 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA B 126 " --> pdb=" O VAL B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 141 No H-bonds generated for 'chain 'B' and resid 139 through 141' Processing helix chain 'B' and resid 161 through 163 No H-bonds generated for 'chain 'B' and resid 161 through 163' Processing helix chain 'B' and resid 166 through 171 removed outlier: 3.840A pdb=" N ARG B 171 " --> pdb=" O PRO B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 196 removed outlier: 3.524A pdb=" N ILE B 196 " --> pdb=" O ARG B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 212 removed outlier: 3.977A pdb=" N ARG B 212 " --> pdb=" O GLU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 231 Processing helix chain 'B' and resid 241 through 251 Processing helix chain 'B' and resid 260 through 272 Processing helix chain 'B' and resid 280 through 287 removed outlier: 3.567A pdb=" N ASN B 286 " --> pdb=" O THR B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 297 Processing helix chain 'B' and resid 299 through 304 Processing helix chain 'B' and resid 319 through 325 Processing helix chain 'C' and resid 32 through 47 Processing helix chain 'C' and resid 65 through 76 removed outlier: 3.700A pdb=" N PHE C 70 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 100 removed outlier: 3.681A pdb=" N ASP C 100 " --> pdb=" O ALA C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 114 No H-bonds generated for 'chain 'C' and resid 112 through 114' Processing helix chain 'C' and resid 117 through 129 removed outlier: 4.291A pdb=" N VAL C 122 " --> pdb=" O ALA C 118 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N SER C 125 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA C 126 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU C 128 " --> pdb=" O TYR C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 163 No H-bonds generated for 'chain 'C' and resid 161 through 163' Processing helix chain 'C' and resid 166 through 171 removed outlier: 3.942A pdb=" N ARG C 171 " --> pdb=" O PRO C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 196 removed outlier: 3.552A pdb=" N ILE C 196 " --> pdb=" O ARG C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 212 removed outlier: 3.923A pdb=" N ARG C 212 " --> pdb=" O GLU C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 233 Processing helix chain 'C' and resid 241 through 251 removed outlier: 3.677A pdb=" N ASP C 245 " --> pdb=" O ASP C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 272 Processing helix chain 'C' and resid 280 through 287 Processing helix chain 'C' and resid 291 through 297 Processing helix chain 'C' and resid 299 through 304 Processing helix chain 'C' and resid 319 through 325 Processing helix chain 'D' and resid 32 through 46 removed outlier: 3.658A pdb=" N ILE D 40 " --> pdb=" O ASP D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 76 removed outlier: 3.674A pdb=" N ALA D 69 " --> pdb=" O LYS D 65 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N PHE D 70 " --> pdb=" O THR D 66 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL D 71 " --> pdb=" O THR D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 87 No H-bonds generated for 'chain 'D' and resid 85 through 87' Processing helix chain 'D' and resid 91 through 100 removed outlier: 3.621A pdb=" N ASP D 100 " --> pdb=" O ALA D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 114 No H-bonds generated for 'chain 'D' and resid 112 through 114' Processing helix chain 'D' and resid 117 through 129 removed outlier: 4.606A pdb=" N VAL D 122 " --> pdb=" O ALA D 118 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU D 123 " --> pdb=" O VAL D 119 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N TYR D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N SER D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA D 126 " --> pdb=" O VAL D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 141 No H-bonds generated for 'chain 'D' and resid 139 through 141' Processing helix chain 'D' and resid 161 through 163 No H-bonds generated for 'chain 'D' and resid 161 through 163' Processing helix chain 'D' and resid 166 through 171 removed outlier: 3.892A pdb=" N ARG D 171 " --> pdb=" O PRO D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 196 removed outlier: 4.598A pdb=" N GLU D 188 " --> pdb=" O PRO D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 212 removed