Starting phenix.real_space_refine on Mon Mar 18 17:36:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qd2_4517/03_2024/6qd2_4517.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qd2_4517/03_2024/6qd2_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_4517/03_2024/6qd2_4517.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qd2_4517/03_2024/6qd2_4517.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qd2_4517/03_2024/6qd2_4517.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qd2_4517/03_2024/6qd2_4517.pdb" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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 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. 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-5265/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: 9.71, per 1000 atoms: 0.45 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: 17.82 Conformation dependent library (CDL) restraints added in 2.2 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: 1.84 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: 8.05 Time building geometry restraints manager: 18.43 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: 9559 15.07 - 30.14: 450 30.14 - 45.21: 171 45.21 - 60.28: 100 60.28 - 75.35: 8 Dihedral angle restraints: 10288 sinusoidal: 5604 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 10285 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 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: 0.040 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: 0.270 Extract box with map and model: 1.340 Check model and map are aligned: 0.310 Set scattering table: 0.180 Process input model: 74.720 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6440 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 % Allowed : 1.47 % Favored : 98.53 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 167 HIS 0.005 0.003 HIS C 323 PHE 0.015 0.002 PHE A 236 TYR 0.016 0.003 TYR C 10 ARG 0.005 0.001 ARG B 63 *********************** 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 : 1.651 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 REVERT: A 78 ASP cc_start: 0.7643 (m-30) cc_final: 0.7419 (m-30) REVERT: A 227 TRP cc_start: 0.7345 (t60) cc_final: 0.6917 (t60) REVERT: B 36 ARG cc_start: 0.7788 (mtt180) cc_final: 0.7105 (mtm180) REVERT: B 78 ASP cc_start: 0.7648 (m-30) cc_final: 0.7405 (m-30) REVERT: B 133 THR cc_start: 0.6578 (m) cc_final: 0.6376 (m) REVERT: B 151 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7592 (mm-30) REVERT: B 227 TRP cc_start: 0.7408 (t60) cc_final: 0.6856 (t60) REVERT: C 36 ARG cc_start: 0.7784 (mtt180) cc_final: 0.7160 (mtm180) REVERT: C 78 ASP cc_start: 0.7710 (m-30) cc_final: 0.7470 (m-30) REVERT: C 133 THR cc_start: 0.6595 (m) cc_final: 0.6366 (m) REVERT: C 151 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7540 (mm-30) REVERT: C 197 MET cc_start: 0.8752 (ttm) cc_final: 0.8060 (tpp) REVERT: C 227 TRP cc_start: 0.7499 (t60) cc_final: 0.7014 (t60) REVERT: D 227 TRP cc_start: 0.7546 (t60) cc_final: 0.7073 (t60) outliers start: 0 outliers final: 0 residues processed: 374 average time/residue: 0.5923 time to fit residues: 301.9083 Evaluate side-chains 303 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 303 time to evaluate : 1.456 ------------------------------------------------------------------------------- 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: 5.9990 chunk 106 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 71 optimal weight: 20.0000 chunk 56 optimal