Starting phenix.real_space_refine on Tue Mar 19 09:50:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd1_6634/03_2024/3jd1_6634_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd1_6634/03_2024/3jd1_6634.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd1_6634/03_2024/3jd1_6634.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd1_6634/03_2024/3jd1_6634.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd1_6634/03_2024/3jd1_6634_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd1_6634/03_2024/3jd1_6634_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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 P 24 5.49 5 S 114 5.16 5 C 14976 2.51 5 N 4158 2.21 5 O 4542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23814 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3881 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "B" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3881 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "C" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3881 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "D" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3881 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "E" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3881 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "F" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3881 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'NAI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'NAI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'NAI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'NAI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'NAI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'NAI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 12.45, per 1000 atoms: 0.52 Number of scatterers: 23814 At special positions: 0 Unit cell: (115.596, 129.116, 166.972, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 114 16.00 P 24 15.00 O 4542 8.00 N 4158 7.00 C 14976 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.57 Conformation dependent library (CDL) restraints added in 4.2 seconds 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5400 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 138 helices and 24 sheets defined 50.6% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.14 Creating SS restraints... Processing helix chain 'A' and resid 9 through 31 removed outlier: 3.765A pdb=" N ILE A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ASP A 26 " --> pdb=" O SER A 22 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS A 27 " --> pdb=" O ILE A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 52 Processing helix chain 'A' and resid 101 through 117 removed outlier: 3.676A pdb=" N ALA A 116 " --> pdb=" O THR A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 135 No H-bonds generated for 'chain 'A' and resid 133 through 135' Processing helix chain 'A' and resid 141 through 155 removed outlier: 3.855A pdb=" N ARG A 147 " --> pdb=" O LYS A 143 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 183 removed outlier: 3.757A pdb=" N ASP A 181 " --> pdb=" O SER A 177 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR A 182 " --> pdb=" O TRP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 190 No H-bonds generated for 'chain 'A' and resid 188 through 190' Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 213 through 227 Processing helix chain 'A' and resid 230 through 236 removed outlier: 5.046A pdb=" N ILE A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) 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 254 through 266 removed outlier: 4.691A pdb=" N PHE A 266 " --> pdb=" O TYR A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 297 removed outlier: 3.605A pdb=" N ASP A 293 " --> pdb=" O LYS A 289 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 316 No H-bonds generated for 'chain 'A' and resid 314 through 316' Processing helix chain 'A' and resid 333 through 338 Proline residue: A 337 - end of helix No H-bonds generated for 'chain 'A' and resid 333 through 338' Processing helix chain 'A' and resid 354 through 362 Processing helix chain 'A' and resid 376 through 390 removed outlier: 3.664A pdb=" N SER A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 420 removed outlier: 3.557A pdb=" N ASP A 404 " --> pdb=" O LYS A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 424 No H-bonds generated for 'chain 'A' and resid 422 through 424' Processing helix chain 'A' and resid 434 through 438 removed outlier: 3.529A pdb=" N ASP A 438 " --> pdb=" O ALA A 434 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 434 through 438' Processing helix chain 'A' and resid 445 through 471 removed outlier: 3.519A pdb=" N HIS A 450 " --> pdb=" O LYS A 446 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A 454 " --> pdb=" O HIS A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 495 removed outlier: 3.896A pdb=" N ASN A 484 " --> pdb=" O ALA A 480 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG A 491 " --> pdb=" O GLU A 487 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 492 " --> pdb=" O LYS A 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 31 removed outlier: 3.766A pdb=" N ILE B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ASP B 26 " --> pdb=" O SER B 22 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS B 27 " --> pdb=" O ILE B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 52 Processing helix chain 'B' and resid 101 through 117 removed outlier: 3.676A pdb=" N ALA B 116 " --> pdb=" O THR B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 135 No H-bonds generated for 'chain 'B' and resid 133 through 135' Processing helix chain 'B' and resid 141 through 155 removed outlier: 3.854A pdb=" N ARG B 147 " --> pdb=" O LYS B 143 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET B 150 " --> pdb=" O ARG B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 183 removed outlier: 3.757A pdb=" N ASP B 181 " --> pdb=" O SER B 177 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR B 182 " --> pdb=" O TRP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 190 No H-bonds generated for 'chain 'B' and resid 188 through 190' Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 213 through 227 Processing helix chain 'B' and resid 230 through 236 removed outlier: 5.047A pdb=" N ILE B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 244 No H-bonds generated for 'chain 'B' and resid 242 through 244' Processing helix chain 'B' and resid 254 through 266 removed outlier: 4.691A pdb=" N PHE B 266 " --> pdb=" O TYR B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 297 removed outlier: 3.605A pdb=" N ASP B 293 " --> pdb=" O LYS B 289 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE B 294 " --> pdb=" O GLU B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 316 No H-bonds generated for 'chain 'B' and resid 314 through 316' Processing helix chain 'B' and resid 333 through 338 Proline residue: B 337 - end of helix No H-bonds generated for 'chain 'B' and resid 333 through 338' Processing helix chain 'B' and resid 354 through 362 Processing helix chain 'B' and resid 376 through 390 removed outlier: 3.664A pdb=" N SER B 381 " --> pdb=" O GLY B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 420 removed outlier: 3.557A pdb=" N ASP B 404 " --> pdb=" O LYS B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 424 No H-bonds generated for 'chain 'B' and resid 422 through 424' Processing helix chain 'B' and resid 434 through 438 removed outlier: 3.529A pdb=" N ASP B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 434 through 438' Processing helix chain 'B' and resid 445 through 471 removed outlier: 3.518A pdb=" N HIS B 450 " --> pdb=" O LYS B 446 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA B 454 " --> pdb=" O HIS B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 495 removed outlier: 3.895A pdb=" N ASN B 484 " --> pdb=" O ALA B 480 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG B 491 " --> pdb=" O GLU B 487 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B 492 " --> pdb=" O LYS B 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 31 removed outlier: 3.765A pdb=" N ILE C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ASP C 26 " --> pdb=" O SER C 22 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS C 27 " --> pdb=" O ILE C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 52 Processing helix chain 'C' and resid 101 through 117 removed outlier: 3.676A pdb=" N ALA C 116 " --> pdb=" O THR C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 135 No H-bonds generated for 'chain 'C' and resid 133 through 135' Processing helix chain 'C' and resid 141 through 155 removed outlier: 3.855A pdb=" N ARG C 147 " --> pdb=" O LYS C 143 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET C 150 " --> pdb=" O ARG C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 183 removed outlier: 3.756A pdb=" N ASP C 181 " --> pdb=" O SER C 177 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR C 182 " --> pdb=" O TRP C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 190 No H-bonds generated for 'chain 'C' and resid 188 through 190' Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 213 through 227 Processing helix chain 'C' and resid 230 through 236 removed outlier: 5.047A pdb=" N ILE C 235 " --> pdb=" O SER C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 244 No H-bonds generated for 'chain 'C' and resid 242 through 244' Processing helix chain 'C' and resid 254 through 266 removed outlier: 4.691A pdb=" N PHE C 266 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 297 removed outlier: 3.605A pdb=" N ASP C 293 " --> pdb=" O LYS C 289 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 316 No H-bonds generated for 'chain 'C' and resid 314 through 316' Processing helix chain 'C' and resid 333 through 338 Proline residue: C 337 - end of helix No H-bonds generated for 'chain 'C' and resid 333 through 338' Processing helix chain 'C' and resid 354 through 362 Processing helix chain 'C' and resid 376 through 390 removed outlier: 3.664A pdb=" N SER C 381 " --> pdb=" O GLY C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 420 removed outlier: 3.557A pdb=" N ASP C 404 " --> pdb=" O LYS C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 424 No H-bonds generated for 'chain 'C' and resid 422 through 424' Processing helix chain 'C' and resid 434 through 438 removed outlier: 3.530A pdb=" N ASP C 438 " --> pdb=" O ALA C 434 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 434 through 438' Processing helix chain 'C' and resid 445 through 471 removed outlier: 3.518A pdb=" N HIS C 450 " --> pdb=" O LYS C 446 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA C 454 " --> pdb=" O HIS C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 495 removed outlier: 3.895A pdb=" N ASN C 484 " --> pdb=" O ALA C 480 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL C 492 " --> pdb=" O LYS C 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 31 removed outlier: 3.765A pdb=" N ILE D 23 " --> pdb=" O ARG D 19 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ASP D 26 " --> pdb=" O SER D 22 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS D 27 " --> pdb=" O ILE D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 52 Processing helix chain 'D' and resid 101 through 117 removed outlier: 3.676A pdb=" N ALA D 116 " --> pdb=" O THR D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 135 No H-bonds generated for 'chain 'D' and resid 133 through 135' Processing helix chain 'D' and resid 141 through 155 removed outlier: 3.855A pdb=" N ARG D 147 " --> pdb=" O LYS D 143 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET D 150 " --> pdb=" O ARG D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 183 removed outlier: 3.757A pdb=" N ASP D 181 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR D 182 " --> pdb=" O TRP D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 190 No H-bonds generated for 'chain 'D' and resid 188 through 190' Processing helix chain 'D' and resid 194 through 197 Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 213 through 227 Processing helix chain 'D' and resid 230 through 236 removed outlier: 5.046A pdb=" N ILE D 235 " --> pdb=" O SER D 231 " (cutoff:3.500A) 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 254 through 266 removed outlier: 4.691A pdb=" N PHE D 266 " --> pdb=" O TYR D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 297 removed outlier: 3.605A pdb=" N ASP D 293 " --> pdb=" O LYS D 289 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE D 294 " --> pdb=" O GLU D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 316 No H-bonds generated for 'chain 'D' and resid 314 through 316' Processing helix chain 'D' and resid 333 through 338 Proline residue: D 337 - end of helix No H-bonds generated for 'chain 'D' and resid 333 through 338' Processing helix chain 'D' and resid 354 through 362 Processing helix chain 'D' and resid 376 through 390 removed outlier: 3.664A pdb=" N SER D 381 " --> pdb=" O GLY D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 420 removed outlier: 3.557A pdb=" N ASP D 404 " --> pdb=" O LYS D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 424 No H-bonds generated for 'chain 'D' and resid 422 through 424' Processing helix chain 'D' and resid 434 through 438 removed outlier: 3.529A pdb=" N ASP D 438 " --> pdb=" O ALA D 434 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 434 through 438' Processing helix chain 'D' and resid 445 through 471 removed outlier: 3.519A pdb=" N HIS D 450 " --> pdb=" O LYS D 446 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA D 454 " --> pdb=" O HIS D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 495 removed outlier: 3.896A pdb=" N ASN D 484 " --> pdb=" O ALA D 480 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG D 491 " --> pdb=" O GLU D 487 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL D 492 " --> pdb=" O LYS D 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 31 removed outlier: 3.766A pdb=" N ILE E 23 " --> pdb=" O ARG E 19 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ASP E 26 " --> pdb=" O SER E 22 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS E 27 " --> pdb=" O ILE E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 52 Processing helix chain 'E' and resid 101 through 117 removed outlier: 3.676A pdb=" N ALA E 116 " --> pdb=" O THR E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 135 No H-bonds generated for 'chain 'E' and resid 133 through 135' Processing helix chain 'E' and resid 141 through 155 removed outlier: 3.854A pdb=" N ARG E 147 " --> pdb=" O LYS E 143 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET E 150 " --> pdb=" O ARG E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 183 removed outlier: 3.757A pdb=" N ASP E 181 " --> pdb=" O SER E 177 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR E 182 " --> pdb=" O TRP E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 190 No H-bonds generated for 'chain 'E' and resid 188 through 190' Processing helix chain 'E' and resid 194 through 197 Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 213 through 227 Processing helix chain 'E' and resid 230 through 236 removed outlier: 5.047A pdb=" N ILE E 235 " --> pdb=" O SER E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 244 No H-bonds generated for 'chain 'E' and resid 242 through 244' Processing helix chain 'E' and resid 254 through 266 removed outlier: 4.691A pdb=" N PHE E 266 " --> pdb=" O TYR E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 297 removed outlier: 3.605A pdb=" N ASP E 293 " --> pdb=" O LYS E 289 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE E 294 " --> pdb=" O GLU E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 316 No H-bonds generated for 'chain 'E' and resid 314 through 316' Processing helix chain 'E' and resid 333 through 338 Proline residue: E 337 - end of helix No H-bonds generated for 'chain 'E' and resid 333 through 