Starting phenix.real_space_refine (version: dev) on Fri Feb 24 01:24:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qd2_4517/02_2023/6qd2_4517.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qd2_4517/02_2023/6qd2_4517.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qd2_4517/02_2023/6qd2_4517.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qd2_4517/02_2023/6qd2_4517.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qd2_4517/02_2023/6qd2_4517.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qd2_4517/02_2023/6qd2_4517.pdb" } resolution = 4.8 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= 1.000 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 None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 21746 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 5436 Classifications: {'peptide': 355} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 333} Chain: "B" Number of atoms: 5436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 5436 Classifications: {'peptide': 355} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 333} Chain: "C" Number of atoms: 5436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 5436 Classifications: {'peptide': 355} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 333} Chain: "D" Number of atoms: 5436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 5436 Classifications: {'peptide': 355} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 333} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.31, per 1000 atoms: 0.47 Number of scatterers: 21746 At special positions: 0 Unit cell: (102.7, 102.7, 94.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 2 19.00 S 44 16.00 O 1844 8.00 N 1820 7.00 C 6936 6.00 H 11100 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: 17.28 Conformation dependent library (CDL) restraints added in 2.1 seconds 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2608 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 8 sheets defined 64.2% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 12 through 17 Processing helix chain 'A' and resid 17 through 24 Processing helix chain 'A' and resid 24 through 29 removed outlier: 4.535A pdb=" N LEU A 28 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR A 29 " --> pdb=" O VAL A 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 24 through 29' Processing helix chain 'A' and resid 34 through 61 removed outlier: 3.544A pdb=" N ARG A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU A 39 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA A 40 " --> pdb=" O ARG A 36 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA A 42 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 76 Processing helix chain 'A' and resid 77 through 92 removed outlier: 3.925A pdb=" N VAL A 82 " --> pdb=" O ASP A 78 " (cutoff:3.500A) Proline residue: A 85 - end of helix removed outlier: 3.585A pdb=" N LEU A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 101 Processing helix chain 'A' and resid 105 through 111 removed outlier: 4.241A pdb=" N LEU A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 152 removed outlier: 4.047A pdb=" N VAL A 121 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA A 123 " --> pdb=" O GLY A 119 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ASN A 124 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ARG A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ASN A 128 " --> pdb=" O ASN A 124 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ALA A 146 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA A 147 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N TYR A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A 149 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG A 152 " --> pdb=" O TYR A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 160 Processing helix chain 'A' and resid 162 through 174 Processing helix chain 'A' and resid 186 through 192 removed outlier: 4.042A pdb=" N ALA A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 225 removed outlier: 4.083A pdb=" N GLY A 208 " --> pdb=" O GLY A 204 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU A 210 " --> pdb=" O TRP A 206 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY A 213 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLN A 216 " --> pdb=" O THR A 212 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 248 removed outlier: 3.973A pdb=" N GLU A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE A 247 " --> pdb=" O VAL A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 323 through 334 Processing helix chain 'A' and resid 334 through 354 removed outlier: 4.021A pdb=" N ALA A 338 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU A 339 " --> pdb=" O PRO A 335 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ARG A 349 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALA A 353 " --> pdb=" O ARG A 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 17 Processing helix chain 'B' and resid 17 through 24 Processing helix chain 'B' and resid 24 through 29 removed outlier: 4.536A pdb=" N LEU B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR B 29 " --> pdb=" O