outlier: 3.773A pdb=" N ARG D 212 " --> pdb=" O GLU D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 233 Processing helix chain 'D' and resid 241 through 250 Processing helix chain 'D' and resid 260 through 273 Processing helix chain 'D' and resid 280 through 287 removed outlier: 3.561A pdb=" N ASN D 286 " --> pdb=" O THR D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 296 Processing helix chain 'D' and resid 299 through 304 Processing helix chain 'D' and resid 319 through 325 removed outlier: 3.513A pdb=" N HIS D 324 " --> pdb=" O LYS D 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 27 No H-bonds generated for 'chain 'E' and resid 25 through 27' Processing helix chain 'E' and resid 32 through 48 removed outlier: 3.705A pdb=" N ILE E 40 " --> pdb=" O ASP E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 76 removed outlier: 3.648A pdb=" N PHE E 70 " --> pdb=" O THR E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 87 No H-bonds generated for 'chain 'E' and resid 85 through 87' Processing helix chain 'E' and resid 91 through 100 Processing helix chain 'E' and resid 112 through 114 No H-bonds generated for 'chain 'E' and resid 112 through 114' Processing helix chain 'E' and resid 117 through 129 removed outlier: 4.212A pdb=" N VAL E 122 " --> pdb=" O ALA E 118 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N SER E 125 " --> pdb=" O GLU E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 171 removed outlier: 3.993A pdb=" N ARG E 171 " --> pdb=" O PRO E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 196 Processing helix chain 'E' and resid 203 through 213 Processing helix chain 'E' and resid 217 through 231 Processing helix chain 'E' and resid 241 through 250 Processing helix chain 'E' and resid 260 through 273 Processing helix chain 'E' and resid 280 through 286 Processing helix chain 'E' and resid 291 through 297 Processing helix chain 'E' and resid 299 through 304 Processing helix chain 'E' and resid 319 through 325 Processing helix chain 'F' and resid 32 through 47 removed outlier: 3.755A pdb=" N GLN F 37 " --> pdb=" O LYS F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 76 removed outlier: 3.506A pdb=" N ALA F 69 " --> pdb=" O LYS F 65 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE F 70 " --> pdb=" O THR F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 87 No H-bonds generated for 'chain 'F' and resid 85 through 87' Processing helix chain 'F' and resid 91 through 100 removed outlier: 3.695A pdb=" N ASP F 100 " --> pdb=" O ALA F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 114 No H-bonds generated for 'chain 'F' and resid 112 through 114' Processing helix chain 'F' and resid 117 through 129 removed outlier: 4.599A pdb=" N VAL F 122 " --> pdb=" O ALA F 118 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU F 123 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR F 124 " --> pdb=" O GLU F 120 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER F 125 " --> pdb=" O GLU F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 141 No H-bonds generated for 'chain 'F' and resid 139 through 141' Processing helix chain 'F' and resid 166 through 171 removed outlier: 4.138A pdb=" N ARG F 171 " --> pdb=" O PRO F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 196 Processing helix chain 'F' and resid 203 through 211 Processing helix chain 'F' and resid 217 through 233 removed outlier: 3.560A pdb=" N ASP F 229 " --> pdb=" O LYS F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 250 removed outlier: 3.680A pdb=" N GLN F 246 " --> pdb=" O LYS F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 272 Processing helix chain 'F' and resid 280 through 286 removed outlier: 3.901A pdb=" N VAL F 285 " --> pdb=" O GLY F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 296 Processing helix chain 'F' and resid 299 through 304 Processing helix chain 'F' and resid 319 through 325 Processing helix chain 'G' and resid 157 through 169 Processing helix chain 'G' and resid 174 through 182 Processing helix chain 'G' and resid 191 through 201 Processing helix chain 'H' and resid 159 through 169 Processing helix chain 'H' and resid 174 through 183 Processing helix chain 'H' and resid 191 through 198 Processing sheet with id= A, first strand: chain 'A' and resid 174 through 177 Processing sheet with id= B, first strand: chain 'A' and resid 131 through 136 Processing sheet with id= C, first