Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 19:40:34 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nps_12518/12_2021/7nps_12518.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nps_12518/12_2021/7nps_12518.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nps_12518/12_2021/7nps_12518.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nps_12518/12_2021/7nps_12518.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nps_12518/12_2021/7nps_12518.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nps_12518/12_2021/7nps_12518.pdb" } resolution = 3.81 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= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "P3 TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/modules/chem_data/mon_lib" Total number of atoms: 55350 Number of models: 1 Model: "" Number of chains: 9 Chain: "B1" Number of atoms: 6214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 6214 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 44, 'TRANS': 369} Chain breaks: 3 Chain: "B2" Number of atoms: 6214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 6214 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 44, 'TRANS': 369} Chain breaks: 3 Chain: "B3" Number of atoms: 6214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 6214 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 44, 'TRANS': 369} Chain breaks: 3 Chain: "B4" Number of atoms: 6208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 6208 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 44, 'TRANS': 371} Chain breaks: 1 Chain: "B5" Number of atoms: 6208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 6208 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 44, 'TRANS': 371} Chain breaks: 1 Chain: "B6" Number of atoms: 6208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 6208 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 44, 'TRANS': 371} Chain breaks: 1 Chain: "P1" Number of atoms: 6028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 6028 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 47, 'TRANS': 365, 'PCIS': 1} Chain breaks: 1 Chain: "P2" Number of atoms: 6028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 6028 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 47, 'TRANS': 365, 'PCIS': 1} Chain breaks: 1 Chain: "P3" Number of atoms: 6028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 6028 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 47, 'TRANS': 365, 'PCIS': 1} Chain breaks: 1 Time building chain proxies: 18.90, per 1000 atoms: 0.34 Number of scatterers: 55350 At special positions: 0 Unit cell: (210.1, 202.4, 114.4, 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 87 16.00 O 5271 8.00 N 4851 7.00 C 17460 6.00 H 27681 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYSB1 162 " - pdb=" SG CYSB1 363 " distance=2.03 Simple disulfide: pdb=" SG CYSB2 162 " - pdb=" SG CYSB2 363 " distance=2.02 Simple disulfide: pdb=" SG CYSB3 162 " - pdb=" SG CYSB3 363 " distance=2.03 Simple disulfide: pdb=" SG CYSB4 162 " - pdb=" SG CYSB4 363 " distance=2.02 Simple disulfide: pdb=" SG CYSB5 162 " - pdb=" SG CYSB5 363 " distance=2.02 Simple disulfide: pdb=" SG CYSB6 162 " - pdb=" SG CYSB6 363 " distance=2.03 Simple disulfide: pdb=" SG CYSP1 68 " - pdb=" SG CYSP1 138 " distance=2.04 Simple disulfide: pdb=" SG CYSP1 334 " - pdb=" SG CYSP1 373 " distance=2.03 Simple disulfide: pdb=" SG CYSP2 68 " - pdb=" SG CYSP2 138 " distance=2.04 Simple disulfide: pdb=" SG CYSP2 334 " - pdb=" SG CYSP2 373 " distance=2.03 Simple disulfide: pdb=" SG CYSP3 68 " - pdb=" SG CYSP3 138 " distance=2.04 Simple disulfide: pdb=" SG CYSP3 334 " - pdb=" SG CYSP3 373 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amimo acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 33.13 Conformation dependent library (CDL) restraints added in 3.8 seconds 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6828 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 51 sheets defined 22.8% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'B1' and resid 109 through 118 Processing helix chain 'B1' and resid 127 through 132 removed outlier: 3.523A pdb=" N ILEB1 131 " --> pdb=" O ARGB1 127 " (cutoff:3.500A) Processing helix chain 'B1' and resid 224 through 232 Proline residue: B1 230 - end of helix Processing helix chain 'B1' and resid 234 through 240 Processing helix chain 'B1' and resid 245 through 252 Processing helix chain 'B1' and resid 306 through 316 Processing helix chain 'B1' and resid 328 through 335 Processing helix chain 'B1' and resid 390 through 395 removed outlier: 4.217A pdb=" N ASNB1 393 " --> pdb=" O THRB1 390 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VALB1 395 " --> pdb=" O METB1 392 " (cutoff:3.500A) Processing helix chain 'B1' and resid 451 through 458 Processing helix chain 'B1' and resid 468 through 473 Processing helix chain 'B1' and resid 482 through 487 removed outlier: 3.843A pdb=" N LEUB1 487 " --> pdb=" O ARGB1 483 " (cutoff:3.500A) Processing helix chain 'B2' and resid 109 through 118 Processing helix chain 'B2' and resid 127 through 132 removed outlier: 3.576A pdb=" N ILEB2 131 " --> pdb=" O ARGB2 127 " (cutoff:3.500A) Processing helix chain 'B2' and resid 224 through 232 Proline residue: B2 230 - end of helix Processing helix chain 'B2' and resid 234 through 240 Processing helix chain 'B2' and resid 245 through 252 removed outlier: 3.869A pdb=" N ALAB2 251 " --> pdb=" O ALAB2 247 " (cutoff:3.500A) Processing helix chain 'B2' and resid 306 through 314 Processing helix chain 'B2' and resid 328 