weight: 10.0000 chunk 109 optimal weight: 20.0000 chunk 42 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 127 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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: 0.6517 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 10880 Z= 0.234 Angle : 0.682 7.206 14852 Z= 0.370 Chirality : 0.040 0.135 1784 Planarity : 0.006 0.038 1872 Dihedral : 6.165 23.781 1536 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % 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: -3.55 (0.21), residues: 1412 helix: -2.52 (0.16), residues: 704 sheet: -2.72 (0.72), residues: 40 loop : -2.04 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 104 HIS 0.003 0.002 HIS B 323 PHE 0.011 0.001 PHE A 114 TYR 0.010 0.002 TYR C 178 ARG 0.007 0.001 ARG A 220 *********************** 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 347 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 347 time to evaluate : 1.716 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: A 17 LEU cc_start: 0.9220 (mt) cc_final: 0.9017 (tp) REVERT: A 133 THR cc_start: 0.7133 (m) cc_final: 0.6915 (m) REVERT: A 227 TRP cc_start: 0.7479 (t60) cc_final: 0.7084 (t60) REVERT: B 158 LYS cc_start: 0.9219 (mptt) cc_final: 0.8936 (mmmt) REVERT: B 197 MET cc_start: 0.8645 (ttm) cc_final: 0.8010 (tpp) REVERT: B 214 PHE cc_start: 0.9190 (t80) cc_final: 0.8945 (t80) REVERT: B 227 TRP cc_start: 0.7410 (t60) cc_final: 0.6975 (t60) REVERT: C 17 LEU cc_start: 0.9218 (mt) cc_final: 0.9005 (tp) REVERT: C 158 LYS cc_start: 0.9238 (mptt) cc_final: 0.8960 (mmmt) REVERT: C 197 MET cc_start: 0.8618 (ttm) cc_final: 0.7982 (tpp) REVERT: C 214 PHE cc_start: 0.9261 (t80) cc_final: 0.8995 (t80) REVERT: C 227 TRP cc_start: 0.7478 (t60) cc_final: 0.7062 (t60) REVERT: D 197 MET cc_start: 0.8506 (ttm) cc_final: 0.7854 (tpp) REVERT: D 227 TRP cc_start: 0.7440 (t60) cc_final: 0.7019 (t60) outliers start: 0 outliers final: 0 residues processed: 347 average time/residue: 0.5186 time to fit residues: 250.0493 Evaluate side-chains 296 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 296 time to evaluate : 1.592 ------------------------------------------------------------------------------- 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: 5.9990 chunk 105 optimal weight: 20.0000 chunk 86 optimal weight: 9.9990 chunk 35 optimal weight: 30.0000 chunk 127 optimal weight: 30.0000 chunk 137 optimal weight: 30.0000 chunk 113 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 chunk 43 optimal weight: 20.0000 chunk 102 optimal weight: 20.0000 overall best weight: 10.3994 ------------------------------------------------------------------------------- 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: 0.6672 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 10880 Z= 0.289 Angle : 0.695 5.120 14852 Z= 0.384 Chirality : 0.040 0.130 1784 Planarity : 0.006 0.047 1872 Dihedral : 5.988 22.621 1536 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % 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: -3.30 (0.21), residues: 1412 helix: -1.92 (0.17), residues: 800 sheet: None (None), residues: 0 loop : -2.45 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 167 HIS 0.012 0.007 HIS A 323 PHE 0.014 0.002 PHE D 136 TYR 0.012 0.002 TYR B 178 ARG 0.012 0.001 ARG C 189 *********************** 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 : 1.790 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: A 101 CYS cc_start: 0.8804 (m) cc_final: 0.8444 (m) REVERT: A 196 