strand: chain 'A' and resid 308 through 311 Processing sheet with id= D, first strand: chain 'B' and resid 174 through 177 Processing sheet with id= E, first strand: chain 'B' and resid 131 through 136 Processing sheet with id= F, first strand: chain 'B' and resid 308 through 311 Processing sheet with id= G, first strand: chain 'C' and resid 174 through 177 Processing sheet with id= H, first strand: chain 'C' and resid 131 through 136 Processing sheet with id= I, first strand: chain 'C' and resid 308 through 311 Processing sheet with id= J, first strand: chain 'D' and resid 174 through 177 Processing sheet with id= K, first strand: chain 'D' and resid 131 through 136 Processing sheet with id= L, first strand: chain 'D' and resid 308 through 311 Processing sheet with id= M, first strand: chain 'E' and resid 174 through 177 Processing sheet with id= N, first strand: chain 'E' and resid 131 through 136 Processing sheet with id= O, first strand: chain 'E' and resid 308 through 310 Processing sheet with id= P, first strand: chain 'F' and resid 174 through 177 Processing sheet with id= Q, first strand: chain 'F' and resid 131 through 136 Processing sheet with id= R, first strand: chain 'F' and resid 308 through 310 672 hydrogen bonds defined for protein. 1968 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 30 hydrogen bonds 60 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 12.38 Time building geometry restraints manager: 24.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.06: 15818 1.06 - 1.28: 2720 1.28 - 1.50: 6914 1.50 - 1.72: 6773 1.72 - 1.94: 199 Bond restraints: 32424 Sorted by residual: bond pdb=" N THR B 19 " pdb=" H1 THR B 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" N THR D 19 " pdb=" H1 THR D 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" N THR E 19 " pdb=" H1 THR E 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" N THR C 19 " pdb=" H1 THR C 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" N THR A 19 " pdb=" H1 THR A 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.50e+01 ... (remaining 32419 not shown) Histogram of bond angle deviations from ideal: 99.52 - 106.96: 857 106.96 - 114.40: 39816 114.40 - 121.84: 12698 121.84 - 129.27: 5248 129.27 - 136.71: 70 Bond angle restraints: 58689 Sorted by residual: angle pdb=" OP1 DT V 4 " pdb=" P DT V 4 " pdb=" OP2 DT V 4 " ideal model delta sigma weight residual 120.00 109.94 10.06 3.00e+00 1.11e-01 1.13e+01 angle pdb=" N GLY E 215 " pdb=" CA GLY E 215 " pdb=" C GLY E 215 " ideal model delta sigma weight residual 115.36 119.79 -4.43 1.33e+00 5.65e-01 1.11e+01 angle pdb=" O3' DT V 3 " pdb=" P DT V 4 " pdb=" OP1 DT V 4 " ideal model delta sigma weight residual 108.00 117.80 -9.80 3.00e+00 1.11e-01 1.07e+01 angle pdb=" C1' ADP E 600 " pdb=" C2' ADP E 600 " pdb=" C3' ADP E 600 " ideal model delta sigma weight residual 111.00 101.77 9.23 3.00e+00 1.11e-01 9.47e+00 angle pdb=" N PRO B 60 " pdb=" CA PRO B 60 " pdb=" C PRO B 60 " ideal model delta sigma weight residual 110.70 114.37 -3.67 1.22e+00 6.72e-01 9.04e+00 ... (remaining 58684 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.36: 14319 28.36 - 56.71: 612 56.71 - 85.07: 98 85.07 - 113.42: 4 113.42 - 141.78: 6 Dihedral angle restraints: 15039 sinusoidal: 8606 harmonic: 6433 Sorted by residual: dihedral pdb=" O2A ADP F 600 " pdb=" O3A ADP F 600 " pdb=" PA ADP F 600 " pdb=" PB ADP F 600 " ideal model delta sinusoidal sigma weight residual -60.00 81.49 -141.49 1 2.00e+01 2.50e-03 4.28e+01 dihedral pdb=" O2A ADP E 600 " pdb=" O3A ADP E 600 " pdb=" PA ADP E 600 " pdb=" PB ADP E 600 " ideal model delta sinusoidal sigma weight residual -60.00 77.02 -137.02 1 2.00e+01 2.50e-03 4.16e+01 dihedral pdb=" C5' ADP A 600 " pdb=" O5' ADP A 600 " pdb=" PA ADP A 600 " pdb=" O2A ADP A 600 " ideal model delta sinusoidal sigma weight residual -60.00 -175.99 115.99 1 2.00e+01 2.50e-03 3.45e+01 ... (remaining 15036 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2355 0.083 - 0.166: 198 0.166 - 0.249: 0 0.249 - 0.332: 0 0.332 - 0.415: 1 Chirality restraints: 2554 Sorted by residual: chirality pdb=" P DT V 4 " pdb=" OP1 DT V 4 " pdb=" OP2 DT V 4 " pdb=" O5' DT V 4 " both_signs ideal model delta sigma weight residual True 2.35 -2.76 -0.42 2.00e-01 2.50e+01 4.31e+00 chirality pdb=" CA ARG E 214 " pdb=" N ARG E 214 " pdb=" C ARG E 214 " pdb=" CB ARG E 214 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.89e-01 