Starting phenix.real_space_refine on Fri Sep 27 22:41:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v00_20966/09_2024/6v00_20966.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v00_20966/09_2024/6v00_20966.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v00_20966/09_2024/6v00_20966.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v00_20966/09_2024/6v00_20966.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v00_20966/09_2024/6v00_20966.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v00_20966/09_2024/6v00_20966.cif" } resolution = 3.1 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: 5 Type Number sf(0) Gaussians Ca 8 9.91 5 S 88 5.16 5 C 11264 2.51 5 N 2988 2.21 5 O 3112 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 17460 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2864 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 346} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1105 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ASP:plan': 6} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 394 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 45} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: D, G, J, F, I, L, E, H, K Residues with excluded nonbonded symmetry interactions: 4 residue: pdb="CA CA B 202 " occ=0.83 residue: pdb="CA CA E 202 " occ=0.83 residue: pdb="CA CA H 202 " occ=0.83 residue: pdb="CA CA K 202 " occ=0.83 Time building chain proxies: 7.82, per 1000 atoms: 0.45 Number of scatterers: 17460 At special positions: 0 Unit cell: (110.21, 110.21, 125.66, 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) Ca 8 19.99 S 88 16.00 O 3112 8.00 N 2988 7.00 C 11264 6.00 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: 4.17 Conformation dependent library (CDL) restraints added in 2.1 seconds 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4056 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 4 sheets defined 77.7% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 104 through 115 Processing helix chain 'A' and resid 120 through 142 Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 148 through 152 removed outlier: 3.684A pdb=" N ALA A 152 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 178 removed outlier: 3.769A pdb=" N TYR A 171 " --> pdb=" O PHE A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 194 removed outlier: 3.741A pdb=" N GLY A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 216 Processing helix chain 'A' and resid 223 through 237 Processing helix chain 'A' and resid 238 through 241 removed outlier: 3.625A pdb=" N VAL A 241 " --> pdb=" O MET A 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 238 through 241' Processing helix chain 'A' and resid 242 through 244 No H-bonds generated for 'chain 'A' and resid 242 through 244' Processing helix chain 'A' and resid 245 through 258 removed outlier: 3.705A pdb=" N LEU A 250 " --> pdb=" O GLY A 246 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 284 removed outlier: 3.837A pdb=" N THR A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 311 removed outlier: 3.821A pdb=" N THR A 311 " --> pdb=" O VAL A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 358 removed outlier: 4.109A pdb=" N PHE A 335 " --> pdb=" O CYS A 331 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N SER A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE A 339 " --> pdb=" O PHE A 335 " (cutoff:3.500A) Proline residue: A 343 - end of helix Processing helix chain 'A' and resid 363 through 366 Processing helix chain 'A' and resid 367 through 385 removed outlier: 3.904A pdb=" N THR A 377 " --> pdb=" O SER A 373 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU A 385 " --> pdb=" O CYS A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 394 removed outlier: 3.620A pdb=" N LYS A 393 " --> pdb=" O SER A 390 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE A 394 " --> pdb=" O THR A 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 390 through 394' Processing helix chain 'A' and resid 509 through 532 removed outlier: 3.588A pdb=" N THR A 513 " --> pdb=" O HIS A 509 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 564 removed outlier: 3.786A pdb=" N VAL A 541 " --> pdb=" O ASP A 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 22 removed outlier: 3.695A pdb=" N GLU B 12 " --> pdb=" O GLU B 8 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS B 22 " --> pdb=" O SER B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 40 removed outlier: 3.837A pdb=" N VAL B 36 " --> pdb=" O GLU B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 54 removed outlier: 3.518A pdb=" N ILE B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 75 removed outlier: 3.695A pdb=" N MET B 72 " --> pdb=" O GLU B 68 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET B 73 " --> pdb=" O PHE B 69 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 91 removed outlier: 3.714A pdb=" N ILE B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG B 91 " --> pdb=" O ARG B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 98 removed outlier: 5.583A pdb=" N LYS B 95 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ASP B 96 " --> pdb=" O PHE B 93 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY B 97 " --> pdb=" O ASP B 94 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ASN B 98 " --> pdb=" O LYS B 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 92 through 98' Processing helix chain 'B' and resid 103 through 111 Processing helix chain 'B' and resid 118 through 129 removed outlier: 3.767A pdb=" N ARG B 127 " --> pdb=" O ASP B 123 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU B 128 " --> pdb=" O GLU B 124 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ALA B 129 " --> pdb=" O MET B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 149 removed outlier: 3.740A pdb=" N MET B 146 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS B 149 " --> pdb=" O MET B 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 81 removed outlier: 4.381A pdb=" N TYR C 60 " --> pdb=" O ASN C 56 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE C 61 " --> pdb=" O SER C 57 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU C 67 " --> pdb=" O PHE C 63 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG C 81 " --> pdb=" O LEU C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 99 Processing helix chain 'D' and resid 105 through 115 Processing helix chain 'D' and resid 120 through 142 Processing helix chain 'D' and resid 143 through 145 No H-bonds generated for 'chain 'D' and resid 143 through 145' Processing helix chain 'D' and resid 148 through 152 removed outlier: 3.684A pdb=" N ALA D 152 " --> pdb=" O ALA D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 178 removed outlier: 3.769A pdb=" N TYR D 171 " --> pdb=" O PHE D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 194 removed outlier: 3.742A pdb=" N GLY D 189 " --> pdb=" O VAL D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 216 Processing helix chain 'D' and resid 223 through 237 Processing helix chain 'D' and resid 238 through 241 removed outlier: 3.625A pdb=" N VAL D 241 " --> pdb=" O MET D 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 238 through 241' Processing helix chain 'D' and resid 242 through 244 No H-bonds generated for 'chain 'D' and resid 242 through 244' Processing helix chain 'D' and resid 245 through 258 removed outlier: 3.705A pdb=" N LEU D 250 " --> pdb=" O GLY D 246 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL D 254 " --> pdb=" O LEU D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 284 removed outlier: 3.837A pdb=" N THR D 265 " --> pdb=" O GLU D 261 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU D 266 " --> pdb=" O LEU D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 311 removed outlier: 3.821A pdb=" N THR D 311 " --> pdb=" O VAL D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 358 removed outlier: 4.109A pdb=" N PHE D 335 " --> pdb=" O CYS D 331 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N