338' Processing helix chain 'E' and resid 354 through 362 Processing helix chain 'E' and resid 376 through 390 removed outlier: 3.664A pdb=" N SER E 381 " --> pdb=" O GLY E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 420 removed outlier: 3.557A pdb=" N ASP E 404 " --> pdb=" O LYS E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 424 No H-bonds generated for 'chain 'E' and resid 422 through 424' Processing helix chain 'E' and resid 434 through 438 removed outlier: 3.529A pdb=" N ASP E 438 " --> pdb=" O ALA E 434 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 434 through 438' Processing helix chain 'E' and resid 445 through 471 removed outlier: 3.518A pdb=" N HIS E 450 " --> pdb=" O LYS E 446 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA E 454 " --> pdb=" O HIS E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 477 through 495 removed outlier: 3.895A pdb=" N ASN E 484 " --> pdb=" O ALA E 480 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG E 491 " --> pdb=" O GLU E 487 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL E 492 " --> pdb=" O LYS E 488 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 31 removed outlier: 3.765A pdb=" N ILE F 23 " --> pdb=" O ARG F 19 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ASP F 26 " --> pdb=" O SER F 22 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS F 27 " --> pdb=" O ILE F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 52 Processing helix chain 'F' and resid 101 through 117 removed outlier: 3.676A pdb=" N ALA F 116 " --> pdb=" O THR F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 135 No H-bonds generated for 'chain 'F' and resid 133 through 135' Processing helix chain 'F' and resid 141 through 155 removed outlier: 3.855A pdb=" N ARG F 147 " --> pdb=" O LYS F 143 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET F 150 " --> pdb=" O ARG F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 183 removed outlier: 3.756A pdb=" N ASP F 181 " --> pdb=" O SER F 177 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR F 182 " --> pdb=" O TRP F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 190 No H-bonds generated for 'chain 'F' and resid 188 through 190' Processing helix chain 'F' and resid 194 through 197 Processing helix chain 'F' and resid 203 through 205 No H-bonds generated for 'chain 'F' and resid 203 through 205' Processing helix chain 'F' and resid 213 through 227 Processing helix chain 'F' and resid 230 through 236 removed outlier: 5.047A pdb=" N ILE F 235 " --> pdb=" O SER F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 244 No H-bonds generated for 'chain 'F' and resid 242 through 244' Processing helix chain 'F' and resid 254 through 266 removed outlier: 4.691A pdb=" N PHE F 266 " --> pdb=" O TYR F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 297 removed outlier: 3.605A pdb=" N ASP F 293 " --> pdb=" O LYS F 289 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE F 294 " --> pdb=" O GLU F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 316 No H-bonds generated for 'chain 'F' and resid 314 through 316' Processing helix chain 'F' and resid 333 through 338 Proline residue: F 337 - end of helix No H-bonds generated for 'chain 'F' and resid 333 through 338' Processing helix chain 'F' and resid 354 through 362 Processing helix chain 'F' and resid 376 through 390 removed outlier: 3.664A pdb=" N SER F 381 " --> pdb=" O GLY F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 420 removed outlier: 3.557A pdb=" N ASP F 404 " --> pdb=" O LYS F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 424 No H-bonds generated for 'chain 'F' and resid 422 through 424' Processing helix chain 'F' and resid 434 through 438 removed outlier: 3.530A pdb=" N ASP F 438 " --> pdb=" O ALA F 434 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 434 through 438' Processing helix chain 'F' and resid 445 through 471 removed outlier: 3.518A pdb=" N HIS F 450 " --> pdb=" O LYS F 446 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA F 454 " --> pdb=" O HIS F 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 477 through 495 removed outlier: 3.895A pdb=" N ASN F 484 " --> pdb=" O ALA F 480 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG F 491 " --> pdb=" O GLU F 487 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL F 492 " --> pdb=" O LYS F 488 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 57 through 66 Processing sheet with id= B, first strand: chain 'A' and resid 89 through 92 removed outlier: 3.679A pdb=" N GLY A 91 " --> pdb=" O VAL A 164 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 321 through 324 removed outlier: 6.319A pdb=" N LYS A 269 " --> pdb=" O PHE A 247 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N VAL A 249 " --> pdb=" O LYS A 269 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N ILE A 271 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY A 278 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER A 279 " --> pdb=" O TYR A 310 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 343 through 345 removed outlier: 6.459A pdb=" N MET A 366 " --> pdb=" O ILE A 344 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 57 through 66 Processing sheet with id= F, first strand: chain 'B' and resid 89 through 92 removed outlier: 3.678A pdb=" N GLY B 91 " --> pdb=" O VAL B 164 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 321 through 324 removed outlier: 6.319A pdb=" N LYS B 269 " --> pdb=" O PHE B 247 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N VAL B 249 " --> pdb=" O LYS B 269 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N ILE B 271 " --> pdb=" O VAL B 249 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY B 278 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER B 279 " --> pdb=" O TYR B 310 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 343 through 345 removed outlier: 6.459A pdb=" N MET B 366 " --> pdb=" O ILE B 344 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'C' and resid 57 through 66 Processing sheet with id= J, first strand: chain 'C' and resid 89 through 92 removed outlier: 3.679A pdb=" N GLY C 91 " --> pdb=" O VAL C 164 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 321 through 324 removed outlier: 6.319A pdb=" N LYS C 269 " --> pdb=" O PHE C 247 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N VAL C 249 " --> pdb=" O LYS C 269 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N ILE C 271 " --> pdb=" O VAL C 249 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY C 278 " --> pdb=" O GLU C 275 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER C 279 " --> pdb=" O TYR C 310 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 343 through 345 removed outlier: 6.459A pdb=" N MET C 366 " --> pdb=" O ILE C 344 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'D' and resid 57 through 66 Processing sheet with id= N, first strand: chain 'D' and resid 89 through 92 removed outlier: 3.679A pdb=" N GLY D 91 " --> pdb=" O VAL D 164 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 321 through 324 removed outlier: 6.319A pdb=" N LYS D 269 " --> pdb=" O PHE D 247 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N VAL D 249 " --> pdb=" O LYS D 269 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N ILE D 271 " --> pdb=" O VAL D 249 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY D 278 " --> pdb=" O GLU D 275 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER D 279 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 343 through 345 removed outlier: 6.459A pdb=" N MET D 366 " --> pdb=" O ILE D 344 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'E' and resid 57 through 66 Processing sheet with id= R, first strand: chain 'E' and resid 89 through 92 removed outlier: 3.678A pdb=" N GLY E 91 " --> pdb=" O VAL E 164 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 321 through 324 removed outlier: 6.319A pdb=" N LYS E 269 " --> pdb=" O PHE E 247 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N VAL E 249 " --> pdb=" O