VAL B 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 24 through 29' Processing helix chain 'B' and resid 34 through 61 removed outlier: 3.543A pdb=" N ARG B 38 " --> pdb=" O SER B 34 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU B 39 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA B 40 " --> pdb=" O ARG B 36 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA B 42 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ALA B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 76 Processing helix chain 'B' and resid 77 through 92 removed outlier: 3.925A pdb=" N VAL B 82 " --> pdb=" O ASP B 78 " (cutoff:3.500A) Proline residue: B 85 - end of helix removed outlier: 3.586A pdb=" N LEU B 90 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 101 Processing helix chain 'B' and resid 105 through 111 removed outlier: 4.241A pdb=" N LEU B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP B 111 " --> pdb=" O LYS B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 152 removed outlier: 4.047A pdb=" N VAL B 121 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA B 123 " --> pdb=" O GLY B 119 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ASN B 124 " --> pdb=" O ARG B 120 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ARG B 127 " --> pdb=" O ALA B 123 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ASN B 128 " --> pdb=" O ASN B 124 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA B 147 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N TYR B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL B 149 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE B 150 " --> pdb=" O ALA B 146 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG B 152 " --> pdb=" O TYR B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 160 Processing helix chain 'B' and resid 162 through 174 Processing helix chain 'B' and resid 186 through 192 removed outlier: 4.042A pdb=" N ALA B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 225 removed outlier: 4.084A pdb=" N GLY B 208 " --> pdb=" O GLY B 204 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU B 210 " --> pdb=" O TRP B 206 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY B 213 " --> pdb=" O ILE B 209 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLN B 216 " --> pdb=" O THR B 212 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N PHE B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 248 removed outlier: 3.974A pdb=" N GLU B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE B 247 " --> pdb=" O VAL B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 302 Processing helix chain 'B' and resid 323 through 334 Processing helix chain 'B' and resid 334 through 354 removed outlier: 4.021A pdb=" N ALA B 338 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU B 339 " --> pdb=" O PRO B 335 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ILE B 340 " --> pdb=" O GLU B 336 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ARG B 349 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY B 350 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ALA B 353 " --> pdb=" O ARG B 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 17 Processing helix chain 'C' and resid 17 through 24 Processing helix chain 'C' and resid 24 through 29 removed outlier: 4.535A pdb=" N LEU C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR C 29 " --> pdb=" O VAL C 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 24 through 29' Processing helix chain 'C' and resid 34 through 61 removed outlier: 3.543A pdb=" N ARG C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU C 39 " --> pdb=" O GLY C 35 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA C 40 " --> pdb=" O ARG C 36 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA C 42 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA C 57 " --> pdb=" O LEU C 53 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA C 58 " --> pdb=" O LEU C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 76 Processing helix chain 'C' and resid 77 through 92 removed outlier: 3.925A pdb=" N VAL C 82 " --> pdb=" O ASP C 78 " (cutoff:3.500A) Proline residue: C 85 - end of helix removed outlier: 3.585A pdb=" N LEU C 90 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 101 Processing helix chain 'C' and resid 105 through 111 removed outlier: 4.241A pdb=" N LEU C 109 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP C 111 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 152 removed outlier: 4.047A pdb=" N VAL C 121 " --> pdb=" O VAL C 117 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU C 122 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA C 123 " --> pdb=" O GLY C 119 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASN C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ARG C 127 " --> pdb=" O ALA C 123 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ASN C 128 " --> pdb=" O ASN C 124 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA C 146 " --> pdb=" O ALA C 142 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA C 147 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N TYR C 148 " --> pdb=" O