SER D 338 " --> pdb=" O VAL D 334 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE D 339 " --> pdb=" O PHE D 335 " (cutoff:3.500A) Proline residue: D 343 - end of helix Processing helix chain 'D' and resid 363 through 366 Processing helix chain 'D' and resid 367 through 385 removed outlier: 3.903A pdb=" N THR D 377 " --> pdb=" O SER D 373 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU D 385 " --> pdb=" O CYS D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 394 removed outlier: 3.619A pdb=" N LYS D 393 " --> pdb=" O SER D 390 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE D 394 " --> pdb=" O THR D 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 390 through 394' Processing helix chain 'D' and resid 509 through 532 removed outlier: 3.589A pdb=" N THR D 513 " --> pdb=" O HIS D 509 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL D 516 " --> pdb=" O ALA D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 564 removed outlier: 3.786A pdb=" N VAL D 541 " --> pdb=" O ASP D 537 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 22 removed outlier: 3.695A pdb=" N GLU E 12 " --> pdb=" O GLU E 8 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE E 20 " --> pdb=" O ALA E 16 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS E 22 " --> pdb=" O SER E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 40 removed outlier: 3.837A pdb=" N VAL E 36 " --> pdb=" O GLU E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 54 removed outlier: 3.519A pdb=" N ILE E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 75 removed outlier: 3.696A pdb=" N MET E 72 " --> pdb=" O GLU E 68 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET E 73 " --> pdb=" O PHE E 69 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG E 75 " --> pdb=" O THR E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 91 removed outlier: 3.714A pdb=" N ILE E 86 " --> pdb=" O SER E 82 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG E 91 " --> pdb=" O ARG E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 98 removed outlier: 5.583A pdb=" N LYS E 95 " --> pdb=" O VAL E 92 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ASP E 96 " --> pdb=" O PHE E 93 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY E 97 " --> pdb=" O ASP E 94 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ASN E 98 " --> pdb=" O LYS E 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 92 through 98' Processing helix chain 'E' and resid 103 through 111 Processing helix chain 'E' and resid 118 through 129 removed outlier: 3.768A pdb=" N ARG E 127 " --> pdb=" O ASP E 123 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU E 128 " --> pdb=" O GLU E 124 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA E 129 " --> pdb=" O MET E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 149 removed outlier: 3.741A pdb=" N MET E 146 " --> pdb=" O PHE E 142 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS E 149 " --> pdb=" O MET E 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 81 removed outlier: 4.381A pdb=" N TYR F 60 " --> pdb=" O ASN F 56 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE F 61 " --> pdb=" O SER F 57 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU F 67 " --> pdb=" O PHE F 63 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG F 81 " --> pdb=" O LEU F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 99 Processing helix chain 'G' and resid 105 through 115 Processing helix chain 'G' and resid 120 through 142 Processing helix chain 'G' and resid 143 through 145 No H-bonds generated for 'chain 'G' and resid 143 through 145' Processing helix chain 'G' and resid 148 through 152 removed outlier: 3.684A pdb=" N ALA G 152 " --> pdb=" O ALA G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 178 removed outlier: 3.769A pdb=" N TYR G 171 " --> pdb=" O PHE G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 194 removed outlier: 3.742A pdb=" N GLY G 189 " --> pdb=" O VAL G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 216 Processing helix chain 'G' and resid 223 through 237 Processing helix chain 'G' and resid 238 through 241 removed outlier: 3.625A pdb=" N VAL G 241 " --> pdb=" O MET G 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 238 through 241' Processing helix chain 'G' and resid 242 through 244 No H-bonds generated for 'chain 'G' and resid 242 through 244' Processing helix chain 'G' and resid 245 through 258 removed outlier: 3.705A pdb=" N LEU G 250 " --> pdb=" O GLY G 246 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL G 254 " --> pdb=" O LEU G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 284 removed outlier: 3.837A pdb=" N THR G 265 " --> pdb=" O GLU G 261 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU G 266 " --> pdb=" O LEU G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 311 removed outlier: 3.821A pdb=" N THR G 311 " --> pdb=" O VAL G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 322 through 358 removed outlier: 4.109A pdb=" N PHE G 335 " --> pdb=" O CYS G 331 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N SER G 338 " --> pdb=" O VAL G 334 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE G 339 " --> pdb=" O PHE G 335 " (cutoff:3.500A) Proline residue: G 343 - end of helix Processing helix chain 'G' and resid 363 through 366 Processing helix chain 'G' and resid 367 through 385 removed outlier: 3.903A pdb=" N THR G 377 " --> pdb=" O SER G 373 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU G 385 " --> pdb=" O CYS G 381 " (cutoff:3.500A) Processing helix chain 'G' and resid 390 through 394 removed outlier: 3.619A pdb=" N LYS G 393 " --> pdb=" O SER G 390 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE G 394 " --> pdb=" O THR G 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 390 through 394' Processing helix chain 'G' and resid 509 through 532 removed outlier: 3.589A pdb=" N THR G 513 " --> pdb=" O HIS G 509 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL G 516 " --> pdb=" O ALA G 512 " (cutoff:3.500A) Processing helix chain 'G' and resid 537 through 564 removed outlier: 3.786A pdb=" N VAL G 541 " --> pdb=" O ASP G 537 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 22 removed outlier: 3.695A pdb=" N GLU H 12 " --> pdb=" O GLU H 8 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE H 20 " --> pdb=" O ALA H 16 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS H 22 " --> pdb=" O SER H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 40 removed outlier: 3.837A pdb=" N VAL H 36 " --> pdb=" O GLU H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 54 removed outlier: 3.519A pdb=" N ILE H 53 " --> pdb=" O LEU H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 75 removed outlier: 3.697A pdb=" N MET H 72 " --> pdb=" O GLU H 68 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET H 73 " --> pdb=" O PHE H 69 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG H 75 " --> pdb=" O THR H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 91 removed outlier: 3.714A pdb=" N ILE H 86 " --> pdb=" O SER H 82 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG H 91 " --> pdb=" O ARG H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 98 removed outlier: 5.583A pdb=" N LYS H 95 " --> pdb=" O VAL H 92 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ASP H 96 " --> pdb=" O PHE H 93 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY H 97 " --> pdb=" O ASP H 94 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ASN H 98 " --> pdb=" O LYS H 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 92 through 98' Processing helix chain 'H' and resid 103 through 111 Processing helix chain 'H' and resid 118 through 129 removed outlier: 3.768A pdb=" N ARG H 127 " --> pdb=" O ASP H 123 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU H 128 " --> pdb=" O GLU H 124 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA H 129 " --> pdb=" O MET H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 149 removed outlier: 3.741A pdb=" N MET H 