LYS E 269 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N ILE E 271 " --> pdb=" O VAL E 249 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY E 278 " --> pdb=" O GLU E 275 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER E 279 " --> pdb=" O TYR E 310 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 343 through 345 removed outlier: 6.459A pdb=" N MET E 366 " --> pdb=" O ILE E 344 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'F' and resid 57 through 66 Processing sheet with id= V, first strand: chain 'F' and resid 89 through 92 removed outlier: 3.679A pdb=" N GLY F 91 " --> pdb=" O VAL F 164 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 321 through 324 removed outlier: 6.319A pdb=" N LYS F 269 " --> pdb=" O PHE F 247 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N VAL F 249 " --> pdb=" O LYS F 269 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N ILE F 271 " --> pdb=" O VAL F 249 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY F 278 " --> pdb=" O GLU F 275 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER F 279 " --> pdb=" O TYR F 310 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 343 through 345 removed outlier: 6.459A pdb=" N MET F 366 " --> pdb=" O ILE F 344 " (cutoff:3.500A) No H-bonds generated for sheet with id= X 1020 hydrogen bonds defined for protein. 2988 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.76 Time building geometry restraints manager: 10.30 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: 7792 1.34 - 1.45: 4474 1.45 - 1.57: 11854 1.57 - 1.69: 48 1.69 - 1.81: 192 Bond restraints: 24360 Sorted by residual: bond pdb=" C4A NAI F 602 " pdb=" C5A NAI F 602 " ideal model delta sigma weight residual 1.386 1.471 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" C4A NAI C 602 " pdb=" C5A NAI C 602 " ideal model delta sigma weight residual 1.386 1.471 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" C4A NAI D 601 " pdb=" C5A NAI D 601 " ideal model delta sigma weight residual 1.386 1.471 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" C4A NAI A 601 " pdb=" C5A NAI A 601 " ideal model delta sigma weight residual 1.386 1.471 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" C4A NAI E 602 " pdb=" C5A NAI E 602 " ideal model delta sigma weight residual 1.386 1.470 -0.084 2.00e-02 2.50e+03 1.78e+01 ... (remaining 24355 not shown) Histogram of bond angle deviations from ideal: 96.53 - 105.11: 486 105.11 - 113.68: 13946 113.68 - 122.25: 14764 122.25 - 130.83: 3672 130.83 - 139.40: 126 Bond angle restraints: 32994 Sorted by residual: angle pdb=" CA PRO A 7 " pdb=" N PRO A 7 " pdb=" CD PRO A 7 " ideal model delta sigma weight residual 112.00 106.02 5.98 1.40e+00 5.10e-01 1.82e+01 angle pdb=" CA PRO D 7 " pdb=" N PRO D 7 " pdb=" CD PRO D 7 " ideal model delta sigma weight residual 112.00 106.02 5.98 1.40e+00 5.10e-01 1.82e+01 angle pdb=" CA PRO E 7 " pdb=" N PRO E 7 " pdb=" CD PRO E 7 " ideal model delta sigma weight residual 112.00 106.07 5.93 1.40e+00 5.10e-01 1.80e+01 angle pdb=" CA PRO B 7 " pdb=" N PRO B 7 " pdb=" CD PRO B 7 " ideal model delta sigma weight residual 112.00 106.07 5.93 1.40e+00 5.10e-01 1.80e+01 angle pdb=" CA PRO C 7 " pdb=" N PRO C 7 " pdb=" CD PRO C 7 " ideal model delta sigma weight residual 112.00 106.08 5.92 1.40e+00 5.10e-01 1.79e+01 ... (remaining 32989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 14196 16.94 - 33.88: 462 33.88 - 50.83: 294 50.83 - 67.77: 18 67.77 - 84.71: 12 Dihedral angle restraints: 14982 sinusoidal: 6504 harmonic: 8478 Sorted by residual: dihedral pdb=" CA GLY C 497 " pdb=" C GLY C 497 " pdb=" N VAL C 498 " pdb=" CA VAL C 498 " ideal model delta harmonic sigma weight residual -180.00 -147.53 -32.47 0 5.00e+00 4.00e-02 4.22e+01 dihedral pdb=" CA GLY B 497 " pdb=" C GLY B 497 " pdb=" N VAL B 498 " pdb=" CA VAL B 498 " ideal model delta harmonic sigma weight residual -180.00 -147.57 -32.43 0 5.00e+00 4.00e-02 4.21e+01 dihedral pdb=" CA GLY A 497 " pdb=" C GLY A 497 " pdb=" N VAL A 498 " pdb=" CA VAL A 498 " ideal model delta harmonic sigma weight residual -180.00 -147.57 -32.43 0 5.00e+00 4.00e-02 4.21e+01 ... (remaining 14979 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2078 0.042 - 0.083: 978 0.083 - 0.125: 388 0.125 - 0.166: 100 0.166 - 0.208: 44 Chirality restraints: 3588 Sorted by residual: chirality pdb=" C1B NAI A 602 " pdb=" C2B NAI A 602 " pdb=" N9A NAI A 602 " pdb=" O4B NAI A 602 " both_signs ideal model delta sigma weight residual False 2.31 2.52 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" C1B NAI D 602 " pdb=" C2B NAI D 602 " pdb=" N9A NAI D 602 " pdb=" O4B NAI D 602 " both_signs ideal model delta sigma weight residual False 2.31 2.52 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" C1B NAI F 602 " pdb=" C2B NAI F 602 " pdb=" N9A NAI F 602 " pdb=" O4B NAI F 602 " both_signs ideal model delta sigma weight residual False 2.31 2.52 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 3585 not shown) Planarity restraints: 4224 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 166 " -0.048 5.00e-02 4.00e+02 7.23e-02 8.37e+00 pdb=" N PRO D 167 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO D 167 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 167 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 166 " -0.048 5.00e-02 4.00e+02 7.23e-02 8.37e+00 pdb=" N PRO A 167 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 167 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 167 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 166 " -0.048 5.00e-02 4.00e+02 7.21e-02 8.31e+00 pdb=" N PRO B 167 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO B 167 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 167 " -0.040 5.00e-02 4.00e+02 ... (remaining 4221 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 300 2.53 - 3.12: 20848 3.12 - 3.71: 35773 3.71 - 4.31: 54533 4.31 - 4.90: 88917 Nonbonded interactions: 200371 Sorted by model distance: nonbonded pdb=" OG1 THR D 272 " pdb=" O ILE D 280 " model vdw 1.935 2.440 nonbonded pdb=" OG1 THR A 272 " pdb=" O ILE A 280 " model vdw 1.935 2.440 nonbonded pdb=" OG1 THR F 272 " pdb=" O ILE F 280 " model vdw 1.935 2.440 nonbonded pdb=" OG1 THR C 272 " pdb=" O ILE C 280 " model vdw 1.935 2.440 nonbonded pdb=" OG1 THR E 272 " pdb=" O ILE E 280 " model vdw 1.935 2.440 ... (remaining 200366 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 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: 0.020 Extract box with map and model: 5.170 Check model and map are aligned: 0.350 Set scattering table: 0.210 Process input model: 63.450 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.150 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 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 : 0.015 0.124 24360 Z= 0.965 Angle : 1.013 14.400 32994 Z= 0.544 Chirality : 0.058 0.208 3588 Planarity : 0.006 0.072 4224 Dihedral : 11.303 84.712 9582 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.16 % Favored : 91.63 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -5.08 (0.12), residues: 2964 helix: -3.93 (0.08), residues: 1410 sheet: -2.39 (0.22), residues: 426 loop : -2.66 (0.16), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.004 TRP E 385 HIS 0.014 0.002 HIS D 450 PHE 0.025 0.003 PHE C 16 TYR 0.026 0.003 TYR B 372 ARG 0.005 0.001 ARG B 86 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 604 time to evaluate : 2.