ALA C 144 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL C 149 " --> pdb=" O LEU C 145 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE C 150 " --> pdb=" O ALA C 146 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG C 152 " --> pdb=" O TYR C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 160 Processing helix chain 'C' and resid 162 through 174 Processing helix chain 'C' and resid 186 through 192 removed outlier: 4.042A pdb=" N ALA C 192 " --> pdb=" O GLY C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 225 removed outlier: 4.083A pdb=" N GLY C 208 " --> pdb=" O GLY C 204 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU C 210 " --> pdb=" O TRP C 206 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA C 211 " --> pdb=" O ALA C 207 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY C 213 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLN C 216 " --> pdb=" O THR C 212 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N PHE C 223 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 248 removed outlier: 3.974A pdb=" N GLU C 246 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE C 247 " --> pdb=" O VAL C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 302 Processing helix chain 'C' and resid 323 through 334 Processing helix chain 'C' and resid 334 through 354 removed outlier: 4.021A pdb=" N ALA C 338 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU C 339 " --> pdb=" O PRO C 335 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE C 340 " --> pdb=" O GLU C 336 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ARG C 349 " --> pdb=" O ALA C 345 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY C 350 " --> pdb=" O LEU C 346 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALA C 353 " --> pdb=" O ARG C 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 17 Processing helix chain 'D' and resid 17 through 24 Processing helix chain 'D' and resid 24 through 29 removed outlier: 4.535A pdb=" N LEU D 28 " --> pdb=" O ALA D 24 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR D 29 " --> pdb=" O VAL D 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 24 through 29' Processing helix chain 'D' and resid 34 through 61 removed outlier: 3.543A pdb=" N ARG D 38 " --> pdb=" O SER D 34 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU D 39 " --> pdb=" O GLY D 35 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA D 40 " --> pdb=" O ARG D 36 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA D 42 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA D 57 " --> pdb=" O LEU D 53 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ALA D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 76 Processing helix chain 'D' and resid 77 through 92 removed outlier: 3.925A pdb=" N VAL D 82 " --> pdb=" O ASP D 78 " (cutoff:3.500A) Proline residue: D 85 - end of helix removed outlier: 3.586A pdb=" N LEU D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 101 Processing helix chain 'D' and resid 105 through 111 removed outlier: 4.240A pdb=" N LEU D 109 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP D 111 " --> pdb=" O LYS D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 152 removed outlier: 4.047A pdb=" N VAL D 121 " --> pdb=" O VAL D 117 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA D 123 " --> pdb=" O GLY D 119 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASN D 124 " --> pdb=" O ARG D 120 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ARG D 127 " --> pdb=" O ALA D 123 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ASN D 128 " --> pdb=" O ASN D 124 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA D 146 " --> pdb=" O ALA D 142 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA D 147 " --> pdb=" O VAL D 143 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N TYR D 148 " --> pdb=" O ALA D 144 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL D 149 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE D 150 " --> pdb=" O ALA D 146 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG D 152 " --> pdb=" O TYR D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 160 Processing helix chain 'D' and resid 162 through 174 Processing helix chain 'D' and resid 186 through 192 removed outlier: 4.041A pdb=" N ALA D 192 " --> pdb=" O GLY D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 225 removed outlier: 4.083A pdb=" N GLY D 208 " --> pdb=" O GLY D 204 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU D 210 " --> pdb=" O TRP D 206 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA D 211 " --> pdb=" O ALA D 207 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY D 213 " --> pdb=" O ILE D 209 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLN D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 248 removed outlier: 3.973A pdb=" N GLU D 246 " --> pdb=" O ALA D 242 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE D 247 " --> pdb=" O VAL D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 302 Processing helix chain 'D' and resid 323 through 334 Processing helix chain 'D' and resid 334 through 354 removed outlier: 4.022A pdb=" N