146 " --> pdb=" O PHE H 142 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS H 149 " --> pdb=" O MET H 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 56 through 81 removed outlier: 4.381A pdb=" N TYR I 60 " --> pdb=" O ASN I 56 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE I 61 " --> pdb=" O SER I 57 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU I 67 " --> pdb=" O PHE I 63 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG I 81 " --> pdb=" O LEU I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 99 Processing helix chain 'J' and resid 105 through 115 Processing helix chain 'J' and resid 120 through 142 Processing helix chain 'J' and resid 143 through 145 No H-bonds generated for 'chain 'J' and resid 143 through 145' Processing helix chain 'J' and resid 148 through 152 removed outlier: 3.684A pdb=" N ALA J 152 " --> pdb=" O ALA J 149 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 178 removed outlier: 3.768A pdb=" N TYR J 171 " --> pdb=" O PHE J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 185 through 194 removed outlier: 3.742A pdb=" N GLY J 189 " --> pdb=" O VAL J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 196 through 216 Processing helix chain 'J' and resid 223 through 237 Processing helix chain 'J' and resid 238 through 241 removed outlier: 3.625A pdb=" N VAL J 241 " --> pdb=" O MET J 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 238 through 241' Processing helix chain 'J' and resid 242 through 244 No H-bonds generated for 'chain 'J' and resid 242 through 244' Processing helix chain 'J' and resid 245 through 258 removed outlier: 3.705A pdb=" N LEU J 250 " --> pdb=" O GLY J 246 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL J 254 " --> pdb=" O LEU J 250 " (cutoff:3.500A) Processing helix chain 'J' and resid 258 through 284 removed outlier: 3.837A pdb=" N THR J 265 " --> pdb=" O GLU J 261 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU J 266 " --> pdb=" O LEU J 262 " (cutoff:3.500A) Processing helix chain 'J' and resid 298 through 311 removed outlier: 3.821A pdb=" N THR J 311 " --> pdb=" O VAL J 307 " (cutoff:3.500A) Processing helix chain 'J' and resid 322 through 358 removed outlier: 4.109A pdb=" N PHE J 335 " --> pdb=" O CYS J 331 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N SER J 338 " --> pdb=" O VAL J 334 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE J 339 " --> pdb=" O PHE J 335 " (cutoff:3.500A) Proline residue: J 343 - end of helix Processing helix chain 'J' and resid 363 through 366 Processing helix chain 'J' and resid 367 through 385 removed outlier: 3.903A pdb=" N THR J 377 " --> pdb=" O SER J 373 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU J 385 " --> pdb=" O CYS J 381 " (cutoff:3.500A) Processing helix chain 'J' and resid 390 through 394 removed outlier: 3.620A pdb=" N LYS J 393 " --> pdb=" O SER J 390 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ILE J 394 " --> pdb=" O THR J 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 390 through 394' Processing helix chain 'J' and resid 509 through 532 removed outlier: 3.588A pdb=" N THR J 513 " --> pdb=" O HIS J 509 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL J 516 " --> pdb=" O ALA J 512 " (cutoff:3.500A) Processing helix chain 'J' and resid 537 through 564 removed outlier: 3.786A pdb=" N VAL J 541 " --> pdb=" O ASP J 537 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 22 removed outlier: 3.695A pdb=" N GLU K 12 " --> pdb=" O GLU K 8 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE K 20 " --> pdb=" O ALA K 16 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS K 22 " --> pdb=" O SER K 18 " (cutoff:3.500A) Processing helix chain 'K' and resid 29 through 40 removed outlier: 3.837A pdb=" N VAL K 36 " --> pdb=" O GLU K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 54 removed outlier: 3.518A pdb=" N ILE K 53 " --> pdb=" O LEU K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 65 through 75 removed outlier: 3.695A pdb=" N MET K 72 " --> pdb=" O GLU K 68 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET K 73 " --> pdb=" O PHE K 69 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 91 removed outlier: 3.714A pdb=" N ILE K 86 " --> pdb=" O SER K 82 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG K 91 " --> pdb=" O ARG K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 98 removed outlier: 5.583A pdb=" N LYS K 95 " --> pdb=" O VAL K 92 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ASP K 96 " --> pdb=" O PHE K 93 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY K 97 " --> pdb=" O ASP K 94 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ASN K 98 " --> pdb=" O LYS K 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 92 through 98' Processing helix chain 'K' and resid 103 through 111 Processing helix chain 'K' and resid 118 through 129 removed outlier: 3.767A pdb=" N ARG K 127 " --> pdb=" O ASP K 123 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU K 128 " --> pdb=" O GLU K 124 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA K 129 " --> pdb=" O MET K 125 " (cutoff:3.500A) Processing helix chain 'K' and resid 139 through 149 removed outlier: 3.741A pdb=" N MET K 146 " --> pdb=" O PHE K 142 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS K 149 " --> pdb=" O MET K 145 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 81 removed outlier: 4.381A pdb=" N TYR L 60 " --> pdb=" O ASN L 56 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE L 61 " --> pdb=" O SER L 57 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU L 67 " --> pdb=" O PHE L 63 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG L 81 " --> pdb=" O LEU L 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 90 through 99 Processing sheet with id=AA1, first strand: chain 'B' and resid 100 through 102 Processing sheet with id=AA2, first strand: chain 'E' and resid 100 through 102 Processing sheet with id=AA3, first strand: chain 'H' and resid 100 through 102 Processing sheet with id=AA4, first strand: chain 'K' and resid 100 through 102 1069 hydrogen bonds defined for protein. 3183 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: 5.09 Time building geometry restraints manager: 4.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5360 1.34 - 1.46: 3419 1.46 - 1.57: 8889 1.57 - 1.69: 0 1.69 - 1.81: 152 Bond restraints: 17820 Sorted by residual: bond pdb=" CB VAL A 310 " pdb=" CG1 VAL A 310 " ideal model delta sigma weight residual 1.521 1.419 0.102 3.30e-02 9.18e+02 9.51e+00 bond pdb=" CB VAL J 310 " pdb=" CG1 VAL J 310 " ideal model delta sigma weight residual 1.521 1.419 0.102 3.30e-02 9.18e+02 9.48e+00 bond pdb=" CB VAL D 310 " pdb=" CG1 VAL D 310 " ideal model delta sigma weight residual 1.521 1.420 0.101 3.30e-02 9.18e+02 9.43e+00 bond pdb=" CB VAL G 310 " pdb=" CG1 VAL G 310 " ideal model delta sigma weight residual 1.521 1.420 0.101 3.30e-02 9.18e+02 9.43e+00 bond pdb=" CB CYS A 122 " pdb=" SG CYS A 122 " ideal model delta sigma weight residual 1.808 1.752 0.056 3.30e-02 9.18e+02 2.89e+00 ... (remaining 17815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 22479 1.70 - 3.41: 1309 3.41 - 5.11: 200 5.11 - 6.82: 60 6.82 - 8.52: 24 Bond angle restraints: 24072 Sorted by residual: angle pdb=" C LYS K 95 " pdb=" N ASP K 96 " pdb=" CA ASP K 96 " ideal model delta sigma weight residual 121.54 129.23 -7.69 1.91e+00 2.74e-01 1.62e+01 angle pdb=" C LYS B 95 " pdb=" N ASP B 96 " pdb=" CA ASP B 96 " ideal model delta sigma weight residual 121.54 129.20 -7.66 1.91e+00 2.74e-01 1.61e+01 angle pdb=" C LYS E 95 " pdb=" N ASP E 96 " pdb=" CA ASP E 96 " ideal model delta sigma weight residual 121.54 129.20 -7.66 1.91e+00 2.74e-01 1.61e+01 angle pdb=" C LYS H 95 " pdb=" N ASP H 96 " pdb=" CA ASP H 96 " ideal model delta sigma weight residual 121.54 129.20 -7.66 1.91e+00 2.74e-01 1.61e+01 angle pdb=" C ARG J 243 " pdb=" N GLN J 244 " pdb=" CA GLN J 244 " ideal model delta sigma weight residual 121.54 129.17 -7.63 1.91e+00 2.74e-01 1.60e+01 ... (remaining 