MET cc_start: 0.8676 (mpp) cc_final: 0.8472 (mmt) REVERT: A 197 MET cc_start: 0.8749 (ttm) cc_final: 0.8157 (tpp) REVERT: A 227 TRP cc_start: 0.7664 (t60) cc_final: 0.7340 (t60) REVERT: A 281 SER cc_start: 0.7887 (t) cc_final: 0.7567 (m) REVERT: B 36 ARG cc_start: 0.8137 (mtt180) cc_final: 0.7233 (mtm180) REVERT: B 101 CYS cc_start: 0.8831 (m) cc_final: 0.8423 (m) REVERT: B 133 THR cc_start: 0.6883 (m) cc_final: 0.6651 (m) REVERT: B 197 MET cc_start: 0.8736 (ttm) cc_final: 0.8065 (tpp) REVERT: B 214 PHE cc_start: 0.9188 (t80) cc_final: 0.8954 (t80) REVERT: B 227 TRP cc_start: 0.7558 (t60) cc_final: 0.7103 (t60) REVERT: C 17 LEU cc_start: 0.9273 (mt) cc_final: 0.9035 (tp) REVERT: C 36 ARG cc_start: 0.8152 (mtt180) cc_final: 0.7209 (mpp80) REVERT: C 101 CYS cc_start: 0.8797 (m) cc_final: 0.8394 (m) REVERT: C 196 MET cc_start: 0.8499 (mpp) cc_final: 0.8192 (mmt) REVERT: C 197 MET cc_start: 0.8810 (ttm) cc_final: 0.8124 (tpp) REVERT: C 214 PHE cc_start: 0.9325 (t80) cc_final: 0.9093 (t80) REVERT: C 227 TRP cc_start: 0.7659 (t60) cc_final: 0.7211 (t60) REVERT: C 243 VAL cc_start: 0.8349 (t) cc_final: 0.8078 (m) REVERT: D 101 CYS cc_start: 0.8767 (m) cc_final: 0.8395 (m) REVERT: D 196 MET cc_start: 0.8476 (mpp) cc_final: 0.8134 (mmt) REVERT: D 197 MET cc_start: 0.8692 (ttm) cc_final: 0.8052 (tpp) REVERT: D 227 TRP cc_start: 0.7682 (t60) cc_final: 0.7219 (t60) REVERT: D 281 SER cc_start: 0.7291 (t) cc_final: 0.6752 (m) outliers start: 0 outliers final: 0 residues processed: 307 average time/residue: 0.4559 time to fit residues: 205.0672 Evaluate side-chains 289 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 289 time to evaluate : 1.713 ------------------------------------------------------------------------------- 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: 0.7980 chunk 95 optimal weight: 8.9990 chunk 66 optimal weight: 50.0000 chunk 14 optimal weight: 20.0000 chunk 60 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 127 optimal weight: 10.0000 chunk 135 optimal weight: 0.9980 chunk 121 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 112 optimal weight: 7.9990 overall best weight: 5.1586 ------------------------------------------------------------------------------- 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: 0.6620 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10880 Z= 0.183 Angle : 0.577 5.860 14852 Z= 0.309 Chirality : 0.038 0.121 1784 Planarity : 0.005 0.048 1872 Dihedral : 5.278 19.191 1536 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % 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: -2.25 (0.22), residues: 1412 helix: -1.04 (0.19), residues: 764 sheet: None (None), residues: 0 loop : -1.99 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 206 HIS 0.008 0.005 HIS D 323 PHE 0.010 0.001 PHE A 223 TYR 0.009 0.001 TYR C 52 ARG 0.008 0.000 ARG B 220 *********************** 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 308 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 308 time to evaluate : 1.580 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: A 101 CYS cc_start: 0.8487 (m) cc_final: 0.8061 (m) REVERT: A 197 MET cc_start: 0.8758 (ttm) cc_final: 0.8219 (tpp) REVERT: A 227 TRP cc_start: 0.7518 (t60) cc_final: 0.7188 (t60) REVERT: A 281 SER cc_start: 0.7778 (t) cc_final: 0.7491 (m) REVERT: B 101 CYS cc_start: 0.8557 (m) cc_final: 0.8146 (m) REVERT: B 197 MET cc_start: 0.8800 (ttm) cc_final: 0.8154 (tpp) REVERT: B 214 PHE cc_start: 0.9180 (t80) cc_final: 0.8898 (t80) REVERT: B 227 TRP cc_start: 