Starting phenix.real_space_refine on Fri Nov 15 23:37:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g13_29660/11_2024/8g13_29660.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g13_29660/11_2024/8g13_29660.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g13_29660/11_2024/8g13_29660.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g13_29660/11_2024/8g13_29660.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g13_29660/11_2024/8g13_29660.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g13_29660/11_2024/8g13_29660.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 5 Type Number sf(0) Gaussians S 48 5.16 5 C 6316 2.51 5 N 1736 2.21 5 O 1896 1.98 5 H 12 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 10008 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2502 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Restraints were copied for chains: C, B, D Time building chain proxies: 5.07, per 1000 atoms: 0.51 Number of scatterers: 10008 At special positions: 0 Unit cell: (94.355, 99.365, 91.015, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 O 1896 8.00 N 1736 7.00 C 6316 6.00 H 12 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 - 3.00 Amino acid : True - 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: 2.54 Conformation dependent library (CDL) restraints added in 1.3 seconds 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2408 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 12 sheets defined 39.5% alpha, 31.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'B' and resid 12 through 26 Processing helix chain 'B' and resid 39 through 49 Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'B' and resid 86 through 91 removed outlier: 3.552A pdb=" N ALA B 90 " --> pdb=" O LYS B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 109 Processing helix chain 'B' and resid 109 through 114 removed outlier: 3.998A pdb=" N GLN B 113 " --> pdb=" O GLY B 109 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 109 through 114' Processing helix chain 'B' and resid 136 through 140 Processing helix chain 'B' and resid 151 through 169 Proline residue: B 159 - end of helix Processing helix chain 'B' and resid 196 through 200 Processing helix chain 'B' and resid 212 through 221 removed outlier: 3.721A pdb=" N GLY B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS B 219 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 225 Processing helix chain 'B' and resid 254 through 268 Processing helix chain 'B' and resid 282 through 287 Processing helix chain 'B' and resid 317 through 335 Processing helix chain 'A' and resid 12 through 26 Processing helix chain 'A' and resid 39 through 49 Processing helix chain 'A' and resid 81 through 85 Processing helix chain 'A' and resid 86 through 91 removed outlier: 3.552A pdb=" N ALA A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 109 through 114 removed outlier: 3.999A pdb=" N GLN A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 109 through 114' Processing helix chain 'A' and resid 136 through 140 Processing helix chain 'A' and resid 151 through 169 Proline residue: A 159 - end of helix Processing helix chain 'A' and resid 196 through 200 Processing helix chain 'A' and resid 212 through 221 removed outlier: 3.721A pdb=" N GLY A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS A 219 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 225 Processing helix chain 'A' and resid 254 through 268 Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 317 through 335 Processing helix chain 'C' and resid 12 through 26 Processing helix chain 'C' and resid 39 through 49 Processing helix chain 'C' and resid 81 through 85 Processing helix chain 'C' and resid 86 through 91 removed outlier: 3.552A pdb=" N ALA C 90 " --> pdb=" O LYS C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 109 Processing helix chain 'C' and resid 109 through 114 removed outlier: 3.999A pdb=" N GLN C 113 " --> pdb=" O GLY C 109 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY C 114 " --> pdb=" O ALA C 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 109 through 114' Processing helix chain 'C' and resid 136 through 140 Processing helix chain 'C' and resid 151 through 169 Proline residue: C 159 - end of helix Processing helix chain 'C' and resid 196 through 200 Processing helix chain 'C' and resid 212 through 221 removed outlier: 3.721A pdb=" N GLY C 218 " --> pdb=" O ALA C 214 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS C 219 