24067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.40: 9843 14.40 - 28.80: 465 28.80 - 43.20: 125 43.20 - 57.60: 15 57.60 - 72.00: 20 Dihedral angle restraints: 10468 sinusoidal: 4164 harmonic: 6304 Sorted by residual: dihedral pdb=" CA HIS J 363 " pdb=" C HIS J 363 " pdb=" N PHE J 364 " pdb=" CA PHE J 364 " ideal model delta harmonic sigma weight residual -180.00 -152.17 -27.83 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA HIS A 363 " pdb=" C HIS A 363 " pdb=" N PHE A 364 " pdb=" CA PHE A 364 " ideal model delta harmonic sigma weight residual -180.00 -152.18 -27.82 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA HIS G 363 " pdb=" C HIS G 363 " pdb=" N PHE G 364 " pdb=" CA PHE G 364 " ideal model delta harmonic sigma weight residual 180.00 -152.21 -27.79 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 10465 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1459 0.039 - 0.077: 879 0.077 - 0.116: 226 0.116 - 0.154: 106 0.154 - 0.193: 18 Chirality restraints: 2688 Sorted by residual: chirality pdb=" CA ARG A 116 " pdb=" N ARG A 116 " pdb=" C ARG A 116 " pdb=" CB ARG A 116 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.29e-01 chirality pdb=" CA ARG J 116 " pdb=" N ARG J 116 " pdb=" C ARG J 116 " pdb=" CB ARG J 116 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.20e-01 chirality pdb=" CA ARG D 116 " pdb=" N ARG D 116 " pdb=" C ARG D 116 " pdb=" CB ARG D 116 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.20e-01 ... (remaining 2685 not shown) Planarity restraints: 3028 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE G 332 " -0.032 2.00e-02 2.50e+03 2.30e-02 9.24e+00 pdb=" CG PHE G 332 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE G 332 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE G 332 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE G 332 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE G 332 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE G 332 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 332 " -0.032 2.00e-02 2.50e+03 2.30e-02 9.24e+00 pdb=" CG PHE D 332 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE D 332 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE D 332 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE D 332 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE D 332 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE D 332 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 332 " 0.032 2.00e-02 2.50e+03 2.29e-02 9.14e+00 pdb=" CG PHE A 332 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE A 332 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 332 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 332 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 332 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 332 " 0.022 2.00e-02 2.50e+03 ... (remaining 3025 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 5479 2.83 - 3.35: 16710 3.35 - 3.87: 28038 3.87 - 4.38: 31098 4.38 - 4.90: 55323 Nonbonded interactions: 136648 Sorted by model distance: nonbonded pdb=" OE2 GLU A 284 " pdb=" OG1 THR A 322 " model vdw 2.315 3.040 nonbonded pdb=" OE2 GLU D 284 " pdb=" OG1 THR D 322 " model vdw 2.315 3.040 nonbonded pdb=" OE2 GLU G 284 " pdb=" OG1 THR G 322 " model vdw 2.315 3.040 nonbonded pdb=" OE2 GLU J 284 " pdb=" OG1 THR J 322 " model vdw 2.315 3.040 nonbonded pdb=" O LYS A 183 " pdb=" NH2 ARG A 192 " model vdw 2.359 3.120 ... (remaining 136643 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 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' } 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=0.83 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: 20.070 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: 0.000 Extract box with map and model: 0.390 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 35.480 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 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 : 0.007 0.102 17820 Z= 0.460 Angle : 0.954 8.521 24072 Z= 0.545 Chirality : 0.053 0.193 2688 Planarity : 0.007 0.048 3028 Dihedral : 10.226 72.001 6412 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.30 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % 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: -3.43 (0.14), residues: 2140 helix: -2.24 (0.09), residues: 1616 sheet: None (None), residues: 0 loop : -1.56 (0.25), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP D 305 HIS 0.013 0.002 HIS A 363 PHE 0.046 0.003 PHE G 332 TYR 0.021 0.003 TYR G 315 ARG 0.008 0.001 ARG G 243 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 480 time to evaluate : 2.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 LEU cc_start: 0.8401 (tp) cc_final: 0.7913 (mm) REVERT: A 507 ARG cc_start: 0.7501 (mmt-90) cc_final: 0.7100 (mpt180) REVERT: B 18 SER cc_start: 0.8995 (t) cc_final: 0.8666 (p) REVERT: B 19 LEU cc_start: 0.9032 (mp) cc_final: 0.8809 (mt) REVERT: B 123 ASP cc_start: 0.8390 (m-30) cc_final: 0.7878 (m-30) REVERT: C 65 MET cc_start: 0.8697 (mmt) cc_final: 0.8249 (mmt) REVERT: C 81 ARG cc_start: 0.7839 (mtp180) cc_final: 0.7181 (mmt180) REVERT: D 191 LEU cc_start: 0.8395 (tp) cc_final: 0.7927 (mm) REVERT: D 507 ARG cc_start: 0.7541 (mmt-90) cc_final: 0.7086 (mpt180) REVERT: E 18 SER cc_start: 0.9001 (t) cc_final: 0.8673 (p) REVERT: E 123 ASP cc_start: 0.8392 (m-30) cc_final: 0.7842 (m-30) REVERT: F 65 MET cc_start: 0.8695 (mmt) cc_final: 0.8220 (mmt) REVERT: F 81 ARG cc_start: 0.7823 (mtp180) cc_final: 0.7130 (mmt180) REVERT: G 191 LEU cc_start: 0.8394 (tp) cc_final: 0.7924 (mm) REVERT: G 507 ARG cc_start: 0.7541 (mmt-90) cc_final: 0.7085 (mpt180) REVERT: H 18 SER cc_start: 0.9002 (t) cc_final: 0.8674 (p) REVERT: H 123 ASP cc_start: 0.8391 (m-30) cc_final: 0.7842 (m-30) REVERT: I 81 ARG cc_start: 0.7833 (mtp180) cc_final: 0.7058 (mmt180) REVERT: J 191 LEU cc_start: 0.8392 (tp) cc_final: 0.7914 (mm) REVERT: J 507 ARG cc_start: 0.7513 (mmt-90) cc_final: 0.7066 (mpt180) REVERT: K 18 SER cc_start: 0.9004 (t) cc_final: 0.8664 (p) REVERT: K 19 LEU cc_start: 0.9009 (mp) cc_final: 0.8798 (mt) REVERT: K 123 ASP cc_start: 0.8391 (m-30) cc_final: 0.7873 (m-30) REVERT: L 81 ARG cc_start: 0.7817 (mtp180) cc_final: 0.7089 (mmt180) outliers start: 0 outliers final: 0 residues processed: 480 average time/residue: 0.3954 time to fit residues: 256.8551 Evaluate side-chains 304 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 304 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 0.1980 chunk 160 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 101 optimal weight: 0.0470 chunk 123 optimal weight: 0.5980 chunk 192 optimal weight: 0.9990 overall best weight: 0.5480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 GLN A 386 ASN A 560 GLN B 54 ASN C 93 HIS D 376 GLN D 386 ASN D 560 GLN E 54 ASN F 93 HIS G 376 GLN G 386 ASN G 560 GLN H 54 ASN I 93 HIS J 376 GLN J 386 ASN J 560 GLN K 50 GLN K 54 ASN L 93 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17820 Z= 0.153 Angle : 0.514 6.328 24072 Z= 0.278 Chirality : 0.038 0.122 2688 Planarity : 0.004 0.030 3028 Dihedral : 4.461 23.119 2396 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.69 % Allowed : 7.81 % Favored : 90.50 % 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: -0.84 (0.17), residues: 2140 helix: -0.26 (0.12), residues: 1620 sheet: None (None), residues: 0 loop : -1.08 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 379 HIS 0.004 0.001 HIS A 240 PHE 0.021 0.001 PHE K 17 TYR 0.013 0.001 TYR D 545 ARG 0.007 0.001 ARG E 127 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 320 time to evaluate : 1.952 Fit side-chains REVERT: A 191 LEU cc_start: 0.8386 (tp) cc_final: 0.7832 (mm) REVERT: A 286 ASP cc_start: 0.7887 (t0) cc_final: 0.7507 (t0) REVERT: A 562 ARG cc_start: 0.7928 (ttp80) cc_final: 0.7379 (ttp80) REVERT: B 22 LYS cc_start: 0.6289 (mtmm) cc_final: 0.5786 (mttp) REVERT: C 65 MET cc_start: 0.8724 (mmt) cc_final: 0.8454 (mmt) REVERT: C 81 ARG cc_start: 0.7535 (mtp180) cc_final: 0.7193 (mpt180) REVERT: D 191 LEU cc_start: 0.8350 (tp) cc_final: 