ALA D 338 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU D 339 " --> pdb=" O PRO D 335 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE D 340 " --> pdb=" O GLU D 336 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ARG D 349 " --> pdb=" O ALA D 345 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY D 350 " --> pdb=" O LEU D 346 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALA D 353 " --> pdb=" O ARG D 349 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 254 through 256 removed outlier: 4.210A pdb=" N GLU A 277 " --> pdb=" O SER A 318 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 261 through 263 removed outlier: 4.177A pdb=" N THR A 310 " --> pdb=" O ALA A 283 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 254 through 256 removed outlier: 4.210A pdb=" N GLU B 277 " --> pdb=" O SER B 318 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 261 through 263 removed outlier: 4.178A pdb=" N THR B 310 " --> pdb=" O ALA B 283 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 254 through 256 removed outlier: 4.209A pdb=" N GLU C 277 " --> pdb=" O SER C 318 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 261 through 263 removed outlier: 4.177A pdb=" N THR C 310 " --> pdb=" O ALA C 283 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 254 through 256 removed outlier: 4.210A pdb=" N GLU D 277 " --> pdb=" O SER D 318 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 261 through 263 removed outlier: 4.178A pdb=" N THR D 310 " --> pdb=" O ALA D 283 " (cutoff:3.500A) 528 hydrogen bonds defined for protein. 1464 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.15 Time building geometry restraints manager: 17.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 11088 1.03 - 1.22: 12 1.22 - 1.42: 4343 1.42 - 1.61: 6461 1.61 - 1.81: 76 Bond restraints: 21980 Sorted by residual: bond pdb=" CZ ARG C 220 " pdb=" NH2 ARG C 220 " ideal model delta sigma weight residual 1.330 1.311 0.019 1.30e-02 5.92e+03 2.23e+00 bond pdb=" CZ ARG B 220 " pdb=" NH2 ARG B 220 " ideal model delta sigma weight residual 1.330 1.311 0.019 1.30e-02 5.92e+03 2.23e+00 bond pdb=" CZ ARG D 220 " pdb=" NH2 ARG D 220 " ideal model delta sigma weight residual 1.330 1.311 0.019 1.30e-02 5.92e+03 2.06e+00 bond pdb=" CZ ARG A 220 " pdb=" NH2 ARG A 220 " ideal model delta sigma weight residual 1.330 1.312 0.018 1.30e-02 5.92e+03 2.00e+00 bond pdb=" CB TRP A 167 " pdb=" CG TRP A 167 " ideal model delta sigma weight residual 1.498 1.459 0.039 3.10e-02 1.04e+03 1.60e+00 ... (remaining 21975 not shown) Histogram of bond angle deviations from ideal: 99.88 - 106.71: 856 106.71 - 113.55: 26223 113.55 - 120.39: 6830 120.39 - 127.22: 5875 127.22 - 134.06: 156 Bond angle restraints: 39940 Sorted by residual: angle pdb=" C ALA D 11 " pdb=" CA ALA D 11 " pdb=" CB ALA D 11 " ideal model delta sigma weight residual 113.57 108.63 4.94 1.57e+00 4.06e-01 9.89e+00 angle pdb=" C ALA C 11 " pdb=" CA ALA C 11 " pdb=" CB ALA C 11 " ideal model delta sigma weight residual 113.57 108.64 4.93 1.57e+00 4.06e-01 9.85e+00 angle pdb=" C ALA B 11 " pdb=" CA ALA B 11 " pdb=" CB ALA B 11 " ideal model delta sigma weight residual 113.57 108.66 4.91 1.57e+00 4.06e-01 9.79e+00 angle pdb=" C ALA A 11 " pdb=" CA ALA A 11 " pdb=" CB ALA A 11 " ideal model delta sigma weight residual 113.57 108.70 4.87 1.57e+00 4.06e-01 9.61e+00 angle pdb=" CG HIS D 323 " pdb=" CB HIS D 323 " pdb=" HB3 HIS D 323 " ideal model delta sigma weight residual 108.00 99.88 8.12 3.00e+00 1.11e-01 7.33e+00 ... (remaining 39935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.07: 8283 15.07 - 30.14: 362 30.14 - 45.21: 23 45.21 - 60.28: 8 60.28 - 75.35: 8 Dihedral angle restraints: 8684 sinusoidal: 4000 harmonic: 4684 Sorted by residual: dihedral pdb=" CA SER B 112 " pdb=" C SER B 112 " pdb=" N THR B 113 " pdb=" CA THR B 113 " ideal model delta harmonic sigma weight residual 180.00 151.38 28.62 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA SER D 112 " pdb=" C SER D 112 " pdb=" N THR D 113 " pdb=" CA THR D 113 " ideal model delta harmonic sigma weight residual 180.00 151.40 28.60 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA SER C 112 " pdb=" C SER C 112 " pdb=" N THR C 113 " pdb=" CA THR C 113 " ideal model delta harmonic sigma weight residual 180.00 151.43 28.57 0 5.00e+00 4.00e-02 3.27e+01 ... (remaining 8681 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1052 0.030 - 0.060: 435 0.060 - 0.090: 205 0.090 - 0.121: 71 0.121 - 0.151: 21 Chirality restraints: 1784 Sorted by residual: chirality pdb=" CA VAL C 68 " pdb=" N VAL C 68 " pdb=" C VAL C 68 " pdb=" CB VAL C 68 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.68e-01 chirality pdb=" CA VAL A 68 " pdb=" N VAL A 68 " pdb=" C VAL A 68 " pdb=" CB VAL A 68 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.65e-01 chirality pdb=" CA VAL D 68 " pdb=" N VAL D 68 " pdb=" C VAL D 68 " pdb=" CB VAL D 68 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.64e-01 ... (remaining 1781 not shown) Planarity restraints: 3204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 324 " 0.011 2.00e-02 2.50e+03 1.97e-02 3.87e+00 pdb=" N ALA A 325 " -0.034 