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 225 Processing helix chain 'C' and resid 254 through 268 Processing helix chain 'C' and resid 282 through 287 Processing helix chain 'C' and resid 317 through 335 Processing helix chain 'D' and resid 12 through 26 Processing helix chain 'D' and resid 39 through 49 Processing helix chain 'D' and resid 81 through 85 Processing helix chain 'D' and resid 86 through 91 removed outlier: 3.551A pdb=" N ALA D 90 " --> pdb=" O LYS D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 109 Processing helix chain 'D' and resid 109 through 114 removed outlier: 3.999A pdb=" N GLN D 113 " --> pdb=" O GLY D 109 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 109 through 114' Processing helix chain 'D' and resid 136 through 140 Processing helix chain 'D' and resid 151 through 169 Proline residue: D 159 - end of helix Processing helix chain 'D' and resid 196 through 200 Processing helix chain 'D' and resid 212 through 221 removed outlier: 3.722A pdb=" N GLY D 218 " --> pdb=" O ALA D 214 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS D 219 " --> pdb=" O LYS D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 225 Processing helix chain 'D' and resid 254 through 268 Processing helix chain 'D' and resid 282 through 287 Processing helix chain 'D' and resid 317 through 335 Processing sheet with id=AA1, first strand: chain 'B' and resid 60 through 63 removed outlier: 10.105A pdb=" N ASP B 29 " --> pdb=" O PRO B 73 " (cutoff:3.500A) removed outlier: 9.829A pdb=" N THR B 75 " --> pdb=" O ASP B 29 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL B 31 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N PHE B 77 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE B 33 " --> pdb=" O PHE B 77 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N VAL B 8 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE B 33 " --> pdb=" O VAL B 8 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL B 95 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL B 119 " --> pdb=" O ILE B 147 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 208 through 210 removed outlier: 3.577A pdb=" N THR B 229 " --> pdb=" O GLY B 173 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ARG B 248 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY B 173 " --> pdb=" O THR B 246 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR B 246 " --> pdb=" O GLY B 173 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N MET B 175 " --> pdb=" O ASP B 244 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASP B 244 " --> pdb=" O MET B 175 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THR B 177 " --> pdb=" O VAL B 242 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL B 242 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N HIS B 179 " --> pdb=" O VAL B 240 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N VAL B 240 " --> pdb=" O HIS B 179 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ILE B 311 " --> pdb=" O ASP B 296 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 208 through 210 removed outlier: 3.577A pdb=" N THR B 229 " --> pdb=" O GLY B 173 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ARG B 248 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY B 173 " --> pdb=" O THR B 246 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR B 246 " --> pdb=" O GLY B 173 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N MET B 175 " --> pdb=" O ASP B 244 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASP B 244 " --> pdb=" O MET B 175 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THR B 177 " --> pdb=" O VAL B 242 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL B 242 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N HIS B 179 " --> pdb=" O VAL B 240 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N VAL B 240 " --> pdb=" O HIS B 179 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE B 307 " --> pdb=" O LEU B 303 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 60 through 63 removed outlier: 10.106A pdb=" N ASP A 29 " --> pdb=" O PRO A 73 " (cutoff:3.500A) removed outlier: 9.830A pdb=" N THR A 75 " --> pdb=" O ASP A 29 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL A 31 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N PHE A 77 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE A 33 " --> pdb=" O PHE A 77 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N VAL A 8 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE A 33 " --> pdb=" O VAL A 