through 335 Processing helix chain 'B2' and resid 391 through 395 removed outlier: 3.731A pdb=" N VALB2 395 " --> pdb=" O METB2 392 " (cutoff:3.500A) Processing helix chain 'B2' and resid 453 through 458 Processing helix chain 'B2' and resid 468 through 473 Processing helix chain 'B2' and resid 482 through 487 removed outlier: 3.603A pdb=" N LEUB2 487 " --> pdb=" O ARGB2 483 " (cutoff:3.500A) Processing helix chain 'B3' and resid 109 through 118 Processing helix chain 'B3' and resid 127 through 132 removed outlier: 3.612A pdb=" N ALAB3 132 " --> pdb=" O SERB3 128 " (cutoff:3.500A) Processing helix chain 'B3' and resid 224 through 232 Proline residue: B3 230 - end of helix Processing helix chain 'B3' and resid 234 through 240 Processing helix chain 'B3' and resid 245 through 252 Processing helix chain 'B3' and resid 306 through 314 Processing helix chain 'B3' and resid 328 through 335 Processing helix chain 'B3' and resid 391 through 395 removed outlier: 3.770A pdb=" N VALB3 395 " --> pdb=" O METB3 392 " (cutoff:3.500A) Processing helix chain 'B3' and resid 451 through 459 Processing helix chain 'B3' and resid 468 through 473 Processing helix chain 'B3' and resid 482 through 487 removed outlier: 3.855A pdb=" N LEUB3 487 " --> pdb=" O ARGB3 483 " (cutoff:3.500A) Processing helix chain 'B4' and resid 109 through 118 Processing helix chain 'B4' and resid 127 through 132 removed outlier: 3.612A pdb=" N ILEB4 131 " --> pdb=" O ARGB4 127 " (cutoff:3.500A) Processing helix chain 'B4' and resid 224 through 232 Proline residue: B4 230 - end of helix Processing helix chain 'B4' and resid 234 through 240 Processing helix chain 'B4' and resid 245 through 252 removed outlier: 3.510A pdb=" N ALAB4 251 " --> pdb=" O ALAB4 247 " (cutoff:3.500A) Processing helix chain 'B4' and resid 286 through 290 removed outlier: 3.501A pdb=" N SERB4 289 " --> pdb=" O PROB4 286 " (cutoff:3.500A) Processing helix chain 'B4' and resid 306 through 317 removed outlier: 3.612A pdb=" N GLNB4 311 " --> pdb=" O PROB4 307 " (cutoff:3.500A) Processing helix chain 'B4' and resid 328 through 333 Processing helix chain 'B4' and resid 342 through 346 removed outlier: 4.325A pdb=" N ALAB4 345 " --> pdb=" O ASPB4 342 " (cutoff:3.500A) Processing helix chain 'B4' and resid 388 through 395 removed outlier: 4.099A pdb=" N ASNB4 393 " --> pdb=" O THRB4 390 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VALB4 395 " --> pdb=" O METB4 392 " (cutoff:3.500A) Processing helix chain 'B4' and resid 451 through 459 Processing helix chain 'B4' and resid 469 through 473 Processing helix chain 'B4' and resid 482 through 487 Processing helix chain 'B5' and resid 109 through 118 Processing helix chain 'B5' and resid 127 through 132 removed outlier: 3.702A pdb=" N ILEB5 131 " --> pdb=" O ARGB5 127 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALAB5 132 " --> pdb=" O SERB5 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'B5' and resid 127 through 132' Processing helix chain 'B5' and resid 224 through 232 Proline residue: B5 230 - end of helix Processing helix chain 'B5' and resid 234 through 240 Processing helix chain 'B5' and resid 245 through 252 removed outlier: 3.506A pdb=" N ALAB5 251 " --> pdb=" O ALAB5 247 " (cutoff:3.500A) Processing helix chain 'B5' and resid 286 through 290 removed outlier: 3.572A pdb=" N GLYB5 290 " --> pdb=" O GLNB5 287 " (cutoff:3.500A) Processing helix chain 'B5' and resid 306 through 317 removed outlier: 3.516A pdb=" N GLNB5 311 " --> pdb=" O PROB5 307 " (cutoff:3.500A) Processing helix chain 'B5' and resid 328 through 333 Processing helix chain 'B5' and resid 390 through 395 removed outlier: 4.225A pdb=" N ASNB5 393 " --> pdb=" O THRB5 390 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VALB5 395 " --> pdb=" O METB5 392 " (cutoff:3.500A) Processing helix chain 'B5' and resid 451 through 458 Processing helix chain 'B5' and resid 469 through 473 Processing helix chain 'B5' and resid 482 through 487 removed outlier: 3.615A pdb=" N LEUB5 487 " --> pdb=" O ARGB5 483 " (cutoff:3.500A) Processing helix chain 'B6' and resid 109 through 118 Processing helix chain 'B6' and resid 127 through 132 removed outlier: 3.853A pdb=" N ILEB6 131 " --> pdb=" O ARGB6 127 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALAB6 132 " --> pdb=" O SERB6 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'B6' and resid 127 through 132' Processing helix chain 'B6' and resid 224 through 232 Proline residue: B6 230 - end of helix Processing helix chain 'B6' and resid 234 through 240 Processing helix chain 'B6' and resid 245 through 252 removed outlier: 3.589A pdb=" N ALAB6 251 " --> pdb=" O ALAB6 247 " (cutoff:3.500A) Processing helix chain 'B6' and resid 306 through 317 removed outlier: 3.543A pdb=" N GLNB6 311 " --> pdb=" O PROB6 307 " (cutoff:3.500A) Processing helix chain 'B6' and resid 328 through 333 Processing helix chain 'B6' and resid 390 through 395 removed outlier: 4.125A pdb=" N ASNB6 393 " --> pdb=" O THRB6 390 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VALB6 395 " --> pdb=" O METB6 392 " (cutoff:3.500A) Processing helix chain 'B6' and resid 451 through 459 Processing helix chain 'B6' and resid 469 through 473 Processing helix chain 'B6' and resid 482 through 487 removed outlier: 3.547A pdb=" N LEUB6 487 " --> pdb=" O ARGB6 483 " (cutoff:3.500A) Processing helix chain 'P1' and resid 46 through 50 removed outlier: 3.814A pdb=" N LEUP1 50 " --> pdb=" O PROP1 47 " (cutoff:3.500A) Processing helix chain 'P1' and resid 85 through 90 removed outlier: 4.035A pdb=" N LEUP1 89 " --> pdb=" O