chirality pdb=" CA PRO B 300 " pdb=" N PRO B 300 " pdb=" C PRO B 300 " pdb=" CB PRO B 300 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.27e-01 ... (remaining 2551 not shown) Planarity restraints: 4701 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 160 " 0.386 9.50e-02 1.11e+02 1.34e-01 4.68e+01 pdb=" NE ARG F 160 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG F 160 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG F 160 " -0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG F 160 " -0.077 2.00e-02 2.50e+03 pdb="HH11 ARG F 160 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG F 160 " -0.005 2.00e-02 2.50e+03 pdb="HH21 ARG F 160 " -0.003 2.00e-02 2.50e+03 pdb="HH22 ARG F 160 " 0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 211 " -0.331 9.50e-02 1.11e+02 1.15e-01 3.60e+01 pdb=" NE ARG F 211 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG F 211 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG F 211 " 0.020 2.00e-02 2.50e+03 pdb=" NH2 ARG F 211 " 0.067 2.00e-02 2.50e+03 pdb="HH11 ARG F 211 " 0.000 2.00e-02 2.50e+03 pdb="HH12 ARG F 211 " -0.004 2.00e-02 2.50e+03 pdb="HH21 ARG F 211 " 0.002 2.00e-02 2.50e+03 pdb="HH22 ARG F 211 " -0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 31 " 0.038 2.00e-02 2.50e+03 4.74e-02 3.37e+01 pdb=" CD GLN C 31 " -0.032 2.00e-02 2.50e+03 pdb=" OE1 GLN C 31 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 GLN C 31 " -0.076 2.00e-02 2.50e+03 pdb="HE21 GLN C 31 " -0.002 2.00e-02 2.50e+03 pdb="HE22 GLN C 31 " 0.073 2.00e-02 2.50e+03 ... (remaining 4698 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.10: 539 2.10 - 2.72: 53049 2.72 - 3.35: 86268 3.35 - 3.97: 108933 3.97 - 4.60: 176962 Nonbonded interactions: 425751 Sorted by model distance: nonbonded pdb=" HG1 THR F 311 " pdb=" O GLY F 314 " model vdw 1.473 1.850 nonbonded pdb=" HG1 THR E 311 " pdb=" O GLY E 314 " model vdw 1.478 1.850 nonbonded pdb=" HG1 THR F 66 " pdb=" O1B ADP F 600 " model vdw 1.539 1.850 nonbonded pdb=" OE1 GLU A 299 " pdb="HH11 ARG A 315 " model vdw 1.581 1.850 nonbonded pdb=" HG1 THR A 311 " pdb=" O GLY A 314 " model vdw 1.590 1.850 ... (remaining 425746 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' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'B' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'C' and resid 19 through 330) selection = (chain 'D' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'E' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'F' and (resid 19 through 136 or resid 141 through 330)) } ncs_group { reference = (chain 'G' and resid 158 through 203) selection = (chain 'H' and resid 158 through 203) } 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: 5.420 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: 0.480 Extract box with map and model: 11.130 Check model and map are aligned: 0.470 Set scattering table: 0.290 Process input model: 107.090 Find NCS groups from input model: 1.680 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16606 Z= 0.281 Angle : 0.726 10.064 22612 Z= 0.413 Chirality : 0.044 0.415 2554 Planarity : 0.010 0.137 2807 Dihedral : 14.913 141.779 6411 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.12 % Allowed : 1.28 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.18), residues: 1950 helix: -1.01 (0.14), residues: 1036 sheet: 0.40 (0.29), residues: 320 loop : 0.54 (0.27), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.003 HIS F 113 PHE 0.021 0.003 PHE D 25 TYR 0.023 0.004 TYR E 131 ARG 0.026 0.003 ARG B 310 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 420 time to evaluate : 2.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 MET cc_start: 0.9122 (mtp) cc_final: 0.8870 (mtp) REVERT: A 252 ASP cc_start: 0.8078 (t0) cc_final: 0.7838 (t0) REVERT: A 325 MET cc_start: 0.8062 (mmm) cc_final: 0.7199 (mmt) REVERT: B 178 MET cc_start: 0.9362 (mmm) cc_final: 0.8849 (mmt) REVERT: C 135 MET cc_start: 0.7184 (mmm) cc_final: 0.6939 (mmm) REVERT: C 199 MET cc_start: 0.7721 (mmt) cc_final: 0.7502 (tpt) REVERT: C 286 ASN cc_start: 0.9169 (OUTLIER) cc_final: 0.8966 (t0) REVERT: D 114 ARG cc_start: 0.6665 (mtp85) cc_final: 0.6445 (mtt180) REVERT: D 232 GLN cc_start: 0.8328 (pt0) cc_final: 0.8127 (pt0) REVERT: E 65 LYS cc_start: 0.8905 (mtmt) cc_final: 0.8632 (mtpt) REVERT: E 100 ASP cc_start: 0.7475 (t0) cc_final: 0.7143 (t0) REVERT: E 147 LEU cc_start: 0.6900 (mt) cc_final: 0.6564 (mt) REVERT: E 234 MET cc_start: 0.7845 (tpp) cc_final: 0.7606 (mmm) REVERT: F 298 TYR cc_start: 0.8033 (m-80) cc_final: 0.7730 (m-80) REVERT: F 309 MET cc_start: 0.7923 (ttt) cc_final: 0.7659 (mtp) REVERT: G 203 LEU cc_start: 0.7164 (tp) cc_final: 0.6136 (tp) REVERT: H 197 ASP cc_start: 0.7583 (m-30) cc_final: 0.7232 (m-30) REVERT: H 203 LEU cc_start: 0.8130 (tp) cc_final: 0.7923 (tt) outliers start: 2 outliers final: 0 residues processed: 422 average time/residue: 0.8219 time to fit residues: 471.4089 Evaluate side-chains 265 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 264 time to evaluate : 2.