8 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL A 95 " --> pdb=" O ILE A 120 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL A 119 " --> pdb=" O ILE A 147 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 208 through 210 removed outlier: 3.577A pdb=" N THR A 229 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ARG A 248 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLY A 173 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR A 246 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N MET A 175 " --> pdb=" O ASP A 244 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASP A 244 " --> pdb=" O MET A 175 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N THR A 177 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL A 242 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N HIS A 179 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N VAL A 240 " --> pdb=" O HIS A 179 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ILE A 311 " --> pdb=" O ASP A 296 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 208 through 210 removed outlier: 3.577A pdb=" N THR A 229 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ARG A 248 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLY A 173 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR A 246 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N MET A 175 " --> pdb=" O ASP A 244 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASP A 244 " --> pdb=" O MET A 175 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N THR A 177 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL A 242 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N HIS A 179 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N VAL A 240 " --> pdb=" O HIS A 179 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 60 through 63 removed outlier: 10.105A pdb=" N ASP C 29 " --> pdb=" O PRO C 73 " (cutoff:3.500A) removed outlier: 9.830A pdb=" N THR C 75 " --> pdb=" O ASP C 29 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL C 31 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N PHE C 77 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE C 33 " --> pdb=" O PHE C 77 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N VAL C 8 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE C 33 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL C 95 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL C 119 " --> pdb=" O ILE C 147 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 208 through 210 removed outlier: 3.577A pdb=" N THR C 229 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ARG C 248 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLY C 173 " --> pdb=" O THR C 246 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR C 246 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N MET C 175 " --> pdb=" O ASP C 244 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASP C 244 " --> pdb=" O MET C 175 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THR C 177 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL C 242 " --> pdb=" O THR C 177 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N HIS C 179 " --> pdb=" O VAL C 240 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N VAL C 240 " --> pdb=" O HIS C 179 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ILE C 311 " --> pdb=" O ASP C 296 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 208 through 210 removed outlier: 3.577A pdb=" N THR C 229 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ARG C 248 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLY C 173 " --> pdb=" O THR C 246 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR C 246 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N MET C 175 " --> pdb=" O ASP C 244 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASP C 244 " --> pdb=" O MET C 175 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THR C 177 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL C 242 " --> pdb=" O THR C 177 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N HIS C 179 " --> pdb=" O VAL C 240 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N VAL C 240 " --> pdb=" O HIS C 179 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE C 307 " --> pdb=" O LEU C 303 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 60 through 63 removed outlier: 10.105A pdb=" N ASP D 29 " --> pdb=" O PRO D 73 " (cutoff:3.500A) removed outlier: 9.830A pdb=" N THR D 75 " --> pdb=" O ASP D 29 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL D 31 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N PHE D 77 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE D 33 " --> pdb=" O PHE D 77 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N VAL D 8 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE D 33 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL D 95 " --> pdb=" O ILE D 120 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL D 119 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 208 through 210 removed outlier: 3.577A pdb=" N THR D 229 " --> pdb=" O GLY D 173 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ARG D 248 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY D 173 " --> pdb=" O THR D 246 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N THR D 246 " --> pdb=" O GLY D 173 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N MET D 175 " --> pdb=" O ASP D 244 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASP D 244 " --> pdb=" O MET D 175 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THR D 177 " --> pdb=" O VAL D 242 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL D 242 " --> pdb=" O THR D 177 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N HIS D 179 " --> pdb=" O VAL D 240 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N VAL D 240 " --> pdb=" O HIS D 179 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ILE D 311 " --> pdb=" O ASP D 296 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 208 through 210 removed outlier: 3.577A pdb=" N THR D 229 " --> pdb=" O GLY D 173 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ARG D 248 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY D 173 " --> pdb=" O THR D 246 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N THR D 246 " --> pdb=" O GLY D 173 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N MET D 175 " --> pdb=" O ASP D 244 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASP D 244 " --> pdb=" O MET D 175 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THR D 177 " --> pdb=" O VAL D 242 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL D 242 " --> pdb=" O THR D 177 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N HIS D 179 " --> pdb=" O VAL D 240 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N VAL D 240 " --> pdb=" O HIS D 179 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N PHE D 307 " --> pdb=" O LEU D 303 " (cutoff:3.500A) 512 hydrogen bonds defined for protein. 1368 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: 3.38 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.05: 8 1.05 - 1.24: 1364 1.24 - 1.43: 2899 1.43 - 1.62: 5853 1.62 - 1.81: 84 Bond restraints: 10208 Sorted by residual: bond pdb=" CA CYS D 152 " pdb=" HA CYS D 152 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" CA CYS B 152 " pdb=" HA CYS B 152 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" CA CYS C 152 " pdb=" HA CYS C 152 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" CA CYS A 152 " pdb=" HA CYS A 152 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" N VAL C 188 " pdb=" CA VAL C 188 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.11e-02 8.12e+03 1.22e+01 ... (remaining 10203 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 13208 1.25 - 2.51: 493 2.51 - 3.76: 134 3.76 - 5.02: 13 5.02 - 6.27: 16 Bond angle restraints: 13864 Sorted by residual: angle pdb=" C ALA B 150 " pdb=" CA ALA B 150 " pdb=" CB ALA B 150 " ideal model delta sigma weight residual 116.63 110.36 6.27 1.16e+00 7.43e-01 2.92e+01 angle pdb=" C ALA C 150 " pdb=" CA ALA C 150 " pdb=" CB ALA C 150 " ideal model delta sigma weight residual 116.63 110.39 6.24 1.16e+00 7.43e-01 2.89e+01 angle pdb=" C ALA A 150 " pdb=" CA ALA A 150 " pdb=" CB ALA A 150 " ideal model delta sigma weight residual 116.63 110.40 6.23 1.16e+00 7.43e-01 2.88e+01 angle pdb=" C ALA D 150 " pdb=" CA ALA D 150 " pdb=" CB ALA D 150 " ideal model delta sigma weight residual 116.63 110.42 6.21 1.16e+00 7.43e-01 2.87e+01 angle pdb=" N ARG A 80 " pdb=" CA ARG A 80 " pdb=" C ARG A 80 " ideal model delta sigma weight residual 113.41 108.74 4.67 1.22e+00 6.72e-01 1.46e+01 ... (remaining 13859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.09: 5375 17.09 - 34.19: 461 34.19 - 51.28: 147 51.28 - 68.38: 33 68.38 - 85.47: 8 Dihedral angle restraints: 6024 sinusoidal: 2248 harmonic: 3776 Sorted by residual: dihedral pdb=" CG ARG D 197 " pdb=" CD ARG D 197 " pdb=" NE ARG D 197 " pdb=" CZ ARG D 197 " ideal model delta sinusoidal sigma