Starting phenix.real_space_refine (version: dev) on Fri Feb 24 21:33:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd1_6634/02_2023/3jd1_6634_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd1_6634/02_2023/3jd1_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_6634/02_2023/3jd1_6634.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd1_6634/02_2023/3jd1_6634.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd1_6634/02_2023/3jd1_6634_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd1_6634/02_2023/3jd1_6634_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 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-4877/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: 13.13, per 1000 atoms: 0.55 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: 10.46 Conformation dependent library (CDL) restraints added in 3.5 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: 2.65 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: 7.96 Time building geometry restraints manager: 11.22 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: 14088 16.94 - 33.88: 216 33.88 - 50.83: 72 50.83 - 67.77: 0 67.77 - 84.71: 6 Dihedral angle restraints: 14382 sinusoidal: 5904 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 14379 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 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. 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: 0.900 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: 6.110 Check model and map are aligned: 0.380 Process input model: 63.290 Find NCS groups from input model: 1.620 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Set scattering table: 0.230 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 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 : 8.097 84.712 8982 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 % 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 *********************** 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 : 2.909 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 outliers start: 0 outliers final: 0 residues processed: 604 average time/residue: 0.5267 time to fit residues: 447.2006 Evaluate side-chains 230 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 2.750 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0572 ------------------------------------------------------------------------------- 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: 6.9990 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 228 ASN ** 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 228 ASN 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: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.032 24360 Z= 0.313 Angle : 0.690 7.084 32994 Z= 0.358 Chirality : 0.047 0.138 3588 Planarity : 0.006 0.090 4224 Dihedral : 6.650 76.465 3390 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer Outliers : 2.32 % 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: -2.45 (0.14), residues: 2964 helix: -1.29 (0.12), residues: 1446 sheet: -1.74 (0.24), residues: 348 loop : -1.82 (0.17), residues: 1170 *********************** 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 : 2.771 Fit side-chains outliers start: 58 outliers final: 31 residues processed: 334 average time/residue: 0.4555 time to fit residues: 221.4412 Evaluate side-chains 207 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 176 time to evaluate : 3.109 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.3065 time to fit residues: 19.6312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 181 optimal weight: 30.0000 chunk 73 optimal weight: 0.7980 chunk 267 optimal weight: 5.9990 chunk 288 optimal weight: 8.9990 chunk 238 optimal weight: 20.0000 chunk 265 optimal weight: 20.0000 chunk 91 optimal weight: 20.0000 chunk 214 optimal weight: 6.9990 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN B 205 GLN ** B 450 HIS ** 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 205 GLN E 205 GLN ** E 450 HIS ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 24360 Z= 0.315 Angle : 0.648 7.346 32994 Z= 0.334 Chirality : 0.045 0.136 3588 Planarity : 0.005 0.043 4224 Dihedral : 6.548 86.171 3390 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer Outliers : 1.48 % 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: -0.96 (0.15), residues: 2964 helix: 0.15 (0.13), residues: 1446 sheet: -1.54 (0.24), residues: 414 loop : -1.17 (0.18), residues: 1104 *********************** 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 269 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 232 time to evaluate : 3.122 Fit side-chains outliers start: 37 outliers final: 13 residues processed: 261 average time/residue: 0.3330 time to fit residues: 141.8614 Evaluate side-chains 182 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 169 time to evaluate : 2.901 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.3384 time to fit residues: 10.6605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 264 optimal weight: 2.9990 chunk 201 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 127 optimal weight: 40.0000 chunk 179 optimal weight: 20.0000 chunk 268 optimal weight: 20.0000 chunk 284 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 254 optimal weight: 10.0000 chunk 76 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 ASN ** B 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 388 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.5330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 24360 Z= 0.268 Angle : 0.592 7.005 32994 Z= 0.303 Chirality : 0.044 0.137 3588 Planarity : 0.004 0.035 4224 Dihedral : 6.188 81.118 3390 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 1.12 % 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: -0.36 (0.15), residues: 2964 helix: 0.69 (0.14), residues: 1446 sheet: -1.12 (0.24), residues: 450 loop : -0.98 (0.19), residues: 1068 *********************** 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 221 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 193 time to evaluate : 3.137 Fit side-chains outliers start: 28 outliers final: 18 residues processed: 214 average time/residue: 0.3566 time to fit residues: 123.6034 Evaluate side-chains 178 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 160 time to evaluate : 3.216 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2298 time to fit residues: 12.1130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 211 optimal weight: 10.0000 chunk 117 optimal weight: 8.9990 chunk 242 optimal weight: 4.9990 chunk 196 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 145 optimal weight: 2.9990 chunk 255 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN A 388 ASN ** B 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 ASN D 388 ASN E 450 HIS ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.5661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 24360 Z= 0.277 Angle : 0.590 8.805 32994 Z= 0.302 Chirality : 0.044 0.137 3588 Planarity : 0.004 0.034 4224 Dihedral : 5.816 64.948 3390 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 1.32 % 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: -0.07 (0.15), residues: 2964 helix: 0.85 (0.14), residues: 1446 sheet: -1.13 (0.25), residues: 420 loop : -0.67 (0.19), residues: 1098 *********************** 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 212 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 179 time to evaluate : 2.869 Fit side-chains outliers start: 33 outliers final: 13 residues processed: 203 average time/residue: 0.3830 time to fit residues: 123.3131 Evaluate side-chains 175 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 162 time to evaluate : 3.003 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2344 time to fit residues: 9.6402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 95 optimal weight: 5.9990 chunk 255 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 166 optimal weight: 0.0470 chunk 70 optimal weight: 4.9990 chunk 284 optimal weight: 8.9990 chunk 236 optimal weight: 10.0000 chunk 131 optimal weight: 20.0000 chunk 23 optimal weight: 30.0000 chunk 94 optimal weight: 5.9990 chunk 149 optimal weight: 20.0000 overall best weight: 4.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 ASN B 298 HIS B 450 HIS C 56 ASN ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 ASN E 250 GLN F 56 ASN ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.5893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 24360 Z= 0.239 Angle : 0.551 6.712 32994 Z= 0.283 Chirality : 0.043 0.135 3588 Planarity : 0.004 0.031 4224 Dihedral : 5.345 51.545 3390 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer Outliers : 1.28 % 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: 0.20 (0.16), residues: 2964 helix: 1.07 (0.14), residues: 1446 sheet: -0.93 (0.25), residues: 408 loop : -0.58 (0.19), residues: 1110 *********************** 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 216 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 184 time to evaluate : 3.352 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 19 residues processed: 206 average time/residue: 0.3652 time to fit residues: 119.6210 Evaluate side-chains 184 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 165 time to evaluate : 2.884 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2661 time to fit residues: 13.5527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 274 optimal weight: 0.6980 chunk 32 optimal weight: 10.0000 chunk 162 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 160 optimal weight: 0.1980 chunk 239 optimal weight: 20.0000 chunk 158 optimal weight: 1.9990 chunk 283 optimal weight: 3.9990 chunk 177 optimal weight: 10.0000 chunk 172 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 HIS ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.6052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 24360 Z= 0.146 Angle : 0.496 6.150 32994 Z= 0.254 Chirality : 0.041 0.133 3588 Planarity : 0.003 0.032 4224 Dihedral : 4.938 50.029 3390 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer Outliers : 0.24 % 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: 0.53 (0.16), residues: 2964 helix: 1.45 (0.14), residues: 1452 sheet: -0.80 (0.25), residues: 408 loop : -0.58 (0.19), residues: 1104 *********************** 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 205 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 199 time to evaluate : 2.774 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 201 average time/residue: 0.3455 time to fit residues: 112.6251 Evaluate side-chains 176 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 171 time to evaluate : 2.950 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2495 time to fit residues: 6.1181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 175 optimal weight: 20.0000 chunk 113 optimal weight: 6.9990 chunk 169 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 180 optimal weight: 0.9990 chunk 193 optimal weight: 8.9990 chunk 140 optimal weight: 0.0370 chunk 26 optimal weight: 40.0000 chunk 222 optimal weight: 6.9990 overall best weight: 3.