0.7800 (mm) REVERT: D 286 ASP cc_start: 0.7890 (t0) cc_final: 0.7508 (t0) REVERT: D 507 ARG cc_start: 0.7467 (mmt-90) cc_final: 0.7084 (mpt180) REVERT: D 562 ARG cc_start: 0.7955 (ttp80) cc_final: 0.7396 (ttp80) REVERT: E 22 LYS cc_start: 0.6250 (mtmm) cc_final: 0.5750 (mttp) REVERT: F 65 MET cc_start: 0.8730 (mmt) cc_final: 0.8502 (mmt) REVERT: F 81 ARG cc_start: 0.7534 (mtp180) cc_final: 0.7294 (mpt180) REVERT: G 191 LEU cc_start: 0.8348 (tp) cc_final: 0.7801 (mm) REVERT: G 286 ASP cc_start: 0.7891 (t0) cc_final: 0.7511 (t0) REVERT: G 507 ARG cc_start: 0.7466 (mmt-90) cc_final: 0.7083 (mpt180) REVERT: G 562 ARG cc_start: 0.7953 (ttp80) cc_final: 0.7412 (ttp80) REVERT: H 22 LYS cc_start: 0.6280 (mtmm) cc_final: 0.5778 (mttp) REVERT: I 65 MET cc_start: 0.8757 (mmt) cc_final: 0.8334 (mmt) REVERT: I 81 ARG cc_start: 0.7582 (mtp180) cc_final: 0.7176 (mpt180) REVERT: J 191 LEU cc_start: 0.8348 (tp) cc_final: 0.7798 (mm) REVERT: J 286 ASP cc_start: 0.7886 (t0) cc_final: 0.7501 (t0) REVERT: J 507 ARG cc_start: 0.7474 (mmt-90) cc_final: 0.7083 (mpt180) REVERT: J 562 ARG cc_start: 0.7944 (ttp80) cc_final: 0.7389 (ttp80) REVERT: K 22 LYS cc_start: 0.6269 (mtmm) cc_final: 0.5765 (mttp) REVERT: L 65 MET cc_start: 0.8761 (mmt) cc_final: 0.8386 (mmt) outliers start: 31 outliers final: 26 residues processed: 343 average time/residue: 0.4025 time to fit residues: 187.6522 Evaluate side-chains 283 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 257 time to evaluate : 2.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain G residue 214 CYS Chi-restraints excluded: chain G residue 290 GLU Chi-restraints excluded: chain G residue 301 ASP Chi-restraints excluded: chain G residue 514 ILE Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain J residue 214 CYS Chi-restraints excluded: chain J residue 290 GLU Chi-restraints excluded: chain J residue 301 ASP Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 145 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 160 optimal weight: 0.3980 chunk 131 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 192 optimal weight: 4.9990 chunk 208 optimal weight: 0.9990 chunk 171 optimal weight: 0.9990 chunk 191 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 154 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 HIS B 54 ASN B 144 GLN D 510 HIS E 54 ASN E 144 GLN G 510 HIS H 54 ASN H 144 GLN J 510 HIS K 112 ASN K 144 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 17820 Z= 0.167 Angle : 0.477 5.764 24072 Z= 0.255 Chirality : 0.038 0.126 2688 Planarity : 0.003 0.027 3028 Dihedral : 3.988 19.487 2396 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.51 % Allowed : 9.72 % Favored : 87.77 % 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: 0.50 (0.18), residues: 2140 helix: 0.76 (0.12), residues: 1620 sheet: None (None), residues: 0 loop : -0.79 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 379 HIS 0.005 0.001 HIS J 240 PHE 0.020 0.001 PHE A 332 TYR 0.014 0.001 TYR J 545 ARG 0.006 0.000 ARG K 127 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 286 time to evaluate : 2.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 TRP cc_start: 0.6876 (m-90) cc_final: 0.6278 (m100) REVERT: A 188 TRP cc_start: 0.8294 (m100) cc_final: 0.8036 (m-90) REVERT: A 191 LEU cc_start: 0.8376 (tp) cc_final: 0.7781 (mm) REVERT: A 286 ASP cc_start: 0.7926 (t0) cc_final: 0.7506 (t0) REVERT: A 562 ARG cc_start: 0.7947 (ttp80) cc_final: 0.7648 (ttp80) REVERT: B 18 SER cc_start: 0.8944 (t) cc_final: 0.8628 (p) REVERT: B 22 LYS cc_start: 0.6331 (mtmm) cc_final: 0.5912 (mttp) REVERT: B 54 ASN cc_start: 0.8541 (m110) cc_final: 0.8211 (m-40) REVERT: B 70 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8568 (mt) REVERT: C 65 MET cc_start: 0.8691 (mmt) cc_final: 0.8353 (mmt) REVERT: D 188 TRP cc_start: 0.8304 (m100) cc_final: 0.8040 (m-90) REVERT: D 191 LEU cc_start: 0.8370 (tp) cc_final: 0.7787 (mm) REVERT: D 286 ASP cc_start: 0.7913 (t0) cc_final: 0.7486 (t0) REVERT: D 507 ARG cc_start: 0.7571 (mmt-90) cc_final: 0.7124 (mpt180) REVERT: D 562 ARG cc_start: 0.7911 (ttp80) cc_final: 0.7593 (ttp80) REVERT: E 18 SER cc_start: 0.8965 (t) cc_final: 0.8650 (p) REVERT: F 65 MET cc_start: 0.8698 (mmt) cc_final: 0.8365 (mmt) REVERT: G 188 TRP cc_start: 0.8305 (m100) cc_final: 0.8040 (m-90) REVERT: G 191 LEU cc_start: 0.8370 (tp) cc_final: 0.7788 (mm) REVERT: G 286 ASP cc_start: 0.7914 (t0) cc_final: 0.7485 (t0) REVERT: G 507 ARG cc_start: 0.7568 (mmt-90) cc_final: 0.7124 (mpt180) REVERT: G 562 ARG cc_start: 0.7938 (ttp80) cc_final: 0.7623 (ttp80) REVERT: H 18 SER cc_start: 0.8963 (t) cc_final: 0.8648 (p) REVERT: H 54 ASN cc_start: 0.8552 (m110) cc_final: 0.8213 (m-40) REVERT: H 70 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8602 (mt) REVERT: I 65 MET cc_start: 0.8732 (mmt) cc_final: 0.8268 (mmt) REVERT: J 158 TRP cc_start: 0.6874 (m-90) cc_final: 0.6269 (m100) REVERT: J 188 TRP cc_start: 0.8286 (m100) cc_final: 0.8044 (m-90) REVERT: J 191 LEU cc_start: 0.8368 (tp) cc_final: 0.7782 (mm) REVERT: J 286 ASP cc_start: 0.7912 (t0) cc_final: 0.7482 (t0) REVERT: J 507 ARG cc_start: 0.7514 (mmt-90) cc_final: 0.7069 (mpt180) REVERT: J 562 ARG cc_start: 0.7926 (ttp80) cc_final: 0.7610 (ttp80) REVERT: K 18 SER cc_start: 0.8949 (t) cc_final: 0.8632 (p) REVERT: L 65 MET cc_start: 0.8735 (mmt) cc_final: 0.8368 (mmt) outliers start: 46 outliers final: 30 residues processed: 313 average time/residue: 0.3715 time to fit residues: 162.3460 Evaluate side-chains 293 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 261 time to evaluate : 1.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 332 PHE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 214 CYS Chi-restraints excluded: chain G residue 290 GLU Chi-restraints excluded: chain G residue 301 ASP Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 214 CYS Chi-restraints excluded: chain J residue 290 GLU Chi-restraints excluded: chain J residue 301 ASP Chi-restraints excluded: chain J residue 332 PHE Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 140 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 0.2980 chunk 145 optimal weight: 0.0770 chunk 100 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 129 optimal weight: 0.8980 chunk 193 optimal weight: 0.9980 chunk 204 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 183 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 54 ASN K 54 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 17820 Z= 0.141 Angle : 0.449 6.097 24072 Z= 0.239 Chirality : 0.037 0.126 2688 Planarity : 0.003 0.029 3028 Dihedral : 3.701 17.159 2396 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.84 % Allowed : 9.44 % Favored : 87.72 % 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: 1.24 (0.18), residues: 2140 helix: 1.35 (0.13), residues: 1616 sheet: None (None), residues: 0 loop : -0.74 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 379 HIS 0.005 0.001 HIS D 240 PHE 0.015 0.001 PHE J 332 TYR 0.011 0.001 TYR J 545 ARG 0.009 0.000 ARG H 127 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 283 time to evaluate : 2.