weight residual -90.00 -132.92 42.92 2 1.50e+01 4.44e-03 9.89e+00 dihedral pdb=" CG ARG C 197 " pdb=" CD ARG C 197 " pdb=" NE ARG C 197 " pdb=" CZ ARG C 197 " ideal model delta sinusoidal sigma weight residual -90.00 -132.91 42.91 2 1.50e+01 4.44e-03 9.89e+00 dihedral pdb=" CG ARG A 197 " pdb=" CD ARG A 197 " pdb=" NE ARG A 197 " pdb=" CZ ARG A 197 " ideal model delta sinusoidal sigma weight residual -90.00 -132.91 42.91 2 1.50e+01 4.44e-03 9.89e+00 ... (remaining 6021 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1078 0.041 - 0.081: 315 0.081 - 0.122: 167 0.122 - 0.163: 12 0.163 - 0.203: 8 Chirality restraints: 1580 Sorted by residual: chirality pdb=" CA VAL B 188 " pdb=" N VAL B 188 " pdb=" C VAL B 188 " pdb=" CB VAL B 188 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA VAL C 188 " pdb=" N VAL C 188 " pdb=" C VAL C 188 " pdb=" CB VAL C 188 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA VAL A 188 " pdb=" N VAL A 188 " pdb=" C VAL A 188 " pdb=" CB VAL A 188 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 1577 not shown) Planarity restraints: 1800 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 268 " 0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO A 269 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 269 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 269 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 268 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO C 269 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO C 269 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 269 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 268 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO B 269 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 269 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 269 " -0.018 5.00e-02 4.00e+02 ... (remaining 1797 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.59: 76 2.59 - 3.09: 7050 3.09 - 3.59: 11331 3.59 - 4.10: 17078 4.10 - 4.60: 25617 Nonbonded interactions: 61152 Sorted by model distance: nonbonded pdb=" NH2 ARG A 118 " pdb=" OD1 ASN A 142 " model vdw 2.083 2.950 nonbonded pdb=" NH2 ARG B 118 " pdb=" OD1 ASN B 142 " model vdw 2.083 2.950 nonbonded pdb=" NH2 ARG C 118 " pdb=" OD1 ASN C 142 " model vdw 2.083 2.950 nonbonded pdb=" NH2 ARG D 118 " pdb=" OD1 ASN D 142 " model vdw 2.083 2.950 nonbonded pdb=" NZ LYS D 3 " pdb=" O GLY D 26 " model vdw 2.288 2.950 ... (remaining 61147 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.290 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.660 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 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:13.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8954 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10196 Z= 0.288 Angle : 0.597 6.272 13832 Z= 0.407 Chirality : 0.049 0.203 1580 Planarity : 0.003 0.032 1796 Dihedral : 14.969 85.473 3612 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.86 % Allowed : 13.21 % Favored : 85.93 % 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: 0.94 (0.25), residues: 1328 helix: 2.33 (0.26), residues: 368 sheet: 0.27 (0.38), residues: 212 loop : -0.10 (0.25), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 313 HIS 0.003 0.001 HIS A 137 PHE 0.007 0.001 PHE B 318 TYR 0.007 0.001 TYR D 314 ARG 0.002 0.000 ARG D 234 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 1.116 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 94 average time/residue: 1.5878 time to fit residues: 158.4600 Evaluate side-chains 77 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 243 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 119 optimal weight: 7.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 ASN B 185 GLN A 149 ASN A 185 GLN C 149 ASN C 185 GLN D 149 ASN D 185 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9072 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 10196 Z= 0.433 Angle : 0.567 7.471 13832 Z= 0.323 Chirality : 0.048 0.172 1580 Planarity : 0.005 0.051 1796 Dihedral : 4.984 33.192 1420 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.24 % Allowed : 13.97 % Favored : 84.79 % 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: 0.53 (0.25), residues: 1328 helix: 2.05 (0.27), residues: 372 sheet: -0.72 (0.33), residues: 288 loop : -0.03 (0.27), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 87 HIS 0.004 0.001 HIS B 137 PHE 0.014 0.002 PHE B 318 TYR 0.019 0.002 TYR B 42 ARG 0.007 0.001 ARG B 80 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 