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 286 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 153 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 166 ASN C 166 ASN D 79 ASN E 246 GLN ** E 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 16606 Z= 0.295 Angle : 0.639 6.512 22612 Z= 0.341 Chirality : 0.041 0.140 2554 Planarity : 0.005 0.045 2807 Dihedral : 14.685 146.206 2598 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.28 % Allowed : 5.79 % Favored : 92.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.18), residues: 1950 helix: 0.20 (0.15), residues: 1039 sheet: 0.46 (0.31), residues: 297 loop : 0.32 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 324 PHE 0.011 0.001 PHE C 25 TYR 0.010 0.001 TYR F 230 ARG 0.006 0.001 ARG D 171 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 264 time to evaluate : 2.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 ASP cc_start: 0.8209 (t0) cc_final: 0.7960 (t0) REVERT: B 178 MET cc_start: 0.9346 (mmm) cc_final: 0.8827 (mmt) REVERT: C 199 MET cc_start: 0.7863 (mmt) cc_final: 0.7638 (tpt) REVERT: D 135 MET cc_start: 0.7112 (mtm) cc_final: 0.6732 (ptm) REVERT: E 100 ASP cc_start: 0.7414 (t0) cc_final: 0.7204 (t0) REVERT: E 234 MET cc_start: 0.7862 (tpp) cc_final: 0.7642 (mmm) REVERT: F 298 TYR cc_start: 0.7991 (m-80) cc_final: 0.7708 (m-80) REVERT: F 309 MET cc_start: 0.7849 (ttt) cc_final: 0.7634 (mtp) REVERT: G 203 LEU cc_start: 0.7736 (tp) cc_final: 0.7140 (tp) REVERT: H 197 ASP cc_start: 0.7726 (m-30) cc_final: 0.7471 (m-30) REVERT: H 203 LEU cc_start: 0.8068 (tp) cc_final: 0.7864 (tt) outliers start: 21 outliers final: 10 residues processed: 272 average time/residue: 0.7527 time to fit residues: 294.8066 Evaluate side-chains 255 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 245 time to evaluate : 2.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ARG Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 221 ASN Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain H residue 182 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 148 optimal weight: 0.5980 chunk 121 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 chunk 176 optimal weight: 0.8980 chunk 60 optimal weight: 0.1980 chunk 143 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 ASN E 255 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16606 Z= 0.185 Angle : 0.536 6.297 22612 Z= 0.280 Chirality : 0.039 0.131 2554 Planarity : 0.004 0.043 2807 Dihedral : 14.520 156.793 2598 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.34 % Allowed : 6.46 % Favored : 92.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.19), residues: 1950 helix: 0.82 (0.16), residues: 1039 sheet: 0.46 (0.31), residues: 292 loop : 0.34 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 146 PHE 0.008 0.001 PHE D 58 TYR 0.009 0.001 TYR B 260 ARG 0.004 0.000 ARG D 171 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 259 time to evaluate : 2.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 ASP cc_start: 0.8149 (t0) cc_final: 0.7911 (t0) REVERT: B 178 MET cc_start: 0.9365 (mmm) cc_final: 0.8870 (mmt) REVERT: C 291 ARG cc_start: 0.7846 (ttm110) cc_final: 0.7629 (ttp-110) REVERT: D 135 MET cc_start: 0.7110 (mtm) cc_final: 0.6757 (ptm) REVERT: E 100 ASP cc_start: 0.7437 (t0) cc_final: 0.7215 (t0) REVERT: F 298 TYR cc_start: 0.7971 (m-80) cc_final: 0.7706 (m-80) REVERT: F 309 MET cc_start: 0.7859 (ttt) cc_final: 0.7598 (mtp) REVERT: H 197 ASP cc_start: 0.7726 (m-30) cc_final: 0.7506 (m-30) REVERT: H 203 LEU cc_start: 0.8055 (tp) cc_final: 0.7849 (tt) outliers start: 22 outliers final: 16 residues processed: 267 average time/residue: 0.6961 time to fit residues: 269.8182 Evaluate side-chains 269 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 253 time to evaluate : 2.