TYRP1 85 " (cutoff:3.500A) Processing helix chain 'P1' and resid 90 through 95 Processing helix chain 'P1' and resid 96 through 98 No H-bonds generated for 'chain 'P1' and resid 96 through 98' Processing helix chain 'P1' and resid 141 through 151 removed outlier: 3.531A pdb=" N VALP1 145 " --> pdb=" O HISP1 141 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILEP1 149 " --> pdb=" O VALP1 145 " (cutoff:3.500A) Processing helix chain 'P1' and resid 299 through 322 removed outlier: 3.648A pdb=" N GLNP1 304 " --> pdb=" O PROP1 300 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYSP1 305 " --> pdb=" O GLNP1 301 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILEP1 306 " --> pdb=" O THRP1 302 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASPP1 307 " --> pdb=" O ALAP1 303 " (cutoff:3.500A) Processing helix chain 'P1' and resid 343 through 356 Processing helix chain 'P1' and resid 464 through 483 removed outlier: 3.699A pdb=" N SERP1 468 " --> pdb=" O GLYP1 464 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALAP1 470 " --> pdb=" O SERP1 466 " (cutoff:3.500A) Processing helix chain 'P1' and resid 487 through 499 removed outlier: 3.719A pdb=" N THRP1 498 " --> pdb=" O ARGP1 494 " (cutoff:3.500A) Processing helix chain 'P1' and resid 516 through 523 Processing helix chain 'P2' and resid 46 through 50 removed outlier: 3.952A pdb=" N LEUP2 50 " --> pdb=" O PROP2 47 " (cutoff:3.500A) Processing helix chain 'P2' and resid 85 through 90 removed outlier: 3.999A pdb=" N LEUP2 89 " --> pdb=" O TYRP2 85 " (cutoff:3.500A) Processing helix chain 'P2' and resid 90 through 95 Processing helix chain 'P2' and resid 96 through 98 No H-bonds generated for 'chain 'P2' and resid 96 through 98' Processing helix chain 'P2' and resid 140 through 151 removed outlier: 4.052A pdb=" N LEUP2 144 " --> pdb=" O ALAP2 140 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VALP2 145 " --> pdb=" O HISP2 141 " (cutoff:3.500A) Processing helix chain 'P2' and resid 299 through 322 removed outlier: 3.956A pdb=" N LYSP2 305 " --> pdb=" O GLNP2 301 " (cutoff:3.500A) Processing helix chain 'P2' and resid 343 through 356 Processing helix chain 'P2' and resid 389 through 393 removed outlier: 3.720A pdb=" N ALAP2 392 " --> pdb=" O ALAP2 389 " (cutoff:3.500A) Processing helix chain 'P2' and resid 464 through 483 removed outlier: 3.593A pdb=" N SERP2 468 " --> pdb=" O GLYP2 464 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ALAP2 470 " --> pdb=" O SERP2 466 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILEP2 471 " --> pdb=" O PHEP2 467 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALAP2 481 " --> pdb=" O ALAP2 477 " (cutoff:3.500A) Processing helix chain 'P2' and resid 487 through 498 removed outlier: 3.539A pdb=" N THRP2 498 " --> pdb=" O ARGP2 494 " (cutoff:3.500A) Processing helix chain 'P2' and resid 516 through 523 Processing helix chain 'P3' and resid 46 through 50 removed outlier: 3.734A pdb=" N LEUP3 50 " --> pdb=" O PROP3 47 " (cutoff:3.500A) Processing helix chain 'P3' and resid 85 through 90 removed outlier: 3.995A pdb=" N LEUP3 89 " --> pdb=" O TYRP3 85 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASNP3 90 " --> pdb=" O METP3 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'P3' and resid 85 through 90' Processing helix chain 'P3' and resid 90 through 95 Processing helix chain 'P3' and resid 96 through 98 No H-bonds generated for 'chain 'P3' and resid 96 through 98' Processing helix chain 'P3' and resid 141 through 151 removed outlier: 3.590A pdb=" N ILEP3 149 " --> pdb=" O VALP3 145 " (cutoff:3.500A) Processing helix chain 'P3' and resid 299 through 322 removed outlier: 3.653A pdb=" N GLNP3 304 " --> pdb=" O PROP3 300 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYSP3 305 " --> pdb=" O GLNP3 301 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASPP3 307 " --> pdb=" O ALAP3 303 " (cutoff:3.500A) Processing helix chain 'P3' and resid 343 through 356 Processing helix chain 'P3' and resid 464 through 483 removed outlier: 3.634A pdb=" N SERP3 468 " --> pdb=" O GLYP3 464 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALAP3 470 " --> pdb=" O SERP3 466 " (cutoff:3.500A) Processing helix chain 'P3' and resid 487 through 499 removed outlier: 3.656A pdb=" N THRP3 498 " --> pdb=" O ARGP3 494 " (cutoff:3.500A) Processing helix chain 'P3' and resid 516 through 523 Processing sheet with id=AA1, first strand: chain 'B1' and resid 103 through 106 Processing sheet with id=AA2, first strand: chain 'B1' and resid 139 through 140 removed outlier: 3.668A pdb=" N ALAP3 538 " --> pdb=" O GLUB1 489 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B1' and resid 193 through 194 removed outlier: 3.743A pdb=" N THRB1 362 " --> pdb=" O ASPB1 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B1' and resid 216 through 220 removed outlier: 4.349A pdb=" N ALAB1 209 " --> pdb=" O ILEB1 220 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B1' and resid 301 through 305 removed outlier: 4.424A pdb=" N TYRB1 294 " --> pdb=" O LEUB1 305 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B1' and resid 445 through 448 removed outlier: 4.568A pdb=" N LEUB1 436 " --> pdb=" O VALB1 448 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B1' and resid 500 through 501 Processing sheet with id=AA8, first strand: chain 'B2' and resid 103 through 106 removed outlier: 6.872A pdb=" N ILEB2 87 " --> pdb=" O HISB2 124 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N VALB2 126 " --> pdb=" O ILEB2 87 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ALAB2 89 " --> pdb=" O