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 TRP cc_start: 0.8253 (m100) cc_final: 0.7951 (m-90) REVERT: A 191 LEU cc_start: 0.8341 (tp) cc_final: 0.7764 (mm) REVERT: A 286 ASP cc_start: 0.7902 (t0) cc_final: 0.7461 (t0) REVERT: A 366 ARG cc_start: 0.9070 (tpp80) cc_final: 0.8868 (tpp-160) REVERT: A 507 ARG cc_start: 0.7545 (mmt-90) cc_final: 0.7056 (mpt180) REVERT: A 562 ARG cc_start: 0.8033 (ttp80) cc_final: 0.7731 (ttp80) REVERT: B 22 LYS cc_start: 0.6264 (mtmm) cc_final: 0.5880 (mttp) REVERT: B 54 ASN cc_start: 0.8531 (m110) cc_final: 0.8318 (m-40) REVERT: C 65 MET cc_start: 0.8670 (mmt) cc_final: 0.8334 (mmt) REVERT: D 188 TRP cc_start: 0.8269 (m100) cc_final: 0.7964 (m-90) REVERT: D 191 LEU cc_start: 0.8316 (tp) cc_final: 0.7747 (mm) REVERT: D 286 ASP cc_start: 0.7903 (t0) cc_final: 0.7490 (t0) REVERT: D 507 ARG cc_start: 0.7603 (mmt-90) cc_final: 0.7074 (mpt180) REVERT: D 562 ARG cc_start: 0.8048 (ttp80) cc_final: 0.7715 (ttp80) REVERT: E 18 SER cc_start: 0.8943 (t) cc_final: 0.8627 (p) REVERT: E 22 LYS cc_start: 0.6307 (mtmm) cc_final: 0.5908 (mttp) REVERT: E 70 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8585 (mt) REVERT: G 188 TRP cc_start: 0.8269 (m100) cc_final: 0.7964 (m-90) REVERT: G 191 LEU cc_start: 0.8315 (tp) cc_final: 0.7747 (mm) REVERT: G 286 ASP cc_start: 0.7902 (t0) cc_final: 0.7490 (t0) REVERT: G 507 ARG cc_start: 0.7603 (mmt-90) cc_final: 0.7074 (mpt180) REVERT: G 562 ARG cc_start: 0.8063 (ttp80) cc_final: 0.7742 (ttp80) REVERT: H 18 SER cc_start: 0.8943 (t) cc_final: 0.8630 (p) REVERT: H 22 LYS cc_start: 0.6307 (mtmm) cc_final: 0.5909 (mttp) REVERT: H 54 ASN cc_start: 0.8536 (m110) cc_final: 0.8325 (m-40) REVERT: I 65 MET cc_start: 0.8691 (mmt) cc_final: 0.8312 (mmt) REVERT: J 188 TRP cc_start: 0.8260 (m100) cc_final: 0.7969 (m-90) REVERT: J 191 LEU cc_start: 0.8311 (tp) cc_final: 0.7738 (mm) REVERT: J 286 ASP cc_start: 0.7925 (t0) cc_final: 0.7510 (t0) REVERT: J 507 ARG cc_start: 0.7611 (mmt-90) cc_final: 0.7081 (mpt180) REVERT: J 562 ARG cc_start: 0.8045 (ttp80) cc_final: 0.7718 (ttp80) REVERT: K 18 SER cc_start: 0.8944 (t) cc_final: 0.8615 (p) REVERT: K 22 LYS cc_start: 0.6335 (mtmm) cc_final: 0.5938 (mttp) REVERT: K 38 ARG cc_start: 0.8770 (mtm110) cc_final: 0.8524 (mtm-85) REVERT: L 65 MET cc_start: 0.8703 (mmt) cc_final: 0.8334 (mmt) outliers start: 52 outliers final: 25 residues processed: 314 average time/residue: 0.3770 time to fit residues: 164.5137 Evaluate side-chains 283 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 257 time to evaluate : 2.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 376 GLN Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 214 CYS Chi-restraints excluded: chain G residue 290 GLU Chi-restraints excluded: chain G residue 376 GLN Chi-restraints excluded: chain G residue 514 ILE Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 214 CYS Chi-restraints excluded: chain J residue 290 GLU Chi-restraints excluded: chain J residue 376 GLN Chi-restraints excluded: chain K residue 70 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 9.9990 chunk 116 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 152 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 104 optimal weight: 0.6980 chunk 183 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 98 ASN E 50 GLN E 54 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 17820 Z= 0.162 Angle : 0.461 10.140 24072 Z= 0.243 Chirality : 0.037 0.118 2688 Planarity : 0.003 0.031 3028 Dihedral : 3.580 15.422 2396 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.84 % Allowed : 10.32 % Favored : 86.84 % 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: 1.65 (0.18), residues: 2140 helix: 1.69 (0.13), residues: 1608 sheet: None (None), residues: 0 loop : -0.69 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 379 HIS 0.006 0.001 HIS A 240 PHE 0.014 0.001 PHE G 332 TYR 0.014 0.001 TYR J 545 ARG 0.009 0.000 ARG H 127 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 273 time to evaluate : 2.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 LEU cc_start: 0.8385 (tp) cc_final: 0.7818 (mm) REVERT: A 286 ASP cc_start: 0.7910 (t0) cc_final: 0.7506 (t0) REVERT: A 366 ARG cc_start: 0.9018 (tpp80) cc_final: 0.8768 (tpp-160) REVERT: A 507 ARG cc_start: 0.7584 (mmt-90) cc_final: 0.7062 (mpt180) REVERT: A 562 ARG cc_start: 0.8080 (ttp80) cc_final: 0.7771 (ttp80) REVERT: B 22 LYS cc_start: 0.6261 (mtmm) cc_final: 0.5837 (mttp) REVERT: B 54 ASN cc_start: 0.8584 (m110) cc_final: 0.8315 (m-40) REVERT: C 65 MET cc_start: 0.8700 (mmt) cc_final: 0.8314 (mmt) REVERT: D 191 LEU cc_start: 0.8336 (tp) cc_final: 0.7766 (mm) REVERT: D 286 ASP cc_start: 0.7902 (t0) cc_final: 0.7488 (t0) REVERT: D 562 ARG cc_start: 0.8107 (ttp80) cc_final: 0.7805 (ttp80) REVERT: E 22 LYS cc_start: 0.6325 (mtmm) cc_final: 0.5917 (mttp) REVERT: G 191 LEU cc_start: 0.8335 (tp) cc_final: 0.7767 (mm) REVERT: G 286 ASP cc_start: 0.7902 (t0) cc_final: 0.7486 (t0) REVERT: G 507 ARG cc_start: 0.7646 (mmt-90) cc_final: 0.7080 (mpt180) REVERT: G 562 ARG cc_start: 0.8128 (ttp80) cc_final: 0.7841 (ttp80) REVERT: H 22 LYS cc_start: 0.6300 (mtmm) cc_final: 0.5887 (mttp) REVERT: H 54 ASN cc_start: 0.8591 (m110) cc_final: 0.8307 (m-40) REVERT: I 65 MET cc_start: 0.8712 (mmt) cc_final: 0.8286 (mmt) REVERT: J 188 TRP cc_start: 0.8325 (m100) cc_final: 0.8054 (m-90) REVERT: J 191 LEU cc_start: 0.8331 (tp) cc_final: 0.7756 (mm) REVERT: J 286 ASP cc_start: 0.7899 (t0) cc_final: 0.7489 (t0) REVERT: J 507 ARG cc_start: 0.7654 (mmt-90) cc_final: 0.7086 (mpt180) REVERT: J 562 ARG cc_start: 0.8116 (ttp80) cc_final: 0.7821 (ttp80) REVERT: K 22 LYS cc_start: 0.6263 (mtmm) cc_final: 0.5897 (mttp) REVERT: K 38 ARG cc_start: 0.8763 (mtm110) cc_final: 0.8496 (mtm110) REVERT: K 54 ASN cc_start: 0.8517 (m110) cc_final: 0.8225 (m-40) REVERT: L 65 MET cc_start: 0.8716 (mmt) cc_final: 0.8312 (mmt) outliers start: 52 outliers final: 31 residues processed: 305 average time/residue: 0.3922 time to fit residues: 165.3853 Evaluate side-chains 287 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 256 time to evaluate : 2.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 363 HIS Chi-restraints excluded: chain D residue 376 GLN Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 214 CYS Chi-restraints excluded: chain G residue 363 HIS Chi-restraints excluded: chain G residue 376 GLN Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 140 GLU Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 214 CYS Chi-restraints excluded: chain J residue 264 THR Chi-restraints excluded: chain J residue 376 GLN Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 137 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 2.9990 chunk 184 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 205 optimal weight: 0.8980 chunk 170 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 ASN C 56 ASN F 56 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17820 Z= 0.188 Angle : 0.471 8.689 24072 Z= 0.249 Chirality : 0.038 0.124 2688 Planarity : 0.003 0.035 3028 Dihedral : 3.551 14.907 2396 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.62 % Allowed : 11.24 % Favored : 86.14 % 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: 1.88 (0.18), residues: 2140 helix: 1.84 (0.13), residues: 1616 sheet: None (None), residues: 0 loop : -0.58 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 379 HIS 0.006 0.001 HIS G 240 PHE 0.017 0.001 PHE G 332 TYR 0.015 0.001 TYR G 545 ARG 0.011 0.000 ARG E 127 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 277 time to evaluate : 2.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 TRP cc_start: 0.6815 (m-90) cc_final: 0.6246 (m100) REVERT: A 286 ASP cc_start: 0.7911 (t0) cc_final: 0.7488 (t0) REVERT: A 562 ARG cc_start: 0.8208 (ttp80) cc_final: 0.7918 (ttp80) REVERT: B 22 LYS cc_start: 0.6270 (OUTLIER) cc_final: 0.5747 (mttp) REVERT: B 54 ASN cc_start: 0.8608 (m110) cc_final: 0.8299 (m-40) REVERT: C 65 MET cc_start: 0.8738 (mmt) cc_final: 0.8263 (mmt) REVERT: D 158 TRP cc_start: 0.6822 (m-90) cc_final: 0.6224 (m100) REVERT: D 191 LEU cc_start: 0.8386 (tp) cc_final: 0.7814 (mm) REVERT: D 286 ASP cc_start: 0.7918 (t0) cc_final: 0.7492 (t0) REVERT: D 562 ARG cc_start: 0.8234 (ttp80) cc_final: 0.7951 (ttp80) REVERT: E 38 ARG cc_start: 0.8780 (mtm110) cc_final: 0.8492 (mtm110) REVERT: G 158 TRP cc_start: 0.6822 (m-90) cc_final: 0.6225 (m100) REVERT: G 191 LEU cc_start: 0.8385 (tp) cc_final: 0.7818 (mm) REVERT: G 242 ASP cc_start: 0.8345 (t0) cc_final: 0.8089 (t0) REVERT: G 286 ASP cc_start: 0.7917 (t0) cc_final: 0.7495 (t0) REVERT: G 553 MET cc_start: 0.8807 (tpp) cc_final: 0.8322 (tpp) REVERT: G 562 ARG cc_start: 0.8276 (ttp80) cc_final: 0.8003 (ttp80) REVERT: H 54 ASN cc_start: 0.8614 (m110) cc_final: 0.8310 (m-40) REVERT: I 65 MET cc_start: 0.8745 (mmt) cc_final: 0.8234 (mmt) REVERT: J 158 TRP cc_start: 0.6839 (m-90) cc_final: 0.6256 (m100) REVERT: J 191 LEU cc_start: 0.8378 (tp) cc_final: 0.7807 (mm) REVERT: J 286 ASP cc_start: 0.7914 (t0) cc_final: 0.7488 (t0) REVERT: J 562 ARG cc_start: 0.8237 (ttp80) cc_final: 0.7958 (ttp80) REVERT: K 54 ASN cc_start: 0.8526 (m110) cc_final: 0.8216 (m-40) REVERT: L 65 MET cc_start: 0.8745 (mmt) cc_final: 0.8267 (mmt) outliers start: 48 outliers final: 34 residues processed: 310 average time/residue: 0.3655 time to fit residues: 158.9833 Evaluate side-chains 295 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 260 time to evaluate : 2.