0.7489 (t60) cc_final: 0.7036 (t60) REVERT: C 17 LEU cc_start: 0.9210 (mt) cc_final: 0.8778 (tp) REVERT: C 25 VAL cc_start: 0.8769 (t) cc_final: 0.8402 (p) REVERT: C 48 ILE cc_start: 0.9571 (mt) cc_final: 0.9351 (mt) REVERT: C 101 CYS cc_start: 0.8535 (m) cc_final: 0.8144 (m) REVERT: C 196 MET cc_start: 0.8593 (mpp) cc_final: 0.8364 (mmt) REVERT: C 197 MET cc_start: 0.8743 (ttm) cc_final: 0.8216 (tpp) REVERT: C 214 PHE cc_start: 0.9256 (t80) cc_final: 0.8981 (t80) REVERT: C 227 TRP cc_start: 0.7556 (t60) cc_final: 0.7105 (t60) REVERT: D 101 CYS cc_start: 0.8539 (m) cc_final: 0.8132 (m) REVERT: D 197 MET cc_start: 0.8694 (ttm) cc_final: 0.8336 (tpp) REVERT: D 227 TRP cc_start: 0.7573 (t60) cc_final: 0.7164 (t60) REVERT: D 281 SER cc_start: 0.7578 (t) cc_final: 0.7124 (m) outliers start: 0 outliers final: 0 residues processed: 308 average time/residue: 0.4184 time to fit residues: 188.9255 Evaluate side-chains 289 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 289 time to evaluate : 1.426 ------------------------------------------------------------------------------- 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: 50.0000 chunk 55 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 93 optimal weight: 40.0000 chunk 0 optimal weight: 40.0000 chunk 69 optimal weight: 20.0000 chunk 121 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 overall best weight: 9.5994 ------------------------------------------------------------------------------- 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: 0.6741 moved from start: 0.5513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10880 Z= 0.267 Angle : 0.645 5.360 14852 Z= 0.356 Chirality : 0.039 0.129 1784 Planarity : 0.006 0.055 1872 Dihedral : 5.452 18.143 1536 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % 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: -2.48 (0.21), residues: 1412 helix: -1.19 (0.18), residues: 776 sheet: None (None), residues: 0 loop : -2.18 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 168 HIS 0.009 0.004 HIS C 323 PHE 0.013 0.001 PHE A 136 TYR 0.015 0.002 TYR A 178 ARG 0.011 0.001 ARG B 220 *********************** 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 299 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 CYS cc_start: 0.8729 (m) cc_final: 0.8353 (m) REVERT: A 197 MET cc_start: 0.8865 (ttm) cc_final: 0.8395 (tpp) REVERT: A 214 PHE cc_start: 0.9518 (t80) cc_final: 0.9283 (t80) REVERT: A 227 TRP cc_start: 0.7758 (t60) cc_final: 0.7414 (t60) REVERT: A 281 SER cc_start: 0.7789 (t) cc_final: 0.7515 (m) REVERT: B 101 CYS cc_start: 0.8880 (m) cc_final: 0.8514 (m) REVERT: B 197 MET cc_start: 0.8904 (ttm) cc_final: 0.8458 (tpp) REVERT: B 214 PHE cc_start: 0.9226 (t80) cc_final: 0.8985 (t80) REVERT: B 227 TRP cc_start: 0.7750 (t60) cc_final: 0.7327 (t60) REVERT: C 17 LEU cc_start: 0.9298 (mt) cc_final: 0.9055 (tp) REVERT: C 36 ARG cc_start: 0.8020 (mtt180) cc_final: 0.7089 (mtm180) REVERT: C 197 MET cc_start: 0.8833 (ttm) cc_final: 0.8321 (tpp) REVERT: C 214 PHE cc_start: 0.9269 (t80) cc_final: 0.9037 (t80) REVERT: C 227 TRP cc_start: 0.7820 (t60) cc_final: 0.7434 (t60) REVERT: C 323 HIS cc_start: 0.4672 (m-70) cc_final: 0.4366 (m-70) REVERT: D 101 CYS cc_start: 0.8795 (m) cc_final: 0.8408 (m) REVERT: D 197 MET cc_start: 0.8819 (ttm) cc_final: 0.8374 (tpp) REVERT: D 214 PHE cc_start: 0.9465 (t80) cc_final: 0.9255 (t80) REVERT: D 227 TRP cc_start: 0.7804 (t60) cc_final: 0.7443 (t60) REVERT: D 281 SER cc_start: 0.7299 (t) cc_final: 0.6817 (m) outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.4024 time to fit residues: 178.6273 Evaluate side-chains 280 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 280 time to evaluate : 1.618 ------------------------------------------------------------------------------- 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: 9.9990 chunk 26 optimal weight: 20.0000 chunk 79 optimal weight: 20.0000 chunk 33 optimal weight: 40.0000 chunk 135 optimal weight: 40.0000 chunk 112 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 chunk 44 optimal weight: 9.9990 chunk 71 optimal weight: 30.0000 chunk 130 optimal weight: 50.0000 overall best weight: 11.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 GLN B 328 GLN C 328 GLN D 328 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.6258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10880 Z= 0.292 Angle : 0.684 5.509 14852 Z= 0.377 Chirality : 0.040 0.134 1784 Planarity : 0.006 0.061 1872 Dihedral : 5.613 17.886 1536 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.05 % Favored : 88.95 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % 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: -2.90 (0.21), residues: 1412 helix: -1.67 (0.17), residues: 820 sheet: None (None), residues: 0 loop : -2.16 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 227 HIS 0.011 0.006 HIS B 323 PHE 0.014 0.002 PHE D 186 TYR 0.025 0.002 TYR A 178 ARG 0.008 0.001 ARG B 220 *********************** 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 291 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 291 time to evaluate : 1.601 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: A 92 ASP cc_start: 0.6717 (t0) cc_final: 0.6417 (t70) REVERT: A 101 CYS cc_start: 0.8728 (m) cc_final: 0.8471 (m) REVERT: A 197 MET cc_start: 0.8835 (ttm) cc_final: 0.8454 (tpp) REVERT: A 227 TRP cc_start: 0.7883 (t60) cc_final: 0.7588 (t60) REVERT: A 281 SER cc_start: 0.7801 (t) cc_final: 0.7543 (m) REVERT: B 101 CYS cc_start: 0.8851 (m) cc_final: 0.8574 (m) REVERT: B 197 MET cc_start: 0.8955 (ttm) cc_final: 0.8559 (tpp) REVERT: B 227 TRP cc_start: 0.8027 (t60) cc_final: 0.7551 (t60) REVERT: C 197 MET cc_start: 0.8787 (ttm) cc_final: 0.8455 (tpp) REVERT: C 214 PHE cc_start: 0.9354 (t80) cc_final: 0.9137 (t80) REVERT: C 227 TRP cc_start: 0.8108 (t60) cc_final: 0.7619 (t60) REVERT: D 92 ASP cc_start: 0.6462 (t0) cc_final: 0.6199 (t70) REVERT: D 101 CYS cc_start: 0.8795 (m) cc_final: 0.8524 (m) REVERT: D 197 MET cc_start: 0.8803 (ttm) cc_final: 0.8408 (tpp) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.3892 time to fit residues: 170.6602 Evaluate side-chains 271 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 1.612 ------------------------------------------------------------------------------- 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: 7.9990 chunk 77 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 chunk 76 optimal weight: 20.0000 chunk 114 optimal weight: 20.0000 chunk 75 optimal weight: 8.9990 chunk 134 optimal weight: 50.0000 chunk 84 optimal weight: 20.0000 chunk 82 optimal weight: 20.0000 chunk 62 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 overall best weight: 9.