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7906 (tt0) cc_final: 0.7646 (tt0) REVERT: A 402 GLU cc_start: 0.7885 (tp30) cc_final: 0.7383 (tp30) REVERT: A 469 MET cc_start: 0.7160 (mmp) cc_final: 0.6814 (mmt) REVERT: B 25 GLU cc_start: 0.7987 (tt0) cc_final: 0.7660 (tt0) REVERT: B 228 ASN cc_start: 0.6833 (p0) cc_final: 0.6355 (t0) REVERT: B 402 GLU cc_start: 0.7882 (tp30) cc_final: 0.7393 (tp30) REVERT: B 469 MET cc_start: 0.7154 (mmp) cc_final: 0.6827 (mmt) REVERT: C 25 GLU cc_start: 0.7932 (tt0) cc_final: 0.7687 (tt0) REVERT: C 402 GLU cc_start: 0.7844 (tp30) cc_final: 0.7386 (tp30) REVERT: C 469 MET cc_start: 0.7211 (mmp) cc_final: 0.6858 (mmt) REVERT: D 25 GLU cc_start: 0.7906 (tt0) cc_final: 0.7652 (tt0) REVERT: D 402 GLU cc_start: 0.7885 (tp30) cc_final: 0.7384 (tp30) REVERT: D 469 MET cc_start: 0.7158 (mmp) cc_final: 0.6811 (mmt) REVERT: E 25 GLU cc_start: 0.7987 (tt0) cc_final: 0.7590 (tt0) REVERT: E 228 ASN cc_start: 0.6832 (p0) cc_final: 0.6352 (t0) REVERT: E 402 GLU cc_start: 0.7880 (tp30) cc_final: 0.7393 (tp30) REVERT: E 469 MET cc_start: 0.7147 (mmp) cc_final: 0.6820 (mmt) REVERT: F 25 GLU cc_start: 0.7935 (tt0) cc_final: 0.7688 (tt0) REVERT: F 402 GLU cc_start: 0.7838 (tp30) cc_final: 0.7380 (tp30) REVERT: F 469 MET cc_start: 0.7210 (mmp) cc_final: 0.6855 (mmt) outliers start: 0 outliers final: 0 residues processed: 604 average time/residue: 0.4792 time to fit residues: 405.3116 Evaluate side-chains 243 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 2.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 5.9990 chunk 222 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 76 optimal weight: 40.0000 chunk 150 optimal weight: 8.9990 chunk 119 optimal weight: 5.9990 chunk 230 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 140 optimal weight: 8.9990 chunk 171 optimal weight: 8.9990 chunk 266 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 209 HIS A 450 HIS A 494 ASN B 40 GLN B 209 HIS ** B 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 494 ASN C 40 GLN ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 ASN D 40 GLN D 209 HIS D 450 HIS D 494 ASN E 40 GLN E 209 HIS E 258 HIS ** E 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 494 ASN F 40 GLN ** F 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 ASN ** F 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 494 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 24360 Z= 0.317 Angle : 0.671 6.743 32994 Z= 0.354 Chirality : 0.046 0.160 3588 Planarity : 0.006 0.082 4224 Dihedral : 10.040 85.959 3990 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.32 % Allowed : 5.69 % Favored : 91.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.47 (0.14), residues: 2964 helix: -1.31 (0.12), residues: 1446 sheet: -1.76 (0.24), residues: 348 loop : -1.83 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 281 HIS 0.011 0.002 HIS D 221 PHE 0.022 0.003 PHE A 9 TYR 0.016 0.002 TYR A 382 ARG 0.013 0.001 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 292 time to evaluate : 2.712 Fit side-chains REVERT: A 292 GLU cc_start: 0.7119 (pp20) cc_final: 0.6793 (pp20) REVERT: A 402 GLU cc_start: 0.7787 (tp30) cc_final: 0.7392 (tp30) REVERT: B 402 GLU cc_start: 0.7755 (tp30) cc_final: 0.7337 (tp30) REVERT: C 111 MET cc_start: 0.8548 (tpp) cc_final: 0.8339 (tpp) REVERT: C 402 GLU cc_start: 0.7815 (tp30) cc_final: 0.7315 (tp30) REVERT: D 292 GLU cc_start: 0.7120 (pp20) cc_final: 0.6801 (pp20) REVERT: D 402 GLU cc_start: 0.7796 (tp30) cc_final: 0.7396 (tp30) REVERT: E 402 GLU cc_start: 0.7756 (tp30) cc_final: 0.7337 (tp30) REVERT: F 111 MET cc_start: 0.8549 (tpp) cc_final: 0.8339 (tpp) REVERT: F 402 GLU cc_start: 0.7815 (tp30) cc_final: 0.7317 (tp30) outliers start: 58 outliers final: 34 residues processed: 334 average time/residue: 0.4134 time to fit residues: 202.2908 Evaluate side-chains 214 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 180 time to evaluate : 2.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 338 ARG Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 139 ASN Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 332 THR Chi-restraints excluded: chain E residue 338 ARG Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 238 MET Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 338 ARG Chi-restraints excluded: chain F residue 417 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 148 optimal weight: 9.9990 chunk 82 optimal weight: 8.9990 chunk 222 optimal weight: 10.0000 chunk 181 optimal weight: 20.0000 chunk 73 optimal weight: 0.2980 chunk 267 optimal weight: 10.0000 chunk 288 optimal weight: 20.0000 chunk 238 optimal weight: 0.9980 chunk 265 optimal weight: 20.0000 chunk 91 optimal weight: 0.5980 chunk 214 optimal weight: 6.9990 overall best weight: 3.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN A 205 GLN B 205 GLN B 388 ASN ** B 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 GLN ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 GLN D 205 GLN E 205 GLN E 388 ASN ** E 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 GLN ** F 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 24360 Z= 0.221 Angle : 0.563 7.873 32994 Z= 0.294 Chirality : 0.043 0.131 3588 Planarity : 0.004 0.039 4224 Dihedral : 9.297 77.200 3990 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.28 % Allowed : 7.33 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 (0.15), residues: 2964 helix: 0.27 (0.13), residues: 1446 sheet: -1.27 (0.25), residues: 348 loop : -1.27 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 281 HIS 0.004 0.001 HIS D 408 PHE 0.018 0.002 PHE B 9 TYR 0.012 0.001 TYR C 78 ARG 0.005 0.001 ARG C 217 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 229 time to evaluate : 2.583 Fit side-chains REVERT: A 402 GLU cc_start: 0.7788 (tp30) cc_final: 0.7353 (tp30) REVERT: B 238 MET cc_start: 0.6224 (mtm) cc_final: 0.5954 (tpt) REVERT: B 402 GLU cc_start: 0.7806 (tp30) cc_final: 0.7399 (tp30) REVERT: C 296 LEU cc_start: 0.7609 (mt) cc_final: 0.7258 (pp) REVERT: C 402 GLU cc_start: 0.7807 (tp30) cc_final: 0.7420 (tp30) REVERT: D 238 MET cc_start: 0.6254 (mtm) cc_final: 0.5791 (tpt) REVERT: D 402 GLU cc_start: 0.7786 (tp30) cc_final: 0.7345 (tp30) REVERT: E 402 GLU cc_start: 0.7811 (tp30) cc_final: 0.7400 (tp30) REVERT: F 296 LEU cc_start: 0.7599 (mt) cc_final: 0.7253 (pp) REVERT: F 402 GLU cc_start: 0.7805 (tp30) cc_final: 0.7420 (tp30) outliers start: 57 outliers final: 32 residues processed: 267 average time/residue: 0.3306 time to fit residues: 141.4149 Evaluate side-chains 215 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 183 time to evaluate : 2.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 338 ARG Chi-restraints excluded: chain B residue 372 TYR Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 338 ARG Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 332 THR Chi-restraints excluded: chain E residue 338 ARG Chi-restraints excluded: chain E residue 372 TYR Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 338 ARG Chi-restraints excluded: chain F residue 417 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 264 optimal weight: 0.3980 chunk 201 optimal weight: 7.9990 chunk 138 optimal weight: 2.9990 chunk 29 optimal weight: 0.0000 chunk 127 optimal weight: 40.0000 chunk 179 optimal weight: 40.0000 chunk 268 optimal weight: 6.9990 chunk 284 optimal weight: 6.9990 chunk 140 optimal weight: 1.9990 chunk 254 optimal weight: 9.9990 chunk 76 optimal weight: 20.0000 overall best weight: 2.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 ASN ** E 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.5062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 24360 Z= 0.170 Angle : 0.506 6.254 32994 Z= 0.264 Chirality : 0.042 0.136 3588 Planarity : 0.004 0.031 4224 Dihedral : 9.092 77.702 3990 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.12 % Allowed : 9.25 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.02 (0.16), residues: 2964 helix: 1.09 (0.14), residues: 1440 sheet: -0.81 (0.25), residues: 420 loop : -1.00 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 385 HIS 0.006 0.001 HIS E 298 PHE 0.015 0.002 PHE D 9 TYR 0.010 0.001 TYR E 401 ARG 0.004 0.000 ARG C 217 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 221 time to evaluate : 2.779 Fit side-chains REVERT: A 402 GLU cc_start: 0.7771 (tp30) cc_final: 0.7376 (tp30) REVERT: B 402 GLU cc_start: 0.7794 (tp30) cc_final: 0.7359 (tp30) REVERT: C 238 MET cc_start: 0.6673 (OUTLIER) cc_final: 0.6239 (mmt) REVERT: C 296 LEU cc_start: 0.7643 (mt) cc_final: 0.7350 (pp) REVERT: C 401 TYR cc_start: 0.8020 (t80) cc_final: 0.7702 (t80) REVERT: C 402 GLU cc_start: 0.7780 (tp30) cc_final: 0.7347 (tp30) REVERT: D 238 MET cc_start: 0.6239 (mtm) cc_final: 0.5775 (tpt) REVERT: D 402 GLU cc_start: 0.7766 (tp30) cc_final: 0.7365 (tp30) REVERT: E 402 GLU cc_start: 0.7801 (tp30) cc_final: 0.7364 (tp30) REVERT: F 238 MET cc_start: 0.6675 (OUTLIER) cc_final: 0.6241 (mmt) REVERT: F 401 TYR cc_start: 0.8013 (t80) cc_final: 0.7700 (t80) REVERT: F 402 GLU cc_start: 0.7778 (tp30) cc_final: 0.7349 (tp30) outliers start: 53 outliers final: 40 residues processed: 253 average time/residue: 0.3417 time to fit residues: 138.0681 Evaluate side-chains 223 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 181 time to evaluate : 2.