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ARG Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 272 MET Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain H residue 182 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 0.3980 chunk 134 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 178 optimal weight: 0.6980 chunk 189 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 169 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 ASN D 286 ASN E 246 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16606 Z= 0.209 Angle : 0.530 6.539 22612 Z= 0.275 Chirality : 0.039 0.134 2554 Planarity : 0.004 0.044 2807 Dihedral : 14.415 164.140 2598 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.46 % Allowed : 7.62 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.19), residues: 1950 helix: 1.06 (0.16), residues: 1037 sheet: 0.22 (0.30), residues: 297 loop : 0.23 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 54 PHE 0.006 0.001 PHE C 25 TYR 0.008 0.001 TYR F 230 ARG 0.003 0.000 ARG B 218 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 253 time to evaluate : 2.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7610 (mt-10) REVERT: A 252 ASP cc_start: 0.8204 (t0) cc_final: 0.7968 (t0) REVERT: A 291 ARG cc_start: 0.7732 (tpp80) cc_final: 0.7468 (ttt90) REVERT: B 178 MET cc_start: 0.9368 (mmm) cc_final: 0.8841 (mmt) REVERT: D 135 MET cc_start: 0.7122 (mtm) cc_final: 0.6738 (ptm) REVERT: F 309 MET cc_start: 0.7786 (ttt) cc_final: 0.7495 (mtp) REVERT: H 197 ASP cc_start: 0.7739 (m-30) cc_final: 0.7529 (m-30) outliers start: 24 outliers final: 15 residues processed: 263 average time/residue: 0.7051 time to fit residues: 264.7357 Evaluate side-chains 261 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 246 time to evaluate : 2.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 160 ARG Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 272 MET Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 191 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 141 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 161 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 170 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16606 Z= 0.221 Angle : 0.529 6.488 22612 Z= 0.275 Chirality : 0.039 0.226 2554 Planarity : 0.004 0.046 2807 Dihedral : 14.332 164.494 2596 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.28 % Allowed : 8.78 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.19), residues: 1950 helix: 1.17 (0.17), residues: 1032 sheet: 0.13 (0.30), residues: 295 loop : 0.18 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 54 PHE 0.007 0.001 PHE D 58 TYR 0.007 0.001 TYR F 131 ARG 0.003 0.000 ARG F 143 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 249 time to evaluate : 5.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7622 (mt-10) REVERT: A 252 ASP cc_start: 0.8242 (t0) cc_final: 0.7980 (t0) REVERT: A 291 ARG cc_start: 0.7753 (tpp80) cc_final: 0.7512 (ttt90) REVERT: B 178 MET cc_start: 0.9335 (mmm) cc_final: 0.8782 (mmt) REVERT: C 269 MET cc_start: 0.9080 (OUTLIER) cc_final: 0.8781 (ttp) REVERT: D 135 MET cc_start: 0.7140 (mtm) cc_final: 0.6746 (ptm) REVERT: F 309 MET cc_start: 0.7793 (ttt) cc_final: 0.7490 (mtp) REVERT: H 197 ASP cc_start: 0.7640 (m-30) cc_final: 0.7377 (m-30) outliers start: 21 outliers final: 17 residues processed: 257 average time/residue: 0.7488 time to fit residues: 276.8403 Evaluate side-chains 263 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 245 time to evaluate : 2.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 272 MET Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 232 GLN Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 191 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 0.9980 chunk 170 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 189 optimal weight: 4.9990 chunk 157 optimal weight: 0.0470 chunk 87 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 232 GLN C 54 HIS D 79 ASN D 286 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16606 Z= 0.188 Angle : 0.514 6.321 22612 Z= 0.265 Chirality : 0.038 0.131 2554 Planarity : 0.004 0.046 2807 Dihedral : 14.237 164.974 2596 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.22 % Allowed : 8.90 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: 1.08 (0.19), residues: 1950 helix: 1.33 (0.17), residues: 1031 sheet: 0.09 (0.29), residues: 295 loop : 0.18 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 54 PHE 0.006 0.001 PHE D 58 TYR 0.007 0.001 TYR F 230 ARG 0.005 0.000 ARG H 196 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 249 time to evaluate : 2.