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 GLN ** 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 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.6105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 24360 Z= 0.211 Angle : 0.538 9.067 32994 Z= 0.275 Chirality : 0.043 0.163 3588 Planarity : 0.004 0.033 4224 Dihedral : 5.090 51.892 3390 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer Outliers : 0.68 % 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: 0.54 (0.16), residues: 2964 helix: 1.46 (0.14), residues: 1452 sheet: -0.80 (0.25), residues: 408 loop : -0.58 (0.19), residues: 1104 *********************** 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 191 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 174 time to evaluate : 2.891 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 185 average time/residue: 0.3632 time to fit residues: 107.6894 Evaluate side-chains 180 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 171 time to evaluate : 3.014 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2180 time to fit residues: 7.6689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 257 optimal weight: 8.9990 chunk 271 optimal weight: 9.9990 chunk 247 optimal weight: 7.9990 chunk 264 optimal weight: 8.9990 chunk 158 optimal weight: 9.9990 chunk 115 optimal weight: 8.9990 chunk 207 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 chunk 238 optimal weight: 3.9990 chunk 249 optimal weight: 6.9990 chunk 263 optimal weight: 0.0270 overall best weight: 4.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 ASN ** B 330 GLN ** 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 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.6179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 24360 Z= 0.247 Angle : 0.563 8.518 32994 Z= 0.288 Chirality : 0.043 0.166 3588 Planarity : 0.004 0.033 4224 Dihedral : 5.282 52.308 3390 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer Outliers : 0.68 % 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: 0.46 (0.16), residues: 2964 helix: 1.41 (0.14), residues: 1452 sheet: -0.97 (0.25), residues: 420 loop : -0.58 (0.19), residues: 1092 *********************** 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 196 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 179 time to evaluate : 3.198 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 190 average time/residue: 0.3772 time to fit residues: 116.1122 Evaluate side-chains 177 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 167 time to evaluate : 3.186 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2524 time to fit residues: 9.1139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 173 optimal weight: 20.0000 chunk 279 optimal weight: 10.0000 chunk 170 optimal weight: 7.9990 chunk 132 optimal weight: 10.0000 chunk 194 optimal weight: 5.9990 chunk 292 optimal weight: 7.9990 chunk 269 optimal weight: 10.0000 chunk 233 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 180 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 330 GLN ** 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 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 228 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.6251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 24360 Z= 0.225 Angle : 0.556 8.294 32994 Z= 0.283 Chirality : 0.043 0.179 3588 Planarity : 0.004 0.037 4224 Dihedral : 5.268 51.848 3390 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer Outliers : 0.28 % 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: 0.51 (0.16), residues: 2964 helix: 1.49 (0.14), residues: 1452 sheet: -0.93 (0.25), residues: 420 loop : -0.62 (0.19), residues: 1092 ********************** 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 182 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 175 time to evaluate : 2.851 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 181 average time/residue: 0.3571 time to fit residues: 104.4877 Evaluate side-chains 168 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 164 time to evaluate : 3.371 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3093 time to fit residues: 6.5192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 185 optimal weight: 8.9990 chunk 248 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 chunk 215 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 233 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 239 optimal weight: 20.0000 chunk 29 optimal weight: 4.9990 chunk 43 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** E 135 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.095734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.069416 restraints weight = 58808.049| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.87 r_work: 0.2917 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.6311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 24360 Z= 0.256 Angle : 0.576 8.157 32994 Z= 0.294 Chirality : 0.044 0.178 3588 Planarity : 0.004 0.038 4224 Dihedral : 5.428 52.941 3390 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer Outliers : 0.28 % 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: 0.47 (0.16), residues: 2964 helix: 1.47 (0.14), residues: 1452 sheet: -0.95 (0.25), residues: 420 loop : -0.65 (0.19), residues: 1092 =============================================================================== Job complete usr+sys time: 4644.72 seconds wall clock time: 86 minutes 40.41 seconds (5200.41 seconds total)