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.6557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10880 Z= 0.241 Angle : 0.628 5.418 14852 Z= 0.342 Chirality : 0.039 0.124 1784 Planarity : 0.005 0.052 1872 Dihedral : 5.501 19.249 1536 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: -2.67 (0.21), residues: 1412 helix: -1.48 (0.17), residues: 820 sheet: None (None), residues: 0 loop : -2.07 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 167 HIS 0.012 0.006 HIS B 323 PHE 0.030 0.002 PHE D 214 TYR 0.009 0.001 TYR C 178 ARG 0.007 0.001 ARG A 220 *********************** 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 294 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 294 time to evaluate : 1.551 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: A 197 MET cc_start: 0.8785 (ttm) cc_final: 0.8490 (tpp) REVERT: A 214 PHE cc_start: 0.9510 (t80) cc_final: 0.9246 (t80) REVERT: A 227 TRP cc_start: 0.7998 (t60) cc_final: 0.7696 (t60) REVERT: A 281 SER cc_start: 0.7406 (t) cc_final: 0.7148 (m) REVERT: B 92 ASP cc_start: 0.6389 (t0) cc_final: 0.6024 (t70) REVERT: B 197 MET cc_start: 0.8901 (ttm) cc_final: 0.8476 (tpp) REVERT: B 227 TRP cc_start: 0.8093 (t60) cc_final: 0.7735 (t60) REVERT: C 36 ARG cc_start: 0.8121 (mtt180) cc_final: 0.7082 (mtm180) REVERT: C 92 ASP cc_start: 0.6170 (t0) cc_final: 0.5822 (t70) REVERT: C 148 TYR cc_start: 0.8461 (t80) cc_final: 0.8251 (t80) REVERT: C 197 MET cc_start: 0.8828 (ttm) cc_final: 0.8433 (tpp) REVERT: C 214 PHE cc_start: 0.9207 (t80) cc_final: 0.8877 (t80) REVERT: C 227 TRP cc_start: 0.8167 (t60) cc_final: 0.7769 (t60) REVERT: D 197 MET cc_start: 0.8799 (ttm) cc_final: 0.8462 (tpp) outliers start: 0 outliers final: 0 residues processed: 294 average time/residue: 0.3889 time to fit residues: 172.2437 Evaluate side-chains 268 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 1.725 ------------------------------------------------------------------------------- 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: 7.9990 chunk 80 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 85 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 12 optimal weight: 20.0000 chunk 106 optimal weight: 7.9990 chunk 122 optimal weight: 9.9990 chunk 129 optimal weight: 10.0000 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.6769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10880 Z= 0.197 Angle : 0.595 5.482 14852 Z= 0.317 Chirality : 0.039 0.127 1784 Planarity : 0.005 0.050 1872 Dihedral : 5.189 20.928 1536 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: -2.22 (0.22), residues: 1412 helix: -1.07 (0.18), residues: 820 sheet: None (None), residues: 0 loop : -1.94 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 104 HIS 0.011 0.006 HIS A 323 PHE 0.019 0.001 PHE D 214 TYR 0.012 0.002 TYR A 178 ARG 0.013 0.001 ARG A 110 *********************** 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 300 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 300 time to evaluate : 1.512 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: A 197 MET cc_start: 0.8713 (ttm) cc_final: 0.8351 (tpp) REVERT: A 227 TRP cc_start: 0.8034 (t60) cc_final: 0.7679 (t60) REVERT: A 281 SER cc_start: 0.7729 (t) cc_final: 0.7491 (m) REVERT: B 92 ASP cc_start: 0.6274 (t0) cc_final: 0.5844 (t70) REVERT: B 148 TYR cc_start: 0.8457 (t80) cc_final: 0.8201 (t80) REVERT: B 197 MET cc_start: 0.8863 (ttm) cc_final: 0.8469 (tpp) REVERT: B 227 TRP cc_start: 0.8029 (t60) cc_final: 0.7680 (t60) REVERT: B 281 SER cc_start: 0.7120 (t) cc_final: 0.6750 (m) REVERT: C 92 ASP cc_start: 0.6229 (t0) cc_final: 0.5903 (t70) REVERT: C 148 TYR cc_start: 0.8443 (t80) cc_final: 0.8189 (t80) REVERT: C 197 MET cc_start: 0.8713 (ttm) cc_final: 0.8257 (tpp) REVERT: C 214 PHE cc_start: 0.9174 (t80) cc_final: 0.8837 (t80) REVERT: D 101 CYS cc_start: 0.8751 (m) cc_final: 