2.00e-02 2.50e+03 pdb=" CA ALA A 325 " 0.009 2.00e-02 2.50e+03 pdb=" H ALA A 325 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 30 " 0.029 5.00e-02 4.00e+02 4.38e-02 3.06e+00 pdb=" N PRO C 31 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO C 31 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 31 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 30 " -0.029 5.00e-02 4.00e+02 4.33e-02 3.01e+00 pdb=" N PRO A 31 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 31 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 31 " -0.024 5.00e-02 4.00e+02 ... (remaining 3201 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.38: 8888 2.38 - 3.07: 63279 3.07 - 3.76: 72581 3.76 - 4.45: 112631 4.45 - 5.14: 171226 Nonbonded interactions: 428605 Sorted by model distance: nonbonded pdb=" O LYS A 62 " pdb="HH22 ARG A 69 " model vdw 1.686 1.850 nonbonded pdb=" O LYS C 62 " pdb="HH22 ARG C 69 " model vdw 1.687 1.850 nonbonded pdb=" O LYS B 62 " pdb="HH22 ARG B 69 " model vdw 1.687 1.850 nonbonded pdb=" O LYS D 62 " pdb="HH22 ARG D 69 " model vdw 1.687 1.850 nonbonded pdb="HH11 ARG B 120 " pdb=" OE2 GLU B 217 " model vdw 1.701 1.850 ... (remaining 428600 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 1 through 355) selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 6 Type Number sf(0) Gaussians K 2 8.98 5 S 44 5.16 5 C 6936 2.51 5 N 1820 2.21 5 O 1844 1.98 5 H 11100 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 group one per residue 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: 0.080 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: 0.330 Extract box with map and model: 2.400 Check model and map are aligned: 0.290 Process input model: 68.590 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.180 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6215 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 : 0.006 0.046 10880 Z= 0.390 Angle : 0.857 6.874 14852 Z= 0.468 Chirality : 0.043 0.151 1784 Planarity : 0.006 0.044 1872 Dihedral : 9.036 75.347 3844 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.61 % Favored : 88.39 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.60 (0.19), residues: 1412 helix: -3.82 (0.12), residues: 616 sheet: -4.07 (0.54), residues: 40 loop : -2.26 (0.23), residues: 756 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 374 time to evaluate : 1.591 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: 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: 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: 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: 0 outliers final: 0 residues processed: 374 average time/residue: 0.5821 time to fit residues: 294.0503 Evaluate side-chains 301 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 301 time to evaluate : 1.579 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 0.8980 chunk 106 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 71 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 109 optimal weight: 20.0000 chunk 42 optimal weight: 7.9990 chunk 66 optimal weight: 40.0000 chunk 81 optimal weight: 8.9990 chunk 127 optimal weight: 9.9990 overall best weight: 6.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6288 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 10880 Z= 0.238 Angle : 0.693 7.779 14852 Z= 0.372 Chirality : 0.041 0.133 1784 Planarity : 0.006 0.034 1872 Dihedral : 6.059 23.282 1536 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.21), residues: 1412 helix: -2.39 (0.16), residues: 708 sheet: -2.64 (0.74), residues: 40 loop : -2.03 (0.26), residues: 664 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 341 time to evaluate : 1.537 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: 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: 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: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 341 average time/residue: 0.5125 time to fit residues: 244.4507 Evaluate side-chains 298 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 1.576 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 20.0000 chunk 39 optimal weight: 8.9990 chunk 105 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 127 optimal weight: 20.0000 chunk 137 optimal weight: 7.9990 chunk 113 optimal weight: 9.9990 chunk 126 optimal weight: 6.9990 chunk 43 optimal weight: 0.6980 chunk 102 optimal weight: 8.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6297 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 10880 Z= 0.196 Angle : 0.612 5.397 14852 Z= 0.329 Chirality : 0.038 0.127 1784 Planarity : 0.005 0.035 1872 Dihedral : 5.525 22.037 1536 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.21), residues: 1412 helix: -1.49 (0.18), residues: 776 sheet: None (None), residues: 0 loop : -2.39 (0.24), residues: 636 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 307 time to evaluate : 1.881 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 307 average time/residue: 0.4646 time to fit residues: 206.5427 Evaluate side-chains 278 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 1.748 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 10.0000 chunk 95 optimal weight: 20.0000 chunk 66 optimal weight: 50.0000 chunk 14 optimal weight: 20.0000 chunk 60 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 chunk 127 optimal weight: 30.0000 chunk 135 optimal weight: 0.0170 chunk 121 optimal weight: 8.9990 chunk 36 optimal weight: 30.0000 chunk 112 optimal weight: 9.9990 overall best weight: 7.