Starting phenix.real_space_refine (version: dev) on Tue Feb 28 07:12:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbp_13298/02_2023/7pbp_13298_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbp_13298/02_2023/7pbp_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_2023/7pbp_13298.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbp_13298/02_2023/7pbp_13298.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbp_13298/02_2023/7pbp_13298_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbp_13298/02_2023/7pbp_13298_neut_trim_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 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-4877/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: 14.52, per 1000 atoms: 0.45 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: 25.21 Conformation dependent library (CDL) restraints added in 2.5 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: 14.48 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: 13.03 Time building geometry restraints manager: 26.39 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: 12353 28.36 - 56.71: 364 56.71 - 85.07: 74 85.07 - 113.42: 4 113.42 - 141.78: 6 Dihedral angle restraints: 12801 sinusoidal: 6368 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 12798 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 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. 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: 3.580 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: 1.240 Extract box with map and model: 11.940 Check model and map are aligned: 0.510 Process input model: 107.880 Find NCS groups from input model: 1.600 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.300 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 130.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 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 : 14.688 141.779 6350 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 % 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 *********************** 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 : 2.652 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 outliers start: 2 outliers final: 0 residues processed: 422 average time/residue: 0.8372 time to fit residues: 481.4950 Evaluate side-chains 261 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 2.721 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 50 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 chunk 153 optimal weight: 4.9990 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: 1.1186 ------------------------------------------------------------------------------- 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 D 232 GLN E 246 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 16606 Z= 0.273 Angle : 0.625 6.271 22612 Z= 0.335 Chirality : 0.041 0.139 2554 Planarity : 0.005 0.064 2807 Dihedral : 14.138 144.132 2535 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer Outliers : 1.04 % 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: 0.27 (0.19), residues: 1950 helix: 0.17 (0.15), residues: 1039 sheet: 0.52 (0.31), residues: 298 loop : 0.36 (0.25), residues: 613 *********************** 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 280 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 263 time to evaluate : 2.920 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 outliers start: 17 outliers final: 9 residues processed: 268 average time/residue: 0.7884 time to fit residues: 305.2819 Evaluate side-chains 260 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 251 time to evaluate : 2.622 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.5444 time to fit residues: 11.1873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 178 optimal weight: 0.7980 chunk 192 optimal weight: 7.9990 chunk 158 optimal weight: 0.9990 chunk 176 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 ASN D 232 GLN E 255 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 16606 Z= 0.229 Angle : 0.562 6.379 22612 Z= 0.294 Chirality : 0.040 0.135 2554 Planarity : 0.004 0.043 2807 Dihedral : 14.145 149.355 2535 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer Outliers : 1.04 % 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: 0.67 (0.19), residues: 1950 helix: 0.69 (0.16), residues: 1039 sheet: 0.48 (0.30), residues: 302 loop : 0.29 (0.25), residues: 609 *********************** 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 273 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 256 time to evaluate : 2.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 264 average time/residue: 0.7226 time to fit residues: 277.3578 Evaluate side-chains 257 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 248 time to evaluate : 2.527 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3756 time to fit residues: 9.5145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 0.1980 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: 0.9980 chunk 178 optimal weight: 0.3980 chunk 189 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 169 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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: 0.8345 moved from start: 0.3252 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= 0.183 Angle : 0.525 6.380 22612 Z= 0.271 Chirality : 0.039 0.133 2554 Planarity : 0.004 0.042 2807 Dihedral : 14.077 150.454 2535 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer Outliers : 0.85 % 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: 0.94 (0.19), residues: 1950 helix: 1.10 (0.17), residues: 1037 sheet: 0.17 (0.30), residues: 297 loop : 0.27 (0.25), residues: 616 *********************** 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 265 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 251 time to evaluate : 2.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 257 average time/residue: 0.7337 time to fit residues: 271.7955 Evaluate side-chains 254 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 246 time to evaluate : 2.679 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3551 time to fit residues: 8.4958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 2 optimal weight: 0.9980 chunk 141 optimal weight: 0.0060 chunk 78 optimal weight: 0.0570 chunk 161 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 chunk 96 optimal weight: 0.5980 chunk 170 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 overall best weight: 0.5114 ------------------------------------------------------------------------------- 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: 0.8338 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 16606 Z= 0.157 Angle : 0.505 6.365 22612 Z= 0.258 Chirality : 0.038 0.130 2554 Planarity : 0.004 0.044 2807 Dihedral : 13.986 146.839 2535 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer Outliers : 0.37 % 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: 1.33 (0.17), residues: 1035 sheet: 0.17 (0.29), residues: 297 loop : 0.34 (0.25), residues: 618 *********************** 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 258 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 252 time to evaluate : 2.765 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 outliers start: 6 outliers final: 3 residues processed: 252 average time/residue: 0.7464 time to fit residues: 267.1844 Evaluate side-chains 251 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 248 time to evaluate : 2.629 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3580 time to fit residues: 5.2092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 37 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 189 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 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: 0.8360 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 16606 Z= 0.224 Angle : 0.523 6.471 22612 Z= 0.269 Chirality : 0.039 0.133 2554 Planarity : 0.004 0.044 2807 Dihedral : 14.023 152.281 2535 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer Outliers : 0.30 % 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: 1.09 (0.19), residues: 1950 helix: 1.34 (0.17), residues: 1031 sheet: 0.08 (0.29), residues: 295 loop : 0.19 (0.25), residues: 624 *********************** 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 252 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 247 time to evaluate : 2.