VALB2 126 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B2' and resid 139 through 140 Processing sheet with id=AB1, first strand: chain 'B2' and resid 193 through 194 removed outlier: 3.520A pdb=" N THRB2 362 " --> pdb=" O ASPB2 163 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B2' and resid 216 through 220 removed outlier: 4.135A pdb=" N ALAB2 209 " --> pdb=" O ILEB2 220 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B2' and resid 302 through 305 removed outlier: 4.383A pdb=" N TYRB2 294 " --> pdb=" O LEUB2 305 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VALB2 282 " --> pdb=" O LEUB2 325 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B2' and resid 445 through 448 removed outlier: 4.309A pdb=" N LEUB2 436 " --> pdb=" O VALB2 448 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B2' and resid 500 through 501 Processing sheet with id=AB6, first strand: chain 'B3' and resid 103 through 106 removed outlier: 6.929A pdb=" N ILEB3 87 " --> pdb=" O HISB3 124 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N VALB3 126 " --> pdb=" O ILEB3 87 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ALAB3 89 " --> pdb=" O VALB3 126 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B3' and resid 139 through 140 removed outlier: 3.520A pdb=" N LEUB3 139 " --> pdb=" O HISB3 490 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B3' and resid 193 through 194 Processing sheet with id=AB9, first strand: chain 'B3' and resid 216 through 220 removed outlier: 4.277A pdb=" N ALAB3 209 " --> pdb=" O ILEB3 220 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B3' and resid 301 through 305 removed outlier: 4.481A pdb=" N TYRB3 294 " --> pdb=" O LEUB3 305 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B3' and resid 445 through 448 removed outlier: 4.602A pdb=" N LEUB3 436 " --> pdb=" O VALB3 448 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B3' and resid 500 through 501 removed outlier: 3.531A pdb=" N LEUB6 139 " --> pdb=" O HISB6 490 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B4' and resid 103 through 106 Processing sheet with id=AC5, first strand: chain 'B4' and resid 193 through 194 removed outlier: 3.517A pdb=" N SERB4 361 " --> pdb=" O GLYB4 382 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B4' and resid 216 through 220 removed outlier: 4.091A pdb=" N ALAB4 209 " --> pdb=" O ILEB4 220 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B4' and resid 302 through 305 removed outlier: 4.477A pdb=" N TYRB4 294 " --> pdb=" O LEUB4 305 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B4' and resid 445 through 447 Processing sheet with id=AC9, first strand: chain 'B5' and resid 103 through 106 removed outlier: 6.786A pdb=" N ILEB5 87 " --> pdb=" O HISB5 124 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N VALB5 126 " --> pdb=" O ILEB5 87 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ALAB5 89 " --> pdb=" O VALB5 126 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B5' and resid 193 through 194 Processing sheet with id=AD2, first strand: chain 'B5' and resid 216 through 220 removed outlier: 4.355A pdb=" N ALAB5 209 " --> pdb=" O ILEB5 220 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALAB5 200 " --> pdb=" O GLUB5 352 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B5' and resid 301 through 305 removed outlier: 4.514A pdb=" N TYRB5 294 " --> pdb=" O LEUB5 305 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B5' and resid 445 through 447 Processing sheet with id=AD5, first strand: chain 'B6' and resid 103 through 106 Processing sheet with id=AD6, first strand: chain 'B6' and resid 193 through 194 Processing sheet with id=AD7, first strand: chain 'B6' and resid 216 through 220 removed outlier: 4.191A pdb=" N ALAB6 209 " --> pdb=" O ILEB6 220 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B6' and resid 302 through 305 removed outlier: 4.475A pdb=" N TYRB6 294 " --> pdb=" O LEUB6 305 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B6' and resid 445 through 448 removed outlier: 4.680A pdb=" N LEUB6 436 " --> pdb=" O VALB6 448 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'P1' and resid 62 through 64 Processing sheet with id=AE2, first strand: chain 'P1' and resid 71 through 72 Processing sheet with id=AE3, first strand: chain 'P1' and resid 121 through 126 removed outlier: 7.055A pdb=" N ARGP1 282 " --> pdb=" O GLYP1 124 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ASPP1 126 " --> pdb=" O ARGP1 282 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'P1' and resid 333 through 336 Processing sheet with id=AE5, first strand: chain 'P1' and resid 440 through 441 removed outlier: 3.714A pdb=" N GLYP1 440 " --> pdb=" O ILEP1 449 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'P2' and resid 62 through 64 Processing sheet with id=AE7, first strand: chain 'P2' and resid 71 through 72 Processing sheet with id=AE8, first strand: chain 'P2' and resid 121 through 126 removed outlier: 6.874A pdb=" N ILEP2 122 " --> pdb=" O SERP2 280 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N ARGP2 282 " --> pdb=" O ILEP2 122 " (cutoff:3.500A) removed outlier: 9.360A pdb=" N GLYP2 124 " --> pdb=" O ARGP2 282 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VALP2 326 " --> pdb=" O LYSP2 104 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'P2' and resid 333 through 336 Processing sheet with id=AF1, first strand: chain 'P2' and resid 440 through 441 removed outlier: 3.659A pdb=" N GLYP2 440 " --> pdb=" O ILEP2 449 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'P3' and