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6392 moved from start: 0.4943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 10880 Z= 0.217 Angle : 0.617 5.543 14852 Z= 0.333 Chirality : 0.038 0.124 1784 Planarity : 0.005 0.047 1872 Dihedral : 5.294 19.043 1536 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.22), residues: 1412 helix: -1.14 (0.18), residues: 768 sheet: None (None), residues: 0 loop : -2.11 (0.25), residues: 644 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 293 time to evaluate : 1.647 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: 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: 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: symmetry clash outliers start: 0 outliers final: 0 residues processed: 293 average time/residue: 0.4471 time to fit residues: 196.7662 Evaluate side-chains 274 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 274 time to evaluate : 1.705 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 100 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 chunk 115 optimal weight: 6.9990 chunk 93 optimal weight: 40.0000 chunk 0 optimal weight: 30.0000 chunk 69 optimal weight: 20.0000 chunk 121 optimal weight: 8.9990 chunk 34 optimal weight: 40.0000 chunk 45 optimal weight: 5.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6457 moved from start: 0.5583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 10880 Z= 0.232 Angle : 0.624 5.215 14852 Z= 0.337 Chirality : 0.039 0.131 1784 Planarity : 0.005 0.067 1872 Dihedral : 5.225 18.198 1536 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.22), residues: 1412 helix: -0.80 (0.19), residues: 768 sheet: None (None), residues: 0 loop : -2.02 (0.25), residues: 644 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 289 time to evaluate : 1.495 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: 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: 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: 0 outliers final: 0 residues processed: 289 average time/residue: 0.3896 time to fit residues: 170.5723 Evaluate side-chains 272 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 272 time to evaluate : 1.744 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 10.0000 chunk 26 optimal weight: 20.0000 chunk 79 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 chunk 135 optimal weight: 20.0000 chunk 112 optimal weight: 0.9990 chunk 62 optimal weight: 30.0000 chunk 11 optimal weight: 20.0000 chunk 44 optimal weight: 10.0000 chunk 71 optimal weight: 20.0000 chunk 130 optimal weight: 7.9990 overall best weight: 7.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 HIS A 328 GLN B 328 GLN C 328 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6474 moved from start: 0.6023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 10880 Z= 0.210 Angle : 0.598 5.362 14852 Z= 0.321 Chirality : 0.038 0.121 1784 Planarity : 0.005 0.071 1872 Dihedral : 5.066 17.347 1536 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.92 % Favored : 90.08 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.22), residues: 1412 helix: -0.71 (0.19), residues: 768 sheet: None (None), residues: 0 loop : -1.90 (0.25), residues: 644 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 285 time to evaluate : 1.654 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: 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: 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: 0 outliers final: 0 residues processed: 285 average time/residue: 0.3761 time to fit residues: 163.9855 Evaluate side-chains 270 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 1.605 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 114 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 134 optimal weight: 7.9990 chunk 84 optimal weight: 20.0000 chunk 82 optimal weight: 20.0000 chunk 62 optimal weight: 0.1980 chunk 83 optimal weight: 8.9990 overall best weight: 6.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 328 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6458 moved from start: 0.6283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 10880 Z= 0.186 Angle : 0.569 5.249 14852 Z= 0.302 Chirality : 0.038 0.145 1784 Planarity : 0.005 0.063 1872 Dihedral : 4.926 16.164 1536 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.22), residues: 1412 helix: -0.51 (0.19), residues: 772 sheet: None (None), residues: 0 loop : -1.84 (0.24), residues: 640 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 289 time to evaluate : 1.619 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: 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: 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: 0 outliers final: 0 residues processed: 289 average time/residue: 0.3772 time to fit residues: 168.2867 Evaluate side-chains 273 