0.8542 (m) REVERT: D 148 TYR cc_start: 0.8324 (t80) cc_final: 0.7990 (t80) REVERT: D 197 MET cc_start: 0.8754 (ttm) cc_final: 0.8386 (tpp) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.3838 time to fit residues: 173.7970 Evaluate side-chains 277 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 1.689 ------------------------------------------------------------------------------- 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: 4.9990 chunk 125 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 75 optimal weight: 20.0000 chunk 54 optimal weight: 9.9990 chunk 98 optimal weight: 7.9990 chunk 38 optimal weight: 0.5980 chunk 113 optimal weight: 8.9990 chunk 118 optimal weight: 5.9990 chunk 82 optimal weight: 20.0000 chunk 132 optimal weight: 40.0000 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 moved from start: 0.6941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 10880 Z= 0.168 Angle : 0.564 5.358 14852 Z= 0.298 Chirality : 0.038 0.123 1784 Planarity : 0.005 0.046 1872 Dihedral : 4.934 19.091 1536 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % 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: -0.59 (0.19), residues: 816 sheet: None (None), residues: 0 loop : -1.78 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 206 HIS 0.011 0.006 HIS A 323 PHE 0.027 0.001 PHE D 214 TYR 0.009 0.001 TYR C 178 ARG 0.008 0.000 ARG B 220 *********************** 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 : 1.545 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: A 133 THR cc_start: 0.6555 (m) cc_final: 0.6348 (m) REVERT: A 197 MET cc_start: 0.8753 (ttm) cc_final: 0.8303 (tpp) REVERT: A 227 TRP cc_start: 0.8065 (t60) cc_final: 0.7718 (t60) REVERT: A 281 SER cc_start: 0.7389 (t) cc_final: 0.7164 (m) REVERT: B 92 ASP cc_start: 0.6548 (t0) cc_final: 0.6172 (t70) REVERT: B 148 TYR cc_start: 0.8437 (t80) cc_final: 0.8176 (t80) REVERT: B 197 MET cc_start: 0.8724 (ttm) cc_final: 0.8352 (tpp) REVERT: B 214 PHE cc_start: 0.9475 (t80) cc_final: 0.9272 (t80) REVERT: B 227 TRP cc_start: 0.7984 (t60) cc_final: 0.7663 (t60) REVERT: B 281 SER cc_start: 0.7124 (t) cc_final: 0.6779 (m) REVERT: C 74 LYS cc_start: 0.9341 (ttmt) cc_final: 0.9101 (ttpt) REVERT: C 92 ASP cc_start: 0.6271 (t0) cc_final: 0.5991 (t70) REVERT: C 148 TYR cc_start: 0.8459 (t80) cc_final: 0.8184 (t80) REVERT: C 197 MET cc_start: 0.8717 (ttm) cc_final: 0.8129 (tpp) REVERT: C 214 PHE cc_start: 0.9089 (t80) cc_final: 0.8719 (t80) REVERT: C 227 TRP cc_start: 0.8196 (t60) cc_final: 0.7829 (t60) REVERT: D 25 VAL cc_start: 0.8973 (t) cc_final: 0.8604 (p) REVERT: D 133 THR cc_start: 0.6647 (m) cc_final: 0.6437 (m) REVERT: D 148 TYR cc_start: 0.8377 (t80) cc_final: 0.7752 (t80) REVERT: D 197 MET cc_start: 0.8666 (ttm) cc_final: 0.8227 (tpp) outliers start: 0 outliers final: 0 residues processed: 290 average time/residue: 0.3768 time to fit residues: 166.7616 Evaluate side-chains 274 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 274 time to evaluate : 1.494 ------------------------------------------------------------------------------- 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: 10.0000 chunk 63 optimal weight: 8.9990 chunk 92 optimal weight: 20.0000 chunk 139 optimal weight: 0.8980 chunk 128 optimal weight: 9.9990 chunk 111 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 68 optimal weight: 20.0000 chunk 88 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 overall best weight: 7.