resid 62 through 64 Processing sheet with id=AF3, first strand: chain 'P3' and resid 71 through 72 Processing sheet with id=AF4, first strand: chain 'P3' and resid 121 through 126 removed outlier: 6.818A pdb=" N ILEP3 122 " --> pdb=" O SERP3 280 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N ARGP3 282 " --> pdb=" O ILEP3 122 " (cutoff:3.500A) removed outlier: 8.802A pdb=" N GLYP3 124 " --> pdb=" O ARGP3 282 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LYSP3 104 " --> pdb=" O VALP3 326 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ASNP3 328 " --> pdb=" O LYSP3 104 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALAP3 106 " --> pdb=" O ASNP3 328 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILEP3 327 " --> pdb=" O VALP3 362 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N ALAP3 364 " --> pdb=" O ILEP3 327 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ILEP3 329 " --> pdb=" O ALAP3 364 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILEP3 361 " --> pdb=" O LEUP3 407 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VALP3 409 " --> pdb=" O ILEP3 361 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ALAP3 363 " --> pdb=" O VALP3 409 " (cutoff:3.500A) removed outlier: 8.939A pdb=" N ALAP3 411 " --> pdb=" O ALAP3 363 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'P3' and resid 333 through 336 removed outlier: 3.693A pdb=" N METP3 333 " --> pdb=" O THRP3 398 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'P3' and resid 440 through 441 removed outlier: 3.722A pdb=" N GLYP3 440 " --> pdb=" O ILEP3 449 " (cutoff:3.500A) 885 hydrogen bonds defined for protein. 2349 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: 19.93 Time building geometry restraints manager: 35.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 27361 1.03 - 1.23: 459 1.23 - 1.43: 11188 1.43 - 1.62: 16876 1.62 - 1.82: 150 Bond restraints: 56034 Sorted by residual: bond pdb=" CZ ARGB2 103 " pdb=" NH2 ARGB2 103 " ideal model delta sigma weight residual 1.330 1.224 0.106 1.30e-02 5.92e+03 6.62e+01 bond pdb=" CA ALAP3 538 " pdb=" CB ALAP3 538 " ideal model delta sigma weight residual 1.537 1.426 0.111 1.38e-02 5.25e+03 6.47e+01 bond pdb=" CZ ARGB1 103 " pdb=" NH2 ARGB1 103 " ideal model delta sigma weight residual 1.330 1.226 0.104 1.30e-02 5.92e+03 6.40e+01 bond pdb=" CZ ARGB2 483 " pdb=" NH2 ARGB2 483 " ideal model delta sigma weight residual 1.330 1.230 0.100 1.30e-02 5.92e+03 5.87e+01 bond pdb=" N GLUB2 489 " pdb=" H GLUB2 489 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 ... (remaining 56029 not shown) Histogram of bond angle deviations from ideal: 99.36 - 106.47: 2222 106.47 - 113.58: 68204 113.58 - 120.69: 16779 120.69 - 127.80: 14315 127.80 - 134.90: 555 Bond angle restraints: 102075 Sorted by residual: angle pdb=" C LEUP2 540 " pdb=" N VALP2 541 " pdb=" CA VALP2 541 " ideal model delta sigma weight residual 122.22 130.82 -8.60 1.15e+00 7.56e-01 5.59e+01 angle pdb=" N VALP3 542 " pdb=" CA VALP3 542 " pdb=" CB VALP3 542 " ideal model delta sigma weight residual 110.08 116.55 -6.47 9.30e-01 1.16e+00 4.83e+01 angle pdb=" C VALB2 488 " pdb=" N GLUB2 489 " pdb=" CA GLUB2 489 " ideal model delta sigma weight residual 122.93 132.93 -10.00 1.45e+00 4.76e-01 4.75e+01 angle pdb=" C ARGB3 99 " pdb=" N VALB3 100 " pdb=" CA VALB3 100 " ideal model delta sigma weight residual 123.17 131.59 -8.42 1.28e+00 6.10e-01 4.32e+01 angle pdb=" C PROP3 539 " pdb=" N LEUP3 540 " pdb=" CA LEUP3 540 " ideal model delta sigma weight residual 121.72 131.15 -9.43 1.45e+00 4.76e-01 4.23e+01 ... (remaining 102070 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 20600 17.60 - 35.20: 812 35.20 - 52.79: 185 52.79 - 70.39: 505 70.39 - 87.99: 35 Dihedral angle restraints: 22137 sinusoidal: 10443 harmonic: 11694 Sorted by residual: dihedral pdb=" C VALP2 541 " pdb=" N VALP2 541 " pdb=" CA VALP2 541 " pdb=" CB VALP2 541 " ideal model delta harmonic sigma weight residual -122.00 -134.84 12.84 0 2.50e+00 1.60e-01 2.64e+01 dihedral pdb=" N VALP2 541 " pdb=" C VALP2 541 " pdb=" CA VALP2 541 " pdb=" CB VALP2 541 " ideal model delta harmonic sigma weight residual 123.40 135.86 -12.46 0 2.50e+00 1.60e-01 2.48e+01 dihedral pdb=" C LEUB2 487 " pdb=" N LEUB2 487 " pdb=" CA LEUB2 487 " pdb=" CB LEUB2 487 " ideal model delta harmonic sigma weight residual -122.60 -134.56 11.96 0 2.50e+00 1.60e-01 2.29e+01 ... (remaining 22134 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 4429 0.144 - 0.287: 43 0.287 - 0.431: 21 0.431 - 0.574: 17 0.574 - 0.718: 17 Chirality restraints: 4527 Sorted by residual: chirality pdb=" CG LEUB2 487 " pdb=" CB LEUB2 487 " pdb=" CD1 LEUB2 487 " pdb=" CD2 LEUB2 487 " both_signs ideal model delta sigma weight residual False -2.59 -1.87 -0.72 2.00e-01 2.50e+01 1.29e+01 chirality pdb=" CB VALB3 100 " pdb=" CA VALB3 100 " pdb=" CG1 VALB3 100 " pdb=" CG2 VALB3 100 " both_signs ideal model delta sigma weight residual False -2.63 -1.92 -0.71 2.00e-01 2.50e+01 1.27e+01 chirality pdb=" CB VALP2 541 " pdb=" CA VALP2 541 " pdb=" CG1 VALP2 541 " pdb=" CG2 VALP2 541 " both_signs ideal model delta sigma weight residual False -2.63 -1.93 -0.70 2.00e-01 2.50e+01 1.23e+01 ... (remaining 4524 not shown) Planarity restraints: 8484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARGB2 406 " -0.108 9.50e-02 1.11e+02 5.31e-02 3.56e+01 pdb=" NE ARGB2 406 " 0.056 2.00e-02 2.50e+03 pdb=" CZ ARGB2 406 " -0.094 2.00e-02 2.50e+03 pdb=" NH1 ARGB2 406 " 0.032 2.00e-02 2.50e+03 pdb=" NH2 ARGB2 406 " 0.002 2.00e-02 2.50e+03 pdb="HH11 ARGB2 406 " -0.015 2.00e-02 