1.144 Fit side-chains REVERT: B 223 GLU cc_start: 0.8495 (mp0) cc_final: 0.8256 (mp0) REVERT: A 223 GLU cc_start: 0.8492 (mp0) cc_final: 0.8253 (mp0) REVERT: C 223 GLU cc_start: 0.8492 (mp0) cc_final: 0.8254 (mp0) REVERT: D 223 GLU cc_start: 0.8489 (mp0) cc_final: 0.8251 (mp0) outliers start: 13 outliers final: 8 residues processed: 77 average time/residue: 1.5962 time to fit residues: 130.8803 Evaluate side-chains 72 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 243 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 81 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 106 optimal weight: 7.9990 chunk 119 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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: 0.9070 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.030 10196 Z= 0.372 Angle : 0.528 7.176 13832 Z= 0.300 Chirality : 0.047 0.160 1580 Planarity : 0.004 0.047 1796 Dihedral : 4.713 32.201 1416 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.81 % Allowed : 13.40 % Favored : 84.79 % 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: 0.38 (0.24), residues: 1328 helix: 1.97 (0.26), residues: 372 sheet: -0.73 (0.32), residues: 288 loop : -0.19 (0.26), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 87 HIS 0.004 0.001 HIS D 137 PHE 0.012 0.001 PHE B 318 TYR 0.012 0.002 TYR C 314 ARG 0.007 0.001 ARG B 80 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 1.101 Fit side-chains REVERT: B 223 GLU cc_start: 0.8480 (mp0) cc_final: 0.8239 (mp0) REVERT: A 223 GLU cc_start: 0.8478 (mp0) cc_final: 0.8238 (mp0) REVERT: C 223 GLU cc_start: 0.8477 (mp0) cc_final: 0.8239 (mp0) REVERT: D 223 GLU cc_start: 0.8480 (mp0) cc_final: 0.8239 (mp0) outliers start: 19 outliers final: 8 residues processed: 83 average time/residue: 1.4436 time to fit residues: 128.2302 Evaluate side-chains 72 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 220 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 62 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 80 optimal weight: 0.0980 chunk 120 optimal weight: 7.9990 chunk 127 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- 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: 0.9044 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 10196 Z= 0.227 Angle : 0.457 6.158 13832 Z= 0.259 Chirality : 0.044 0.129 1580 Planarity : 0.004 0.049 1796 Dihedral : 4.149 16.748 1412 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.76 % Allowed : 13.69 % Favored : 85.55 % 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: 0.54 (0.24), residues: 1328 helix: 2.20 (0.27), residues: 372 sheet: -0.72 (0.31), residues: 288 loop : -0.13 (0.26), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 313 HIS 0.003 0.001 HIS D 137 PHE 0.008 0.001 PHE D 286 TYR 0.009 0.001 TYR A 314 ARG 0.008 0.001 ARG B 80 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 1.158 Fit side-chains REVERT: B 223 GLU cc_start: 0.8476 (mp0) cc_final: 0.8235 (mp0) REVERT: A 223 GLU cc_start: 0.8475 (mp0) cc_final: 0.8235 (mp0) REVERT: C 223 GLU cc_start: 0.8476 (mp0) cc_final: 0.8236 (mp0) REVERT: D 223 GLU cc_start: 0.8476 (mp0) cc_final: 0.8235 (mp0) outliers start: 8 outliers final: 8 residues processed: 72 average time/residue: 1.6968 time to fit residues: 129.9681 Evaluate side-chains 72 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 243 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 95 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 chunk 114 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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: 0.9031 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 10196 Z= 0.185 Angle : 0.436 5.818 13832 Z= 0.246 Chirality : 0.043 0.124 1580 Planarity : 0.004 0.044 1796 Dihedral : 4.008 16.706 1412 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.76 % Allowed : 14.07 % Favored : 85.17 % 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: 0.67 (0.25), residues: 1328 helix: 2.38 (0.27), residues: 372 sheet: -0.69 (0.31), residues: 288 loop : -0.07 (0.27), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 313 HIS 0.002 0.001 HIS D 137 PHE 0.007 0.001 PHE B 286 TYR 0.008 0.001 TYR C 314 ARG 0.008 0.001 ARG B 80 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 1.167 Fit side-chains REVERT: B 223 GLU cc_start: 0.8466 (mp0) cc_final: 0.8226 (mp0) REVERT: A 223 GLU cc_start: 0.8466 (mp0) cc_final: 0.8226 (mp0) REVERT: C 223 GLU cc_start: 0.8468 (mp0) cc_final: 0.8229 (mp0) REVERT: D 223 GLU cc_start: 0.8466 (mp0) cc_final: 0.8226 (mp0) outliers start: 8 outliers final: 8 residues processed: 72 average time/residue: 1.6679 time to fit residues: 127.7135 Evaluate side-chains 72 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 243 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 127 optimal weight: 6.9990 chunk 106 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 chunk 67 optimal weight: 8.9990 chunk 123 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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: 0.9092 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.044 10196 Z= 0.595 Angle : 0.603 7.786 13832 Z= 0.340 Chirality : 0.051 0.186 1580 Planarity : 0.005 0.051 1796 Dihedral : 4.526 17.450 1412 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.71 % Allowed : 13.50 % Favored : 84.79 % 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: 0.28 (0.24), residues: 1328 helix: 1.83 (0.26), residues: 372 sheet: -0.63 (0.32), residues: 288 loop : -0.31 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 87 HIS 0.004 0.001 HIS C 53 PHE 0.015 0.002 PHE C 286 TYR 0.014 0.002 TYR A 314 ARG 0.008 0.001 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 1.207 Fit side-chains REVERT: B 223 GLU cc_start: 0.8513 (mp0) cc_final: 0.8263 (mp0) REVERT: A 223 GLU cc_start: 0.8514 (mp0) cc_final: 0.8264 (mp0) REVERT: C 223 GLU cc_start: 0.8513 (mp0) cc_final: 0.8264 (mp0) REVERT: D 223 GLU cc_start: 0.8513 (mp0) cc_final: 0.8264 (mp0) outliers start: 18 outliers final: 8 residues processed: 82 average time/residue: 1.5067 time to fit residues: 132.2171 Evaluate side-chains 72 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 220 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- 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: 0.9030 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 10196 Z= 0.157 Angle : 0.435 5.750 13832 Z= 0.245 Chirality : 0.043 0.125 1580 Planarity : 0.004 0.050 1796 Dihedral : 4.077 17.761 1412 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.14 % Allowed : 14.45 % Favored : 84.41 % 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: 0.62 (0.24), residues: 1328 helix: 2.27 (0.27), residues: 372 sheet: -0.59 (0.31), residues: 288 loop : -0.12 (0.26), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 313 HIS 0.002 0.001 HIS A 137 PHE 0.007 0.001 PHE A 286 TYR 0.007 0.001 TYR B 314 ARG 0.010 0.001 ARG B 80 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 1.242 Fit side-chains REVERT: B 223 GLU cc_start: 0.8480 (mp0) cc_final: 0.8236 (mp0) REVERT: A 223 GLU cc_start: 0.8482 (mp0) cc_final: 0.8237 (mp0) REVERT: C 223 GLU cc_start: 0.8482 (mp0) cc_final: 0.8237 (mp0) REVERT: D 223 GLU cc_start: 0.8481 (mp0) cc_final: 0.8238 (mp0) outliers start: 12 outliers final: 9 residues processed: 76 average time/residue: 1.6513 time to fit residues: 133.8635 Evaluate side-chains 73 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 243 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 0.2980 chunk 38 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 80 optimal weight: 10.0000 chunk 86 optimal weight: 0.8980 chunk 62 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 chunk 115 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- 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: 0.9061 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 10196 Z= 0.303 Angle : 0.487 6.597 13832 Z= 0.275 Chirality : 0.045 0.142 1580 Planarity : 0.004 0.050 1796 Dihedral : 4.227 17.384 1412 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.62 % Allowed : 13.97 % Favored : 84.41 % 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: 0.53 (0.24), residues: 1328 helix: 2.13 (0.26), residues: 372 sheet: -0.60 (0.31), residues: 288 loop : -0.15 (0.26), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 87 HIS 0.003 0.001 HIS D 137 PHE 0.010 0.001 PHE A 286 TYR 0.010 0.001 TYR C 314 ARG 0.010 0.001 ARG D 80 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 1.201 Fit side-chains REVERT: B 223 GLU cc_start: 0.8491 (mp0) cc_final: 0.8239 (mp0) REVERT: A 223 GLU cc_start: 0.8491 (mp0) cc_final: 0.8240 (mp0) REVERT: C 223 GLU cc_start: 0.8492 (mp0) cc_final: 0.8241 (mp0) REVERT: D 223 GLU cc_start: 0.8491 (mp0) cc_final: 0.8242 (mp0) outliers start: 17 outliers final: 12 residues processed: 81 average time/residue: 1.5118 time to fit residues: 130.7114 Evaluate side-chains 76 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 243 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 8.9990 