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 363 HIS Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 376 GLN Chi-restraints excluded: chain D residue 566 SER Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 214 CYS Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 301 ASP Chi-restraints excluded: chain G residue 376 GLN Chi-restraints excluded: chain G residue 566 SER Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 140 GLU Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 214 CYS Chi-restraints excluded: chain J residue 376 GLN Chi-restraints excluded: chain J residue 566 SER Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 140 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 114 optimal weight: 0.6980 chunk 204 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 126 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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: 0.8114 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17820 Z= 0.213 Angle : 0.488 8.410 24072 Z= 0.259 Chirality : 0.039 0.125 2688 Planarity : 0.003 0.044 3028 Dihedral : 3.575 14.308 2396 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.35 % Allowed : 12.72 % Favored : 84.93 % 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: 1.87 (0.18), residues: 2140 helix: 1.82 (0.13), residues: 1620 sheet: None (None), residues: 0 loop : -0.55 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 379 HIS 0.006 0.001 HIS A 240 PHE 0.016 0.001 PHE J 332 TYR 0.016 0.001 TYR J 545 ARG 0.011 0.000 ARG H 127 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 270 time to evaluate : 2.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 TRP cc_start: 0.6783 (m-90) cc_final: 0.6271 (m100) REVERT: A 286 ASP cc_start: 0.7992 (t0) cc_final: 0.7580 (t0) REVERT: A 562 ARG cc_start: 0.8285 (ttp80) cc_final: 0.8002 (ttp80) REVERT: B 22 LYS cc_start: 0.6188 (OUTLIER) cc_final: 0.5741 (mttp) REVERT: B 38 ARG cc_start: 0.8792 (mtm110) cc_final: 0.8535 (mtm110) REVERT: B 54 ASN cc_start: 0.8629 (m110) cc_final: 0.8293 (m-40) REVERT: C 65 MET cc_start: 0.8750 (mmt) cc_final: 0.8272 (mmt) REVERT: D 158 TRP cc_start: 0.6835 (m-90) cc_final: 0.6257 (m100) REVERT: D 286 ASP cc_start: 0.7994 (t0) cc_final: 0.7567 (t0) REVERT: D 562 ARG cc_start: 0.8273 (ttp80) cc_final: 0.7982 (ttp80) REVERT: E 22 LYS cc_start: 0.6263 (mtmm) cc_final: 0.5785 (mttp) REVERT: G 158 TRP cc_start: 0.6837 (m-90) cc_final: 0.6259 (m100) REVERT: G 286 ASP cc_start: 0.7995 (t0) cc_final: 0.7568 (t0) REVERT: G 553 MET cc_start: 0.8802 (tpp) cc_final: 0.8327 (tpp) REVERT: G 562 ARG cc_start: 0.8285 (ttp80) cc_final: 0.8012 (ttp80) REVERT: H 22 LYS cc_start: 0.6266 (mtmm) cc_final: 0.5783 (mttp) REVERT: H 38 ARG cc_start: 0.8786 (mtm110) cc_final: 0.8515 (mtm110) REVERT: H 54 ASN cc_start: 0.8637 (m110) cc_final: 0.8299 (m-40) REVERT: I 65 MET cc_start: 0.8747 (mmt) cc_final: 0.8288 (mmt) REVERT: J 158 TRP cc_start: 0.6843 (m-90) cc_final: 0.6261 (m100) REVERT: J 286 ASP cc_start: 0.7994 (t0) cc_final: 0.7568 (t0) REVERT: J 562 ARG cc_start: 0.8271 (ttp80) cc_final: 0.7980 (ttp80) REVERT: K 22 LYS cc_start: 0.6198 (mtmm) cc_final: 0.5755 (mttp) REVERT: L 65 MET cc_start: 0.8750 (mmt) cc_final: 0.8290 (mmt) outliers start: 43 outliers final: 33 residues processed: 298 average time/residue: 0.3661 time to fit residues: 152.8743 Evaluate side-chains 294 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 260 time to evaluate : 2.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 363 HIS Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 376 GLN Chi-restraints excluded: chain D residue 566 SER Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 214 CYS Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 363 HIS Chi-restraints excluded: chain G residue 376 GLN Chi-restraints excluded: chain G residue 566 SER Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 214 CYS Chi-restraints excluded: chain J residue 264 THR Chi-restraints excluded: chain J residue 376 GLN Chi-restraints excluded: chain J residue 566 SER Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 137 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 139 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 185 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 98 ASN K 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17820 Z= 0.179 Angle : 0.478 8.092 24072 Z= 0.252 Chirality : 0.038 0.127 2688 Planarity : 0.003 0.048 3028 Dihedral : 3.504 14.413 2396 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.40 % Allowed : 13.05 % Favored : 84.55 % 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: 2.02 (0.18), residues: 2140 helix: 1.91 (0.13), residues: 1620 sheet: None (None), residues: 0 loop : -0.44 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 379 HIS 0.005 0.001 HIS A 240 PHE 0.016 0.001 PHE A 332 TYR 0.013 0.001 TYR J 545 ARG 0.012 0.000 ARG K 127 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 270 time to evaluate : 2.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 TRP cc_start: 0.6709 (m-90) cc_final: 0.6168 (m100) REVERT: A 286 ASP cc_start: 0.7996 (t0) cc_final: 0.7592 (t0) REVERT: A 528 LYS cc_start: 0.8246 (mttp) cc_final: 0.7993 (mmtm) REVERT: A 562 ARG cc_start: 0.8297 (ttp80) cc_final: 0.8003 (ttp80) REVERT: B 38 ARG cc_start: 0.8775 (mtm110) cc_final: 0.8559 (mtm110) REVERT: B 54 ASN cc_start: 0.8605 (m110) cc_final: 0.8259 (m-40) REVERT: C 65 MET cc_start: 0.8725 (mmt) cc_final: 0.8234 (mmt) REVERT: D 158 TRP cc_start: 0.6743 (m-90) cc_final: 0.6259 (m100) REVERT: D 286 ASP cc_start: 0.8022 (t0) cc_final: 0.7619 (t0) REVERT: D 562 ARG cc_start: 0.8312 (ttp80) cc_final: 0.8025 (ttp80) REVERT: G 158 TRP cc_start: 0.6744 (m-90) cc_final: 0.6259 (m100) REVERT: G 286 ASP cc_start: 0.8021 (t0) cc_final: 0.7617 (t0) REVERT: G 553 MET cc_start: 0.8809 (tpp) cc_final: 0.8289 (tpp) REVERT: G 562 ARG cc_start: 0.8325 (ttp80) cc_final: 0.8055 (ttp80) REVERT: H 38 ARG cc_start: 0.8794 (mtm110) cc_final: 0.8529 (mtm110) REVERT: H 54 ASN cc_start: 0.8611 (m110) cc_final: 0.8262 (m-40) REVERT: I 65 MET cc_start: 0.8746 (mmt) cc_final: 0.8257 (mmt) REVERT: J 158 TRP cc_start: 0.6732 (m-90) cc_final: 0.6250 (m100) REVERT: J 286 ASP cc_start: 0.8022 (t0) cc_final: 0.7619 (t0) REVERT: J 562 ARG cc_start: 0.8306 (ttp80) cc_final: 0.8017 (ttp80) REVERT: K 22 LYS cc_start: 0.6252 (OUTLIER) cc_final: 0.5735 (mttp) REVERT: L 65 MET cc_start: 0.8731 (mmt) cc_final: 0.8240 (mmt) outliers start: 44 outliers final: 33 residues processed: 302 average time/residue: 0.3549 time to fit residues: 152.4777 Evaluate side-chains 294 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 260 time to evaluate : 2.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 363 HIS Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 376 GLN Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 566 SER Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 214 CYS Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 301 ASP Chi-restraints excluded: chain G residue 376 GLN Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 566 SER Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 140 GLU Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 214 CYS Chi-restraints excluded: chain J residue 264 THR Chi-restraints excluded: chain J residue 376 GLN Chi-restraints excluded: chain K residue 22 LYS Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 140 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 114 optimal weight: 0.5980 chunk 82 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 chunk 58 optimal weight: 0.0030 chunk 172 optimal weight: 6.9990 chunk 180 optimal weight: 1.9990 chunk 189 optimal weight: 0.6980 chunk 125 optimal weight: 0.9980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17820 Z= 0.154 Angle : 0.470 7.884 24072 Z= 0.247 Chirality : 0.037 0.121 2688 Planarity : 0.003 0.053 3028 Dihedral : 3.400 13.789 2396 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.91 % Allowed : 14.14 % Favored : 83.95 % 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: 2.17 (0.18), residues: 2140 helix: 2.02 (0.13), residues: 1620 sheet: None (None), residues: 0 loop : -0.38 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 379 HIS 0.005 0.001 HIS A 363 PHE 0.015 0.001 PHE A 332 TYR 0.011 0.001 TYR D 545 ARG 0.013 0.000 ARG E 127 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 273 time to evaluate : 2.