2.50e+03 pdb="HH12 ARGB2 406 " 0.012 2.00e-02 2.50e+03 pdb="HH21 ARGB2 406 " -0.005 2.00e-02 2.50e+03 pdb="HH22 ARGB2 406 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARGB2 192 " 0.199 9.50e-02 1.11e+02 7.50e-02 3.21e+01 pdb=" NE ARGB2 192 " -0.036 2.00e-02 2.50e+03 pdb=" CZ ARGB2 192 " -0.034 2.00e-02 2.50e+03 pdb=" NH1 ARGB2 192 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARGB2 192 " 0.074 2.00e-02 2.50e+03 pdb="HH11 ARGB2 192 " 0.030 2.00e-02 2.50e+03 pdb="HH12 ARGB2 192 " -0.027 2.00e-02 2.50e+03 pdb="HH21 ARGB2 192 " 0.005 2.00e-02 2.50e+03 pdb="HH22 ARGB2 192 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARGB3 192 " -0.208 9.50e-02 1.11e+02 7.54e-02 2.44e+01 pdb=" NE ARGB3 192 " 0.005 2.00e-02 2.50e+03 pdb=" CZ ARGB3 192 " 0.066 2.00e-02 2.50e+03 pdb=" NH1 ARGB3 192 " -0.020 2.00e-02 2.50e+03 pdb=" NH2 ARGB3 192 " -0.024 2.00e-02 2.50e+03 pdb="HH11 ARGB3 192 " -0.031 2.00e-02 2.50e+03 pdb="HH12 ARGB3 192 " 0.035 2.00e-02 2.50e+03 pdb="HH21 ARGB3 192 " -0.003 2.00e-02 2.50e+03 pdb="HH22 ARGB3 192 " -0.018 2.00e-02 2.50e+03 ... (remaining 8481 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.04: 612 2.04 - 2.68: 81603 2.68 - 3.32: 148581 3.32 - 3.96: 184690 3.96 - 4.60: 294574 Nonbonded interactions: 710060 Sorted by model distance: nonbonded pdb=" HG1 THRP2 113 " pdb=" OD1 ASPP2 137 " model vdw 1.406 1.850 nonbonded pdb=" O LEUB6 259 " pdb=" HH TYRB6 346 " model vdw 1.498 1.850 nonbonded pdb=" O LEUB4 259 " pdb=" HH TYRB4 346 " model vdw 1.502 1.850 nonbonded pdb=" O LEUB5 259 " pdb=" HH TYRB5 346 " model vdw 1.525 1.850 nonbonded pdb=" HG SERP2 336 " pdb=" OD1 ASNP3 457 " model vdw 1.595 1.850 ... (remaining 710055 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 'B1' and resid 74 through 496) selection = (chain 'B2' and resid 74 through 496) selection = (chain 'B3' and resid 74 through 496) selection = (chain 'B4' and (resid 74 through 316 or resid 319 through 424 or resid 433 thro \ ugh 496)) selection = (chain 'B5' and (resid 74 through 316 or resid 319 through 424 or resid 433 thro \ ugh 496)) selection = (chain 'B6' and (resid 74 through 316 or resid 319 through 424 or resid 433 thro \ ugh 496)) } ncs_group { reference = chain 'P1' selection = chain 'P2' selection = chain 'P3' } 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 S 87 5.16 5 C 17460 2.51 5 N 4851 2.21 5 O 5271 1.98 5 H 27681 0.53 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Write .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: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 7.160 Check model and map are aligned: 0.670 Convert atoms to be neutral: 0.360 Process input model: 130.440 Find NCS groups from input model: 2.330 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.960 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 143.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 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 : 0.010 0.134 28353 Z= 0.664 Angle : 1.146 12.994 38931 Z= 0.685 Chirality : 0.078 0.718 4527 Planarity : 0.007 0.127 5181 Dihedral : 11.025 87.991 10410 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 1.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.12), residues: 3684 helix: -1.98 (0.15), residues: 720 sheet: 0.26 (0.19), residues: 618 loop : -0.96 (0.11), residues: 2346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 410 time to evaluate : 3.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 410 average time/residue: 0.8002 time to fit residues: 511.6952 Evaluate side-chains 189 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 3.259 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 311 optimal weight: 0.9980 chunk 279 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 188 optimal weight: 0.3980 chunk 149 optimal weight: 0.2980 chunk 289 optimal weight: 0.0980 chunk 111 optimal weight: 0.9980 chunk 175 optimal weight: 3.9990 chunk 215 optimal weight: 0.9990 chunk 335 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2 339 ASN B4 130 GLN ** B6 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1 391 ASN P1 450 ASN P2 391 ASN P3 391 ASN P3 450 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.086 28353 Z= 0.189 Angle : 0.617 10.356 38931 Z= 0.316 Chirality : 0.046 0.177 4527 Planarity : 0.006 0.100 5181 Dihedral : 4.219 23.973 3975 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.63 (0.13), residues: 3684 helix: -0.68 (0.18), residues: 702 sheet: 0.61 (0.20), residues: 594 loop : -0.58 (0.12), residues: 2388 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 223 time to evaluate : 3.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 11 residues processed: 235 average time/residue: 0.6918 time to fit residues: 261.5716 Evaluate side-chains 195 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 184 time to evaluate : 3.362 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.4712 time to fit residues: 13.8653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 186 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 278 optimal weight: 0.9980 chunk 228 optimal weight: 4.9990 chunk 92 optimal weight: 0.6980 chunk 335 optimal weight: 1.9990 chunk 362 optimal weight: 4.9990 chunk 298 optimal weight: 6.9990 chunk 332 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 269 optimal weight: 7.