chunk 121 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 chunk 36 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 125 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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: 0.9057 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 10196 Z= 0.277 Angle : 0.479 6.554 13832 Z= 0.270 Chirality : 0.045 0.137 1580 Planarity : 0.005 0.051 1796 Dihedral : 4.228 18.059 1412 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.24 % Allowed : 14.35 % Favored : 84.41 % 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: 0.55 (0.24), residues: 1328 helix: 2.21 (0.26), residues: 372 sheet: -0.64 (0.31), residues: 288 loop : -0.15 (0.26), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 313 HIS 0.003 0.001 HIS D 137 PHE 0.009 0.001 PHE C 286 TYR 0.010 0.001 TYR D 314 ARG 0.011 0.001 ARG B 80 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 1.076 Fit side-chains REVERT: B 223 GLU cc_start: 0.8490 (mp0) cc_final: 0.8239 (mp0) REVERT: A 223 GLU cc_start: 0.8490 (mp0) cc_final: 0.8238 (mp0) REVERT: C 223 GLU cc_start: 0.8490 (mp0) cc_final: 0.8241 (mp0) REVERT: D 223 GLU cc_start: 0.8491 (mp0) cc_final: 0.8241 (mp0) outliers start: 13 outliers final: 12 residues processed: 77 average time/residue: 1.5685 time to fit residues: 129.0350 Evaluate side-chains 76 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 243 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 131 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 104 optimal weight: 0.0010 chunk 10 optimal weight: 7.9990 chunk 80 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 83 optimal weight: 8.9990 chunk 111 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 overall best weight: 2.1994 ------------------------------------------------------------------------------- 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: 0.9046 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 10196 Z= 0.226 Angle : 0.458 6.178 13832 Z= 0.258 Chirality : 0.044 0.128 1580 Planarity : 0.004 0.050 1796 Dihedral : 4.129 17.906 1412 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.14 % Allowed : 14.45 % Favored : 84.41 % 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: 0.64 (0.24), residues: 1328 helix: 2.31 (0.27), residues: 372 sheet: -0.60 (0.31), residues: 288 loop : -0.11 (0.26), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 313 HIS 0.003 0.001 HIS D 137 PHE 0.008 0.001 PHE A 286 TYR 0.009 0.001 TYR C 314 ARG 0.011 0.001 ARG D 80 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 1.081 Fit side-chains REVERT: B 223 GLU cc_start: 0.8492 (mp0) cc_final: 0.8242 (mp0) REVERT: A 223 GLU cc_start: 0.8493 (mp0) cc_final: 0.8242 (mp0) REVERT: C 223 GLU cc_start: 0.8492 (mp0) cc_final: 0.8242 (mp0) REVERT: D 223 GLU cc_start: 0.8493 (mp0) cc_final: 0.8243 (mp0) outliers start: 12 outliers final: 12 residues processed: 76 average time/residue: 1.6614 time to fit residues: 134.5233 Evaluate side-chains 76 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 243 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 104 optimal weight: 7.9990 chunk 43 optimal weight: 0.0030 chunk 107 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 overall best weight: 2.9998 ------------------------------------------------------------------------------- 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 = 0.2910 r_free = 0.2910 target = 0.062073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.049044 restraints weight = 19782.850| |-----------------------------------------------------------------------------| r_work (start): 0.2608 rms_B_bonded: 2.49 r_work: 0.2473 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2350 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9080 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 10196 Z= 0.299 Angle : 0.490 6.685 13832 Z= 0.276 Chirality : 0.045 0.144 1580 Planarity : 0.005 0.051 1796 Dihedral : 4.244 17.959 1412 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.14 % Allowed : 14.83 % Favored : 84.03 % 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: 0.55 (0.24), residues: 1328 helix: 2.18 (0.26), residues: 372 sheet: -0.63 (0.31), residues: 288 loop : -0.14 (0.26), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 87 HIS 0.003 0.001 HIS D 53 PHE 0.010 0.001 PHE C 286 TYR 0.010 0.001 TYR D 314 ARG 0.011 0.001 ARG C 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3120.79 seconds wall clock time: 57 minutes 17.23 seconds (3437.23 seconds total)