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 TRP cc_start: 0.6581 (m-90) cc_final: 0.6060 (m100) REVERT: A 191 LEU cc_start: 0.8342 (tp) cc_final: 0.7937 (mm) REVERT: A 286 ASP cc_start: 0.7947 (t0) cc_final: 0.7592 (t0) REVERT: A 528 LYS cc_start: 0.8226 (mttp) cc_final: 0.8005 (mmtm) REVERT: A 562 ARG cc_start: 0.8288 (ttp80) cc_final: 0.8017 (ttp80) REVERT: B 38 ARG cc_start: 0.8728 (mtm110) cc_final: 0.8518 (mtm110) REVERT: B 54 ASN cc_start: 0.8596 (m110) cc_final: 0.8242 (m-40) REVERT: C 65 MET cc_start: 0.8707 (mmt) cc_final: 0.8243 (mmt) REVERT: D 158 TRP cc_start: 0.6660 (m-90) cc_final: 0.6144 (m100) REVERT: D 191 LEU cc_start: 0.8349 (tp) cc_final: 0.7948 (mm) REVERT: D 286 ASP cc_start: 0.7990 (t0) cc_final: 0.7627 (t0) REVERT: D 528 LYS cc_start: 0.8235 (mttp) cc_final: 0.8005 (mmtm) REVERT: D 562 ARG cc_start: 0.8301 (ttp80) cc_final: 0.8033 (ttp80) REVERT: G 158 TRP cc_start: 0.6660 (m-90) cc_final: 0.6146 (m100) REVERT: G 191 LEU cc_start: 0.8347 (tp) cc_final: 0.7950 (mm) REVERT: G 286 ASP cc_start: 0.7991 (t0) cc_final: 0.7628 (t0) REVERT: G 528 LYS cc_start: 0.8267 (mttp) cc_final: 0.8037 (mmtm) REVERT: G 562 ARG cc_start: 0.8319 (ttp80) cc_final: 0.8063 (ttp80) REVERT: H 38 ARG cc_start: 0.8768 (mtm110) cc_final: 0.8554 (mtm110) REVERT: H 54 ASN cc_start: 0.8586 (m110) cc_final: 0.8256 (m-40) REVERT: I 65 MET cc_start: 0.8718 (mmt) cc_final: 0.8265 (mmt) REVERT: J 158 TRP cc_start: 0.6682 (m-90) cc_final: 0.6153 (m100) REVERT: J 191 LEU cc_start: 0.8350 (tp) cc_final: 0.7951 (mm) REVERT: J 286 ASP cc_start: 0.7991 (t0) cc_final: 0.7628 (t0) REVERT: J 528 LYS cc_start: 0.8256 (mttp) cc_final: 0.8035 (mmtm) REVERT: J 562 ARG cc_start: 0.8298 (ttp80) cc_final: 0.8032 (ttp80) REVERT: L 65 MET cc_start: 0.8714 (mmt) cc_final: 0.8251 (mmt) outliers start: 35 outliers final: 29 residues processed: 297 average time/residue: 0.3891 time to fit residues: 161.9165 Evaluate side-chains 294 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 265 time to evaluate : 2.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 376 GLN Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 214 CYS Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 376 GLN Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 140 GLU Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 214 CYS Chi-restraints excluded: chain J residue 264 THR Chi-restraints excluded: chain J residue 376 GLN Chi-restraints excluded: chain J residue 396 ILE Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 140 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 0.8980 chunk 122 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 211 optimal weight: 10.0000 chunk 194 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 17 optimal weight: 0.0570 chunk 129 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 chunk 133 optimal weight: 3.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 144 GLN K 144 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17820 Z= 0.153 Angle : 0.475 7.767 24072 Z= 0.249 Chirality : 0.037 0.120 2688 Planarity : 0.003 0.056 3028 Dihedral : 3.354 13.540 2396 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.64 % Allowed : 14.25 % Favored : 84.12 % 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: 2.26 (0.18), residues: 2140 helix: 2.09 (0.13), residues: 1620 sheet: None (None), residues: 0 loop : -0.37 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 379 HIS 0.004 0.001 HIS A 363 PHE 0.015 0.001 PHE A 332 TYR 0.011 0.001 TYR A 545 ARG 0.014 0.000 ARG K 127 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 270 time to evaluate : 2.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 LEU cc_start: 0.8361 (tp) cc_final: 0.7958 (mm) REVERT: A 286 ASP cc_start: 0.7968 (t0) cc_final: 0.7607 (t0) REVERT: A 528 LYS cc_start: 0.8213 (mttp) cc_final: 0.8012 (mmtm) REVERT: A 562 ARG cc_start: 0.8233 (ttp80) cc_final: 0.7972 (ttp80) REVERT: B 54 ASN cc_start: 0.8594 (m110) cc_final: 0.8258 (m-40) REVERT: C 65 MET cc_start: 0.8706 (mmt) cc_final: 0.8245 (mmt) REVERT: D 158 TRP cc_start: 0.6556 (m-90) cc_final: 0.6038 (m100) REVERT: D 191 LEU cc_start: 0.8314 (tp) cc_final: 0.7906 (mm) REVERT: D 286 ASP cc_start: 0.8009 (t0) cc_final: 0.7642 (t0) REVERT: D 528 LYS cc_start: 0.8228 (mttp) cc_final: 0.8012 (mmtm) REVERT: D 562 ARG cc_start: 0.8301 (ttp80) cc_final: 0.8044 (ttp80) REVERT: E 22 LYS cc_start: 0.6188 (OUTLIER) cc_final: 0.5674 (mttp) REVERT: G 158 TRP cc_start: 0.6558 (m-90) cc_final: 0.6039 (m100) REVERT: G 191 LEU cc_start: 0.8312 (tp) cc_final: 0.7906 (mm) REVERT: G 286 ASP cc_start: 0.7985 (t0) cc_final: 0.7637 (t0) REVERT: G 528 LYS cc_start: 0.8253 (mttp) cc_final: 0.8040 (mmtm) REVERT: G 562 ARG cc_start: 0.8335 (ttp80) cc_final: 0.8091 (ttp80) REVERT: H 38 ARG cc_start: 0.8763 (mtm110) cc_final: 0.8555 (mtm110) REVERT: H 54 ASN cc_start: 0.8557 (m110) cc_final: 0.8217 (m-40) REVERT: I 65 MET cc_start: 0.8716 (mmt) cc_final: 0.8260 (mmt) REVERT: J 158 TRP cc_start: 0.6533 (m-90) cc_final: 0.6024 (m100) REVERT: J 191 LEU cc_start: 0.8312 (tp) cc_final: 0.7908 (mm) REVERT: J 286 ASP cc_start: 0.7989 (t0) cc_final: 0.7639 (t0) REVERT: J 528 LYS cc_start: 0.8244 (mttp) cc_final: 0.8040 (mmtm) REVERT: J 562 ARG cc_start: 0.8295 (ttp80) cc_final: 0.8042 (ttp80) REVERT: L 65 MET cc_start: 0.8712 (mmt) cc_final: 0.8245 (mmt) outliers start: 30 outliers final: 24 residues processed: 291 average time/residue: 0.3648 time to fit residues: 149.0668 Evaluate side-chains 288 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 263 time to evaluate : 2.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 376 GLN Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 214 CYS Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 376 GLN Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 140 GLU Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 214 CYS Chi-restraints excluded: chain J residue 264 THR Chi-restraints excluded: chain J residue 376 GLN Chi-restraints excluded: chain J residue 396 ILE Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 137 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 155 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 172 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 GLN C 98 ASN I 98 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.132917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.099017 restraints weight = 24295.745| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.43 r_work: 0.3128 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17820 Z= 0.178 Angle : 0.492 10.515 24072 Z= 0.255 Chirality : 0.038 0.121 2688 Planarity : 0.003 0.058 3028 Dihedral : 3.374 13.636 2396 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.58 % Allowed : 14.47 % Favored : 83.95 % 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: 2.20 (0.18), residues: 2140 helix: 2.03 (0.13), residues: 1632 sheet: None (None), residues: 0 loop : -0.40 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 379 HIS 0.004 0.001 HIS A 363 PHE 0.016 0.001 PHE A 332 TYR 0.013 0.001 TYR J 545 ARG 0.014 0.000 ARG E 127 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4090.04 seconds wall clock time: 73 minutes 21.95 seconds (4401.95 seconds total)