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7620 (mt-10) REVERT: A 252 ASP cc_start: 0.8236 (t0) cc_final: 0.7990 (t0) REVERT: B 178 MET cc_start: 0.9315 (mmm) cc_final: 0.8779 (mmt) REVERT: D 135 MET cc_start: 0.7151 (mtm) cc_final: 0.6725 (ptm) REVERT: F 309 MET cc_start: 0.7798 (ttt) cc_final: 0.7462 (mtp) REVERT: H 197 ASP cc_start: 0.7477 (m-30) cc_final: 0.7170 (m-30) outliers start: 20 outliers final: 18 residues processed: 257 average time/residue: 0.7183 time to fit residues: 265.3798 Evaluate side-chains 261 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 243 time to evaluate : 2.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 272 MET Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 232 GLN Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 191 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 105 optimal weight: 0.0010 chunk 188 optimal weight: 3.9990 chunk 118 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 overall best weight: 1.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16606 Z= 0.249 Angle : 0.529 6.482 22612 Z= 0.274 Chirality : 0.039 0.134 2554 Planarity : 0.004 0.046 2807 Dihedral : 14.247 164.859 2596 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.40 % Allowed : 8.71 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: 1.02 (0.19), residues: 1950 helix: 1.34 (0.17), residues: 1026 sheet: 0.03 (0.29), residues: 295 loop : 0.08 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 54 PHE 0.009 0.001 PHE E 197 TYR 0.007 0.001 TYR C 124 ARG 0.005 0.000 ARG F 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 248 time to evaluate : 2.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.8534 (tp) cc_final: 0.8307 (tt) REVERT: A 111 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7591 (mt-10) REVERT: A 252 ASP cc_start: 0.8280 (t0) cc_final: 0.8020 (t0) REVERT: B 178 MET cc_start: 0.9301 (mmm) cc_final: 0.8780 (mmt) REVERT: C 269 MET cc_start: 0.9105 (OUTLIER) cc_final: 0.8828 (ttm) REVERT: D 135 MET cc_start: 0.7166 (mtm) cc_final: 0.6719 (ptm) REVERT: F 309 MET cc_start: 0.7796 (ttt) cc_final: 0.7453 (mtp) REVERT: H 197 ASP cc_start: 0.7465 (m-30) cc_final: 0.7174 (m-30) outliers start: 23 outliers final: 21 residues processed: 258 average time/residue: 0.7215 time to fit residues: 266.3069 Evaluate side-chains 267 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 245 time to evaluate : 2.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 272 MET Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 232 GLN Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 191 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 56 optimal weight: 0.0980 chunk 37 optimal weight: 0.4980 chunk 36 optimal weight: 0.9990 chunk 120 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 ASN D 286 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16606 Z= 0.169 Angle : 0.507 7.427 22612 Z= 0.261 Chirality : 0.038 0.129 2554 Planarity : 0.004 0.046 2807 Dihedral : 14.138 165.010 2596 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.16 % Allowed : 9.26 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: 1.27 (0.19), residues: 1950 helix: 1.54 (0.17), residues: 1027 sheet: 0.07 (0.29), residues: 293 loop : 0.23 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 146 PHE 0.006 0.001 PHE D 58 TYR 0.008 0.001 TYR F 230 ARG 0.004 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 249 time to evaluate : 2.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7582 (mt-10) REVERT: A 252 ASP cc_start: 0.8223 (t0) cc_final: 0.7965 (t0) REVERT: B 178 MET cc_start: 0.9318 (mmm) cc_final: 0.8792 (mmt) REVERT: C 135 MET cc_start: 0.6515 (mmm) cc_final: 0.6305 (mmm) REVERT: D 135 MET cc_start: 0.7156 (mtm) cc_final: 0.6685 (ptm) REVERT: F 222 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7076 (mtp85) REVERT: F 309 MET cc_start: 0.7753 (ttt) cc_final: 0.7532 (mtp) REVERT: H 197 ASP cc_start: 0.7446 (m-30) cc_final: 0.7171 (m-30) outliers start: 19 outliers final: 14 residues processed: 258 average time/residue: 0.7297 time to fit residues: 267.0975 Evaluate side-chains 257 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 242 time to evaluate : 2.