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 372 TYR Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 338 ARG Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 252 PHE Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 332 THR Chi-restraints excluded: chain E residue 338 ARG Chi-restraints excluded: chain E residue 372 TYR Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain F residue 238 MET Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 338 ARG Chi-restraints excluded: chain F residue 417 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 236 optimal weight: 5.9990 chunk 161 optimal weight: 9.9990 chunk 4 optimal weight: 0.2980 chunk 211 optimal weight: 6.9990 chunk 117 optimal weight: 0.0570 chunk 242 optimal weight: 8.9990 chunk 196 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 145 optimal weight: 20.0000 chunk 255 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 overall best weight: 3.8704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 HIS ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 472 ASN ** F 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.5301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 24360 Z= 0.218 Angle : 0.535 6.292 32994 Z= 0.276 Chirality : 0.043 0.137 3588 Planarity : 0.004 0.033 4224 Dihedral : 9.158 76.961 3990 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.16 % Allowed : 9.90 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.21 (0.16), residues: 2964 helix: 1.23 (0.14), residues: 1446 sheet: -0.76 (0.25), residues: 420 loop : -0.89 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 385 HIS 0.004 0.001 HIS A 258 PHE 0.017 0.002 PHE D 9 TYR 0.014 0.001 TYR A 401 ARG 0.004 0.001 ARG C 217 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 180 time to evaluate : 2.756 Fit side-chains REVERT: A 402 GLU cc_start: 0.7846 (tp30) cc_final: 0.7477 (tp30) REVERT: B 103 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7224 (tp30) REVERT: B 238 MET cc_start: 0.6195 (OUTLIER) cc_final: 0.5650 (tpt) REVERT: B 402 GLU cc_start: 0.7850 (tp30) cc_final: 0.7446 (tp30) REVERT: C 238 MET cc_start: 0.6731 (OUTLIER) cc_final: 0.6235 (mmt) REVERT: C 296 LEU cc_start: 0.7687 (mt) cc_final: 0.7412 (pp) REVERT: C 402 GLU cc_start: 0.7807 (tp30) cc_final: 0.7449 (tp30) REVERT: D 238 MET cc_start: 0.6324 (mtm) cc_final: 0.5930 (tpt) REVERT: D 402 GLU cc_start: 0.7841 (tp30) cc_final: 0.7471 (tp30) REVERT: E 103 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7223 (tp30) REVERT: E 402 GLU cc_start: 0.7854 (tp30) cc_final: 0.7451 (tp30) REVERT: F 238 MET cc_start: 0.6732 (OUTLIER) cc_final: 0.6232 (mmt) REVERT: F 296 LEU cc_start: 0.7826 (mp) cc_final: 0.7552 (pp) REVERT: F 402 GLU cc_start: 0.7803 (tp30) cc_final: 0.7446 (tp30) outliers start: 54 outliers final: 39 residues processed: 219 average time/residue: 0.3686 time to fit residues: 128.7875 Evaluate side-chains 209 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 167 time to evaluate : 2.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 293 ASP Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 338 ARG Chi-restraints excluded: chain B residue 372 TYR Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 338 ARG Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 252 PHE Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 332 THR Chi-restraints excluded: chain E residue 372 TYR Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 238 MET Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 338 ARG Chi-restraints excluded: chain F residue 417 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 95 optimal weight: 20.0000 chunk 255 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 166 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 284 optimal weight: 3.9990 chunk 236 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 94 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN B 450 HIS B 472 ASN ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 ASN E 450 HIS ** F 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.5554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 24360 Z= 0.208 Angle : 0.520 6.608 32994 Z= 0.268 Chirality : 0.042 0.132 3588 Planarity : 0.004 0.035 4224 Dihedral : 9.182 78.251 3990 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.24 % Allowed : 10.90 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.37 (0.16), residues: 2964 helix: 1.36 (0.14), residues: 1446 sheet: -0.69 (0.25), residues: 420 loop : -0.80 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 281 HIS 0.004 0.001 HIS F 258 PHE 0.015 0.002 PHE D 9 TYR 0.014 0.001 TYR A 401 ARG 0.004 0.000 ARG C 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 182 time to evaluate : 2.584 Fit side-chains REVERT: A 238 MET cc_start: 0.6096 (mtm) cc_final: 0.5748 (tpt) REVERT: A 297 GLN cc_start: 0.7221 (mp10) cc_final: 0.7005 (tt0) REVERT: B 103 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7193 (tp30) REVERT: B 238 MET cc_start: 0.6262 (mtm) cc_final: 0.5795 (tpt) REVERT: B 402 GLU cc_start: 0.7835 (tp30) cc_final: 0.7452 (tp30) REVERT: C 94 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.7937 (ttm-80) REVERT: C 238 MET cc_start: 0.6772 (OUTLIER) cc_final: 0.6226 (mmt) REVERT: C 296 LEU cc_start: 0.7721 (mt) cc_final: 0.7473 (pp) REVERT: C 402 GLU cc_start: 0.7809 (tp30) cc_final: 0.7444 (tp30) REVERT: D 238 MET cc_start: 0.6208 (mtm) cc_final: 0.5790 (tpt) REVERT: D 297 GLN cc_start: 0.7247 (mp10) cc_final: 0.7035 (tt0) REVERT: E 103 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7192 (tp30) REVERT: E 402 GLU cc_start: 0.7842 (tp30) cc_final: 0.7460 (tp30) REVERT: F 94 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.7939 (ttm-80) REVERT: F 238 MET cc_start: 0.6767 (OUTLIER) cc_final: 0.6225 (mmt) REVERT: F 296 LEU cc_start: 0.7903 (mp) cc_final: 0.7653 (pp) REVERT: F 402 GLU cc_start: 0.7804 (tp30) cc_final: 0.7441 (tp30) outliers start: 56 outliers final: 45 residues processed: 225 average time/residue: 0.3505 time to fit residues: 124.2865 Evaluate side-chains 222 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 173 time to evaluate : 2.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 293 ASP Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 372 TYR Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 94 ARG Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 427 THR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 332 THR Chi-restraints excluded: chain E residue 372 TYR Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 94 ARG Chi-restraints excluded: chain F residue 238 MET Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain F residue 294 PHE Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 338 ARG Chi-restraints excluded: chain F residue 417 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 274 optimal weight: 30.0000 chunk 32 optimal weight: 0.1980 chunk 162 optimal weight: 9.9990 chunk 207 optimal weight: 2.9990 chunk 160 optimal weight: 6.9990 chunk 239 optimal weight: 20.0000 chunk 158 optimal weight: 0.8980 chunk 283 optimal weight: 4.9990 chunk 177 optimal weight: 20.0000 chunk 172 optimal weight: 4.9990 chunk 130 optimal weight: 20.0000 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 ASN ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 ASN E 450 HIS ** F 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.5733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 