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1 359 HIS ** B6 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P2 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.080 28353 Z= 0.199 Angle : 0.564 10.672 38931 Z= 0.278 Chirality : 0.045 0.181 4527 Planarity : 0.005 0.095 5181 Dihedral : 4.090 20.752 3975 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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 (0.13), residues: 3684 helix: -0.32 (0.19), residues: 720 sheet: 0.67 (0.20), residues: 612 loop : -0.54 (0.12), residues: 2352 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 186 time to evaluate : 3.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 189 average time/residue: 0.6874 time to fit residues: 212.2023 Evaluate side-chains 181 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 175 time to evaluate : 3.365 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.4510 time to fit residues: 9.2811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 331 optimal weight: 3.9990 chunk 252 optimal weight: 4.9990 chunk 174 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 160 optimal weight: 0.9990 chunk 225 optimal weight: 10.0000 chunk 336 optimal weight: 4.9990 chunk 356 optimal weight: 0.0870 chunk 176 optimal weight: 5.9990 chunk 319 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B3 287 GLN ** B6 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.078 28353 Z= 0.228 Angle : 0.547 10.796 38931 Z= 0.265 Chirality : 0.045 0.179 4527 Planarity : 0.005 0.076 5181 Dihedral : 4.072 20.088 3975 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.43 (0.13), residues: 3684 helix: -0.14 (0.19), residues: 723 sheet: 0.67 (0.20), residues: 612 loop : -0.57 (0.12), residues: 2349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 185 time to evaluate : 3.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 188 average time/residue: 0.7305 time to fit residues: 224.0904 Evaluate side-chains 166 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 164 time to evaluate : 3.319 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4665 time to fit residues: 5.9449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 297 optimal weight: 5.9990 chunk 202 optimal weight: 0.7980 chunk 5 optimal weight: 0.0570 chunk 265 optimal weight: 4.9990 chunk 147 optimal weight: 6.9990 chunk 304 optimal weight: 3.9990 chunk 246 optimal weight: 0.0970 chunk 0 optimal weight: 5.9990 chunk 182 optimal weight: 8.9990 chunk 320 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B6 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P2 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.080 28353 Z= 0.178 Angle : 0.521 10.895 38931 Z= 0.249 Chirality : 0.045 0.175 4527 Planarity : 0.005 0.090 5181 Dihedral : 3.915 19.649 3975 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.26 (0.13), residues: 3684 helix: 0.18 (0.20), residues: 702 sheet: 0.78 (0.20), residues: 603 loop : -0.52 (0.12), residues: 2379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 180 time to evaluate : 3.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 180 average time/residue: 0.7425 time to fit residues: 215.0122 Evaluate side-chains 172 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 168 time to evaluate : 3.287 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.4949 time to fit residues: 7.6941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 120 optimal weight: 4.9990 chunk 321 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 209 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 357 optimal weight: 4.9990 chunk 296 optimal weight: 7.9990 chunk 165 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 187 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B6 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P2 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P3 328 ASN ** P3 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.195 28353 Z= 0.410 Angle : 0.599 13.157 38931 Z= 0.298 Chirality : 0.046 0.194 4527 Planarity : 0.005 0.117 5181 Dihedral : 4.211 21.665 3975 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.64 % Favored : 96.34 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.61 (0.13), residues: 3684 helix: -0.13 (0.19), residues: 726 sheet: 0.63 (0.20), residues: 600 loop : -0.77 (0.12), residues: 2358 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 163 time to evaluate : 3.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 163 average time/residue: 0.7072 time to fit residues: 188.9806 Evaluate side-chains 160 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 156 time to evaluate : 3.270 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.4880 time to fit residues: 7.6699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 344 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 203 optimal weight: 3.9990 chunk 260 optimal weight: 2.9990 chunk 202 optimal weight: 0.8980 chunk 300 optimal weight: 2.9990 chunk 199 optimal weight: 4.9990 chunk 355 optimal weight: 1.9990 chunk 222 optimal weight: 0.7980 chunk 216 optimal weight: 5.9990 chunk 164 optimal weight: 10.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B6 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P2 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P3 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.096 28353 Z= 0.209 Angle : 0.536 10.875 38931 Z= 0.258 Chirality : 0.045 0.178 4527 Planarity : 0.005 0.101 5181 Dihedral : 4.037 20.466 3975 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.44 (0.13), residues: 3684 helix: 0.11 (0.20), residues: 726 sheet: 0.46 (0.20), residues: 630 loop : -0.62 (0.12), residues: 2328 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 163 time to evaluate : 3.