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 248 average time/residue: 0.7465 time to fit residues: 265.2483 Evaluate side-chains 243 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 240 time to evaluate : 2.643 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3320 time to fit residues: 5.1680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 159 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 188 optimal weight: 6.9990 chunk 118 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.046 16606 Z= 0.358 Angle : 0.578 6.620 22612 Z= 0.301 Chirality : 0.041 0.146 2554 Planarity : 0.004 0.050 2807 Dihedral : 14.164 161.014 2535 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer Outliers : 0.67 % 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: 0.79 (0.19), residues: 1950 helix: 1.18 (0.16), residues: 1026 sheet: -0.05 (0.29), residues: 293 loop : -0.09 (0.24), residues: 631 *********************** 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 255 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 244 time to evaluate : 2.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 10 residues processed: 249 average time/residue: 0.7339 time to fit residues: 261.4681 Evaluate side-chains 250 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 240 time to evaluate : 2.465 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.3187 time to fit residues: 9.1208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 112 optimal weight: 0.9980 chunk 56 optimal weight: 0.0770 chunk 37 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 120 optimal weight: 0.3980 chunk 128 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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: 0.8362 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 16606 Z= 0.163 Angle : 0.517 6.171 22612 Z= 0.265 Chirality : 0.038 0.131 2554 Planarity : 0.004 0.045 2807 Dihedral : 14.052 160.024 2535 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer Outliers : 0.43 % 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: 1.13 (0.19), residues: 1950 helix: 1.45 (0.17), residues: 1028 sheet: 0.13 (0.30), residues: 283 loop : 0.05 (0.24), residues: 639 *********************** 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 257 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 250 time to evaluate : 2.565 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 outliers start: 7 outliers final: 4 residues processed: 254 average time/residue: 0.7678 time to fit residues: 277.0327 Evaluate side-chains 250 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 246 time to evaluate : 2.673 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3785 time to fit residues: 5.9089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.4980 chunk 176 optimal weight: 0.4980 chunk 105 optimal weight: 0.9980 chunk 76 optimal weight: 0.4980 chunk 138 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 159 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 175 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.8356 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 16606 Z= 0.173 Angle : 0.507 6.235 22612 Z= 0.260 Chirality : 0.038 0.153 2554 Planarity : 0.004 0.068 2807 Dihedral : 13.938 162.059 2535 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer Outliers : 0.24 % 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: 1.55 (0.17), residues: 1028 sheet: 0.27 (0.29), residues: 291 loop : 0.10 (0.25), residues: 631 *********************** 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 256 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 252 time to evaluate : 2.909 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 outliers start: 4 outliers final: 2 residues processed: 255 average time/residue: 0.7467 time to fit residues: 270.5271 Evaluate side-chains 249 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 247 time to evaluate : 2.693 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3221 time to fit residues: 4.5164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 88 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 155 optimal weight: 0.0970 chunk 16 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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: 0.8364 moved from start: 0.3813 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= 0.202 Angle : 0.516 6.251 22612 Z= 0.264 Chirality : 0.039 0.133 2554 Planarity : 0.004 0.050 2807 Dihedral : 13.915 161.765 2535 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer Outliers : 0.06 % 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: 1.25 (0.19), residues: 1950 helix: 1.55 (0.17), residues: 1029 sheet: 0.25 (0.29), residues: 291 loop : 0.06 (0.24), residues: 630 ********************** 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 250 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 249 time to evaluate : 2.704 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 outliers start: 1 outliers final: 1 residues processed: 249 average time/residue: 0.7551 time to fit residues: 267.5692 Evaluate side-chains 249 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 248 time to evaluate : 2.482 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3265 time to fit residues: 3.8130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 155 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 146 HIS D 79 ASN E 246 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.115688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.082592 restraints weight = 73684.060| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 2.38 r_work: 0.2710 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2583 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 16606 Z= 0.210 Angle : 0.522 6.195 22612 Z= 0.267 Chirality : 0.039 0.153 2554 Planarity : 0.004 0.049 2807 Dihedral : 13.888 162.283 2535 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer Outliers : 0.24 % 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: 1.23 (0.19), residues: 1950 helix: 1.57 (0.17), residues: 1028 sheet: 0.07 (0.29), residues: 285 loop : 0.07 (0.24), residues: 637 =============================================================================== Job complete usr+sys time: 7639.09 seconds wall clock time: 136 minutes 11.31 seconds (8171.31 seconds total)