24360 Z= 0.171 Angle : 0.494 8.130 32994 Z= 0.254 Chirality : 0.042 0.136 3588 Planarity : 0.004 0.032 4224 Dihedral : 9.079 80.852 3990 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.76 % Allowed : 10.66 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.16), residues: 2964 helix: 1.49 (0.14), residues: 1458 sheet: -0.72 (0.24), residues: 450 loop : -0.66 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 281 HIS 0.003 0.001 HIS B 258 PHE 0.014 0.001 PHE F 9 TYR 0.012 0.001 TYR A 401 ARG 0.003 0.000 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 184 time to evaluate : 2.714 Fit side-chains REVERT: A 238 MET cc_start: 0.6143 (mtm) cc_final: 0.5920 (tpt) REVERT: A 435 GLU cc_start: 0.7260 (pm20) cc_final: 0.7017 (pm20) REVERT: B 90 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.7939 (mtpp) REVERT: B 103 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7143 (tp30) REVERT: B 238 MET cc_start: 0.6282 (mtm) cc_final: 0.5809 (tpt) REVERT: B 402 GLU cc_start: 0.7747 (tp30) cc_final: 0.7376 (tp30) REVERT: B 465 MET cc_start: 0.8336 (mtm) cc_final: 0.8126 (mtm) REVERT: C 90 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.7960 (mtpp) REVERT: C 94 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.7940 (ttm-80) REVERT: C 296 LEU cc_start: 0.7868 (mt) cc_final: 0.7547 (pp) REVERT: C 402 GLU cc_start: 0.7779 (tp30) cc_final: 0.7502 (tp30) REVERT: D 238 MET cc_start: 0.6134 (mtm) cc_final: 0.5702 (tpt) REVERT: D 330 GLN cc_start: 0.7418 (mt0) cc_final: 0.6573 (mt0) REVERT: D 435 GLU cc_start: 0.7265 (pm20) cc_final: 0.7022 (pm20) REVERT: E 90 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.7931 (mtpp) REVERT: E 103 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7137 (tp30) REVERT: E 402 GLU cc_start: 0.7756 (tp30) cc_final: 0.7384 (tp30) REVERT: F 90 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.7966 (mtpp) REVERT: F 94 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.7943 (ttm-80) REVERT: F 296 LEU cc_start: 0.7947 (mp) cc_final: 0.7666 (pp) REVERT: F 402 GLU cc_start: 0.7775 (tp30) cc_final: 0.7504 (tp30) outliers start: 69 outliers final: 50 residues processed: 241 average time/residue: 0.3705 time to fit residues: 137.6139 Evaluate side-chains 230 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 174 time to evaluate : 2.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 293 ASP Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 372 TYR Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 94 ARG Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 372 TYR Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 427 THR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 332 THR Chi-restraints excluded: chain E residue 372 TYR Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 90 LYS Chi-restraints excluded: chain F residue 94 ARG Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain F residue 294 PHE Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 372 TYR Chi-restraints excluded: chain F residue 417 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 175 optimal weight: 5.9990 chunk 113 optimal weight: 7.9990 chunk 169 optimal weight: 9.9990 chunk 85 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 chunk 180 optimal weight: 5.9990 chunk 193 optimal weight: 10.0000 chunk 140 optimal weight: 1.9990 chunk 26 optimal weight: 40.0000 chunk 222 optimal weight: 40.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 ASN ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 HIS E 56 ASN E 450 HIS ** F 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 408 HIS ** F 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.5838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 24360 Z= 0.232 Angle : 0.537 7.321 32994 Z= 0.276 Chirality : 0.043 0.145 3588 Planarity : 0.004 0.030 4224 Dihedral : 9.216 82.603 3990 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.60 % Allowed : 11.30 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.16), residues: 2964 helix: 1.45 (0.14), residues: 1458 sheet: -0.92 (0.25), residues: 420 loop : -0.50 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 281 HIS 0.005 0.001 HIS C 258 PHE 0.016 0.002 PHE D 148 TYR 0.013 0.001 TYR A 401 ARG 0.004 0.001 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 176 time to evaluate : 2.698 Fit side-chains REVERT: A 238 MET cc_start: 0.6186 (mtm) cc_final: 0.5893 (tpt) REVERT: A 296 LEU cc_start: 0.7826 (mp) cc_final: 0.7526 (pp) REVERT: B 90 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.7975 (mtpp) REVERT: B 103 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7228 (tp30) REVERT: B 252 PHE cc_start: 0.6642 (OUTLIER) cc_final: 0.6319 (t80) REVERT: B 402 GLU cc_start: 0.7751 (tp30) cc_final: 0.7340 (tp30) REVERT: C 90 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.7981 (mtpp) REVERT: C 94 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.7933 (ttm-80) REVERT: C 238 MET cc_start: 0.6654 (mtp) cc_final: 0.6421 (tpt) REVERT: C 296 LEU cc_start: 0.7912 (mt) cc_final: 0.7594 (pp) REVERT: C 308 LYS cc_start: 0.5033 (pttm) cc_final: 0.4518 (pttm) REVERT: C 402 GLU cc_start: 0.7845 (tp30) cc_final: 0.7485 (tp30) REVERT: D 238 MET cc_start: 0.6195 (mtm) cc_final: 0.5824 (tpt) REVERT: E 90 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.7972 (mtpp) REVERT: E 103 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7223 (tp30) REVERT: E 402 GLU cc_start: 0.7756 (tp30) cc_final: 0.7337 (tp30) REVERT: F 90 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.7997 (mtpp) REVERT: F 94 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.7935 (ttm-80) REVERT: F 238 MET cc_start: 0.6643 (mtp) cc_final: 0.6410 (tpt) REVERT: F 296 LEU cc_start: 0.7954 (mp) cc_final: 0.7687 (pp) REVERT: F 308 LYS cc_start: 0.5035 (pttm) cc_final: 0.4512 (pttm) REVERT: F 402 GLU cc_start: 0.7842 (tp30) cc_final: 0.7486 (tp30) outliers start: 65 outliers final: 48 residues processed: 229 average time/residue: 0.3595 time to fit residues: 128.5539 Evaluate side-chains 230 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 175 time to evaluate : 2.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 293 ASP Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 372 TYR Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 94 ARG Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 63 PHE Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 372 TYR Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 427 THR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 332 THR Chi-restraints excluded: chain E residue 372 TYR Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 90 LYS Chi-restraints excluded: chain F residue 94 ARG Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain F residue 294 PHE Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 372 TYR Chi-restraints excluded: chain F residue 417 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 257 optimal weight: 20.0000 chunk 271 optimal weight: 40.0000 chunk 247 optimal weight: 7.9990 chunk 264 optimal weight: 9.9990 chunk 158 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 238 optimal weight: 30.0000 chunk 249 optimal weight: 0.4980 chunk 263 optimal weight: 1.