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 232 GLN Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain H residue 167 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 176 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 chunk 175 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16606 Z= 0.229 Angle : 0.519 6.256 22612 Z= 0.268 Chirality : 0.039 0.138 2554 Planarity : 0.004 0.046 2807 Dihedral : 14.145 165.240 2596 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.10 % Allowed : 9.08 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: 1.17 (0.19), residues: 1950 helix: 1.50 (0.17), residues: 1028 sheet: -0.00 (0.29), residues: 293 loop : 0.13 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 146 PHE 0.007 0.001 PHE D 58 TYR 0.008 0.001 TYR C 124 ARG 0.004 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 246 time to evaluate : 2.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7593 (mt-10) REVERT: A 252 ASP cc_start: 0.8332 (t0) cc_final: 0.8072 (t0) REVERT: B 178 MET cc_start: 0.9300 (mmm) cc_final: 0.8805 (mmt) REVERT: D 135 MET cc_start: 0.7143 (mtm) cc_final: 0.6636 (ptm) REVERT: F 222 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7077 (mtp85) REVERT: F 309 MET cc_start: 0.7742 (ttt) cc_final: 0.7511 (mtp) REVERT: H 197 ASP cc_start: 0.7558 (m-30) cc_final: 0.7288 (m-30) outliers start: 18 outliers final: 17 residues processed: 254 average time/residue: 0.7418 time to fit residues: 266.9588 Evaluate side-chains 261 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 243 time to evaluate : 2.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 232 GLN Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 191 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 0.9990 chunk 186 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 120 optimal weight: 0.1980 chunk 95 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 ASN E 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16606 Z= 0.184 Angle : 0.513 8.587 22612 Z= 0.264 Chirality : 0.039 0.136 2554 Planarity : 0.005 0.066 2807 Dihedral : 14.083 164.906 2596 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.10 % Allowed : 9.32 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: 1.30 (0.19), residues: 1950 helix: 1.61 (0.17), residues: 1027 sheet: 0.04 (0.29), residues: 291 loop : 0.17 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 146 PHE 0.007 0.001 PHE D 58 TYR 0.008 0.001 TYR C 124 ARG 0.012 0.000 ARG C 160 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 247 time to evaluate : 2.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7590 (mt-10) REVERT: A 252 ASP cc_start: 0.8255 (t0) cc_final: 0.7997 (t0) REVERT: B 178 MET cc_start: 0.9306 (mmm) cc_final: 0.8761 (mmt) REVERT: D 135 MET cc_start: 0.7142 (mtm) cc_final: 0.6752 (ptm) REVERT: F 222 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7111 (mtp85) REVERT: F 309 MET cc_start: 0.7768 (ttt) cc_final: 0.7545 (mtp) REVERT: H 197 ASP cc_start: 0.7549 (m-30) cc_final: 0.7281 (m-30) outliers start: 18 outliers final: 17 residues processed: 255 average time/residue: 0.7736 time to fit residues: 279.5431 Evaluate side-chains 263 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 245 time to evaluate : 2.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 232 GLN Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 191 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 143 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 ASN D 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.115489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.082540 restraints weight = 73783.903| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 2.33 r_work: 0.2738 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2612 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16606 Z= 0.233 Angle : 0.530 9.497 22612 Z= 0.272 Chirality : 0.039 0.135 2554 Planarity : 0.005 0.047 2807 Dihedral : 14.090 165.204 2596 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.28 % Allowed : 9.26 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: 1.20 (0.19), residues: 1950 helix: 1.54 (0.17), residues: 1029 sheet: -0.02 (0.29), residues: 295 loop : 0.11 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 54 PHE 0.007 0.001 PHE D 58 TYR 0.008 0.001 TYR C 124 ARG 0.008 0.000 ARG C 160 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7817.72 seconds wall clock time: 138 minutes 37.04 seconds (8317.04 seconds total)