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 165 average time/residue: 0.7116 time to fit residues: 193.4026 Evaluate side-chains 164 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 159 time to evaluate : 3.297 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.5372 time to fit residues: 8.9079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 220 optimal weight: 6.9990 chunk 142 optimal weight: 0.8980 chunk 212 optimal weight: 0.0570 chunk 107 optimal weight: 8.9990 chunk 69 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 226 optimal weight: 7.9990 chunk 242 optimal weight: 1.9990 chunk 175 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 279 optimal weight: 2.9990 overall best weight: 1.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B6 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P2 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P3 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.107 28353 Z= 0.232 Angle : 0.530 10.759 38931 Z= 0.254 Chirality : 0.045 0.178 4527 Planarity : 0.005 0.080 5181 Dihedral : 3.947 19.583 3975 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.13), residues: 3684 helix: 0.20 (0.20), residues: 726 sheet: 0.72 (0.21), residues: 597 loop : -0.65 (0.12), residues: 2361 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 161 time to evaluate : 3.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 162 average time/residue: 0.7469 time to fit residues: 200.1078 Evaluate side-chains 157 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 3.340 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 323 optimal weight: 1.9990 chunk 340 optimal weight: 8.9990 chunk 310 optimal weight: 10.0000 chunk 331 optimal weight: 2.9990 chunk 199 optimal weight: 3.9990 chunk 144 optimal weight: 9.9990 chunk 260 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 299 optimal weight: 0.8980 chunk 313 optimal weight: 1.9990 chunk 330 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B6 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P2 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.164 28353 Z= 0.179 Angle : 0.513 10.794 38931 Z= 0.243 Chirality : 0.045 0.172 4527 Planarity : 0.004 0.081 5181 Dihedral : 3.781 18.825 3975 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.19 (0.13), residues: 3684 helix: 0.56 (0.21), residues: 690 sheet: 0.75 (0.20), residues: 600 loop : -0.56 (0.12), residues: 2394 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 169 time to evaluate : 3.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 172 average time/residue: 0.7046 time to fit residues: 197.9683 Evaluate side-chains 161 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 159 time to evaluate : 3.308 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.5128 time to fit residues: 5.9575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 217 optimal weight: 3.9990 chunk 350 optimal weight: 0.4980 chunk 213 optimal weight: 0.9990 chunk 166 optimal weight: 3.9990 chunk 243 optimal weight: 0.8980 chunk 367 optimal weight: 4.9990 chunk 338 optimal weight: 4.9990 chunk 292 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 226 optimal weight: 0.0270 chunk 179 optimal weight: 1.9990 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B6 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B6 321 ASN ** P2 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P2 457 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.170 28353 Z= 0.174 Angle : 0.513 12.534 38931 Z= 0.242 Chirality : 0.045 0.167 4527 Planarity : 0.004 0.072 5181 Dihedral : 3.647 18.283 3975 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.05 (0.14), residues: 3684 helix: 0.70 (0.21), residues: 690 sheet: 0.80 (0.20), residues: 600 loop : -0.46 (0.13), residues: 2394 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 168 time to evaluate : 3.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 171 average time/residue: 0.7090 time to fit residues: 197.9162 Evaluate side-chains 167 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 164 time to evaluate : 3.312 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.5065 time to fit residues: 6.9233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 232 optimal weight: 6.9990 chunk 311 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 269 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 81 optimal weight: 0.3980 chunk 293 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 301 optimal weight: 0.6980 chunk 37 optimal weight: 0.0980 chunk 54 optimal weight: 4.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B6 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P2 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.087246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.065819 restraints weight = 199962.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.069064 restraints weight = 85954.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.071233 restraints weight = 50717.588| |-----------------------------------------------------------------------------| r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.199 28353 Z= 0.171 Angle : 0.504 12.724 38931 Z= 0.235 Chirality : 0.045 0.198 4527 Planarity : 0.004 0.074 5181 Dihedral : 3.481 17.874 3975 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: 0.05 (0.14), residues: 3684 helix: 0.78 (0.21), residues: 696 sheet: 0.84 (0.21), residues: 600 loop : -0.38 (0.13), residues: 2388 =============================================================================== Job complete usr+sys time: 6657.26 seconds wall clock time: 115 minutes 27.60 seconds (6927.60 seconds total)