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 ASN B 135 ASN B 189 HIS C 56 ASN ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 250 GLN E 56 ASN E 135 ASN E 189 HIS E 330 GLN F 56 ASN ** F 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.5976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 24360 Z= 0.131 Angle : 0.484 9.170 32994 Z= 0.247 Chirality : 0.041 0.158 3588 Planarity : 0.003 0.030 4224 Dihedral : 8.933 85.854 3990 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.76 % Allowed : 12.22 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.83 (0.16), residues: 2964 helix: 1.81 (0.14), residues: 1452 sheet: -0.70 (0.25), residues: 450 loop : -0.60 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 281 HIS 0.003 0.001 HIS E 258 PHE 0.014 0.001 PHE F 63 TYR 0.009 0.001 TYR E 401 ARG 0.008 0.000 ARG B 462 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 209 time to evaluate : 2.652 Fit side-chains REVERT: A 238 MET cc_start: 0.6105 (mtm) cc_final: 0.5824 (tpt) REVERT: A 293 ASP cc_start: 0.7042 (OUTLIER) cc_final: 0.6244 (t0) REVERT: A 296 LEU cc_start: 0.7882 (mp) cc_final: 0.7546 (pp) REVERT: B 90 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.7897 (mtpp) REVERT: B 103 GLU cc_start: 0.7381 (mm-30) cc_final: 0.7040 (tp30) REVERT: B 238 MET cc_start: 0.5951 (mtm) cc_final: 0.5716 (tpt) REVERT: B 402 GLU cc_start: 0.7643 (tp30) cc_final: 0.7224 (tp30) REVERT: C 90 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.7922 (mtpp) REVERT: C 94 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.7921 (ttm-80) REVERT: C 228 ASN cc_start: 0.6947 (p0) cc_final: 0.6365 (t0) REVERT: C 238 MET cc_start: 0.6638 (mtp) cc_final: 0.6404 (tpt) REVERT: C 308 LYS cc_start: 0.5091 (pttm) cc_final: 0.4552 (pttm) REVERT: C 402 GLU cc_start: 0.7733 (tp30) cc_final: 0.7445 (tp30) REVERT: D 238 MET cc_start: 0.6043 (mtm) cc_final: 0.5801 (tpt) REVERT: D 308 LYS cc_start: 0.5057 (pttm) cc_final: 0.4618 (pttm) REVERT: E 90 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.7886 (mtpp) REVERT: E 103 GLU cc_start: 0.7372 (mm-30) cc_final: 0.7039 (tp30) REVERT: E 293 ASP cc_start: 0.7340 (OUTLIER) cc_final: 0.6571 (t0) REVERT: E 402 GLU cc_start: 0.7649 (tp30) cc_final: 0.7226 (tp30) REVERT: F 90 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.7937 (mtpp) REVERT: F 94 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.7936 (ttm-80) REVERT: F 238 MET cc_start: 0.6623 (mtp) cc_final: 0.6396 (tpt) REVERT: F 293 ASP cc_start: 0.7453 (OUTLIER) cc_final: 0.6402 (t0) REVERT: F 296 LEU cc_start: 0.7928 (mp) cc_final: 0.7657 (pp) REVERT: F 308 LYS cc_start: 0.5085 (pttm) cc_final: 0.4547 (pttm) REVERT: F 402 GLU cc_start: 0.7729 (tp30) cc_final: 0.7446 (tp30) outliers start: 44 outliers final: 30 residues processed: 243 average time/residue: 0.3822 time to fit residues: 142.5075 Evaluate side-chains 227 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 188 time to evaluate : 2.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 293 ASP Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 372 TYR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 94 ARG Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 372 TYR Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 332 THR Chi-restraints excluded: chain E residue 372 TYR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 90 LYS Chi-restraints excluded: chain F residue 94 ARG Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 372 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 173 optimal weight: 10.0000 chunk 279 optimal weight: 2.9990 chunk 170 optimal weight: 0.0970 chunk 132 optimal weight: 5.9990 chunk 194 optimal weight: 8.9990 chunk 292 optimal weight: 6.9990 chunk 269 optimal weight: 0.5980 chunk 233 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 180 optimal weight: 20.0000 chunk 143 optimal weight: 5.9990 overall best weight: 3.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 330 GLN C 56 ASN ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 56 ASN ** F 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.6014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 24360 Z= 0.187 Angle : 0.521 9.856 32994 Z= 0.265 Chirality : 0.042 0.178 3588 Planarity : 0.004 0.030 4224 Dihedral : 8.925 85.961 3990 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.64 % Allowed : 12.42 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.86 (0.16), residues: 2964 helix: 1.79 (0.14), residues: 1452 sheet: -0.79 (0.26), residues: 420 loop : -0.46 (0.20), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 281 HIS 0.011 0.001 HIS D 408 PHE 0.013 0.002 PHE A 148 TYR 0.011 0.001 TYR E 401 ARG 0.003 0.000 ARG D 86 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 190 time to evaluate : 2.743 Fit side-chains REVERT: A 238 MET cc_start: 0.6098 (mtm) cc_final: 0.5831 (tpt) REVERT: A 296 LEU cc_start: 0.7884 (mp) cc_final: 0.7561 (pp) REVERT: B 90 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.7922 (mtpp) REVERT: B 103 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7185 (tp30) REVERT: B 238 MET cc_start: 0.6028 (mtm) cc_final: 0.5679 (tpt) REVERT: B 402 GLU cc_start: 0.7684 (tp30) cc_final: 0.7263 (tp30) REVERT: C 90 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.7966 (mtpp) REVERT: C 94 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.7940 (ttm-80) REVERT: C 228 ASN cc_start: 0.6952 (p0) cc_final: 0.6382 (t0) REVERT: C 238 MET cc_start: 0.6667 (mtp) cc_final: 0.6437 (tpt) REVERT: C 308 LYS cc_start: 0.5080 (pttm) cc_final: 0.4546 (pttm) REVERT: C 338 ARG cc_start: 0.6983 (mtp180) cc_final: 0.6558 (ptp-170) REVERT: C 402 GLU cc_start: 0.7779 (tp30) cc_final: 0.7493 (tp30) REVERT: D 238 MET cc_start: 0.6051 (mtm) cc_final: 0.5781 (tpt) REVERT: D 296 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7617 (pp) REVERT: D 308 LYS cc_start: 0.5084 (pttm) cc_final: 0.4672 (pttm) REVERT: E 90 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.7915 (mtpp) REVERT: E 103 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7142 (tp30) REVERT: E 402 GLU cc_start: 0.7684 (tp30) cc_final: 0.7263 (tp30) REVERT: F 90 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.7976 (mtpp) REVERT: F 94 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.7921 (ttm-80) REVERT: F 228 ASN cc_start: 0.6966 (p0) cc_final: 0.6387 (t0) REVERT: F 238 MET cc_start: 0.6632 (mtp) cc_final: 0.6407 (tpt) REVERT: F 296 LEU cc_start: 0.7872 (mp) cc_final: 0.7645 (pp) REVERT: F 308 LYS cc_start: 0.5066 (pttm) cc_final: 0.4535 (pttm) REVERT: F 402 GLU cc_start: 0.7783 (tp30) cc_final: 0.7493 (tp30) outliers start: 41 outliers final: 33 residues processed: 228 average time/residue: 0.3635 time to fit residues: 129.6910 Evaluate side-chains 219 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 179 time to evaluate : 2.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 293 ASP Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 372 TYR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 94 ARG Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 372 TYR Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 332 THR Chi-restraints excluded: chain E residue 372 TYR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 90 LYS Chi-restraints excluded: chain F residue 94 ARG Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain F residue 294 PHE Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 372 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 185 optimal weight: 10.0000 chunk 248 optimal weight: 5.9990 chunk 71 optimal weight: 20.0000 chunk 215 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 233 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 239 optimal weight: 20.0000 chunk 29 optimal weight: 40.0000 chunk 43 optimal weight: 9.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 HIS ** F 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.096233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.070365 restraints weight = 58045.320| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.81 r_work: 0.2953 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.6082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 24360 Z= 0.185 Angle : 0.522 9.846 32994 Z= 0.265 Chirality : 0.042 0.173 3588 Planarity : 0.004 0.031 4224 Dihedral : 8.901 88.027 3990 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.84 % Allowed : 12.74 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.89 (0.16), residues: 2964 helix: 1.82 (0.14), residues: 1452 sheet: -0.79 (0.26), residues: 420 loop : -0.45 (0.20), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 281 HIS 0.008 0.001 HIS E 408 PHE 0.013 0.002 PHE A 148 TYR 0.011 0.001 TYR B 401 ARG 0.003 0.000 ARG D 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4720.03 seconds wall clock time: 86 minutes 55.11 seconds (5215.11 seconds total)