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 1.651 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 40 optimal weight: 20.0000 chunk 26 optimal weight: 0.3980 chunk 85 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 106 optimal weight: 30.0000 chunk 122 optimal weight: 3.9990 chunk 129 optimal weight: 20.0000 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 323 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6425 moved from start: 0.6542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 10880 Z= 0.163 Angle : 0.555 5.420 14852 Z= 0.291 Chirality : 0.038 0.123 1784 Planarity : 0.005 0.056 1872 Dihedral : 4.698 15.075 1536 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.23), residues: 1412 helix: -0.22 (0.20), residues: 776 sheet: None (None), residues: 0 loop : -1.74 (0.25), residues: 636 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 289 time to evaluate : 1.812 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: 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: 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: 0 outliers final: 0 residues processed: 289 average time/residue: 0.3668 time to fit residues: 164.7341 Evaluate side-chains 265 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 1.789 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 20.0000 chunk 125 optimal weight: 20.0000 chunk 129 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 54 optimal weight: 20.0000 chunk 98 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 113 optimal weight: 20.0000 chunk 118 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 132 optimal weight: 40.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 323 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6493 moved from start: 0.6852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 10880 Z= 0.210 Angle : 0.599 5.049 14852 Z= 0.323 Chirality : 0.039 0.129 1784 Planarity : 0.005 0.067 1872 Dihedral : 4.895 16.752 1536 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.22), residues: 1412 helix: -0.60 (0.18), residues: 800 sheet: None (None), residues: 0 loop : -1.82 (0.25), residues: 612 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 1.719 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: 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: 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: 0 outliers final: 0 residues processed: 290 average time/residue: 0.3831 time to fit residues: 170.8454 Evaluate side-chains 271 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 1.617 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 139 optimal weight: 9.9990 chunk 128 optimal weight: 0.4980 chunk 111 optimal weight: 0.8980 chunk 11 optimal weight: 20.0000 chunk 85 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 88 optimal weight: 0.9990 chunk 118 optimal weight: 8.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6394 moved from start: 0.6909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 10880 Z= 0.145 Angle : 0.543 5.290 14852 Z= 0.280 Chirality : 0.038 0.126 1784 Planarity : 0.004 0.066 1872 Dihedral : 4.526 15.270 1536 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.23), residues: 1412 helix: 0.20 (0.20), residues: 776 sheet: None (None), residues: 0 loop : -1.45 (0.25), residues: 636 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 285 time to evaluate : 1.632 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: 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: 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: 0 outliers final: 0 residues processed: 285 average time/residue: 0.3633 time to fit residues: 161.7208 Evaluate side-chains 263 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 1.546 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 20.0000 chunk 102 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 30 optimal weight: 0.8980 chunk 111 optimal weight: 20.0000 chunk 46 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 14 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 97 optimal weight: 40.0000 chunk 6 optimal weight: 4.9990 overall best weight: 7.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.223301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.186311 restraints weight = 60525.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.191931 restraints weight = 32018.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.195587 restraints weight = 20525.667| |-----------------------------------------------------------------------------| r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6487 moved from start: 0.7165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 10880 Z= 0.209 Angle : 0.592 4.956 14852 Z= 0.317 Chirality : 0.038 0.121 1784 Planarity : 0.005 0.055 1872 Dihedral : 4.750 15.836 1536 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.22), residues: 1412 helix: -0.41 (0.18), residues: 824 sheet: None (None), residues: 0 loop : -1.73 (0.26), residues: 588 =============================================================================== Job complete usr+sys time: 4218.99 seconds wall clock time: 75 minutes 20.81 seconds (4520.81 seconds total)