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 HIS C 323 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.7143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10880 Z= 0.213 Angle : 0.597 4.935 14852 Z= 0.322 Chirality : 0.038 0.125 1784 Planarity : 0.005 0.056 1872 Dihedral : 5.028 19.564 1536 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % 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: -1.86 (0.22), residues: 1412 helix: -0.75 (0.18), residues: 820 sheet: None (None), residues: 0 loop : -1.83 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 167 HIS 0.010 0.006 HIS C 323 PHE 0.012 0.001 PHE D 214 TYR 0.013 0.001 TYR B 178 ARG 0.008 0.001 ARG B 220 ********************** 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 290 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 1.574 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: A 133 THR cc_start: 0.6446 (m) cc_final: 0.6245 (m) REVERT: A 197 MET cc_start: 0.8850 (ttm) cc_final: 0.8406 (tpp) REVERT: A 227 TRP cc_start: 0.8060 (t60) cc_final: 0.7765 (t60) REVERT: A 281 SER cc_start: 0.6908 (t) cc_final: 0.6649 (m) REVERT: B 197 MET cc_start: 0.8766 (ttm) cc_final: 0.8184 (tpp) REVERT: B 214 PHE cc_start: 0.9444 (t80) cc_final: 0.9237 (t80) REVERT: B 227 TRP cc_start: 0.8078 (t60) cc_final: 0.7763 (t60) REVERT: B 281 SER cc_start: 0.7158 (t) cc_final: 0.6799 (m) REVERT: C 133 THR cc_start: 0.6628 (m) cc_final: 0.6425 (m) REVERT: C 197 MET cc_start: 0.8842 (ttm) cc_final: 0.8257 (tpp) REVERT: C 214 PHE cc_start: 0.9198 (t80) cc_final: 0.8889 (t80) REVERT: D 133 THR cc_start: 0.6707 (m) cc_final: 0.6490 (m) REVERT: D 197 MET cc_start: 0.8601 (ttm) cc_final: 0.8213 (tpp) REVERT: D 214 PHE cc_start: 0.9492 (t80) cc_final: 0.9285 (t80) outliers start: 0 outliers final: 0 residues processed: 290 average time/residue: 0.3897 time to fit residues: 170.0958 Evaluate side-chains 270 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 1.227 ------------------------------------------------------------------------------- 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: 10.0000 chunk 102 optimal weight: 30.0000 chunk 16 optimal weight: 9.9990 chunk 30 optimal weight: 20.0000 chunk 111 optimal weight: 10.0000 chunk 46 optimal weight: 20.0000 chunk 114 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 97 optimal weight: 30.0000 chunk 6 optimal weight: 9.9990 overall best weight: 8.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.220431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.182190 restraints weight = 63796.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.188333 restraints weight = 33187.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.192141 restraints weight = 21261.165| |-----------------------------------------------------------------------------| r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.7524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10880 Z= 0.228 Angle : 0.616 4.857 14852 Z= 0.334 Chirality : 0.039 0.125 1784 Planarity : 0.005 0.063 1872 Dihedral : 5.205 20.257 1536 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.99 % Favored : 90.01 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: -2.06 (0.22), residues: 1412 helix: -0.98 (0.18), residues: 820 sheet: -2.29 (0.62), residues: 48 loop : -1.70 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 167 HIS 0.015 0.008 HIS C 323 PHE 0.013 0.001 PHE B 136 TYR 0.016 0.002 TYR B 178 ARG 0.009 0.001 ARG B 220 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4326.05 seconds wall clock time: 76 minutes 51.43 seconds (4611.43 seconds total)