Starting phenix.real_space_refine on Sat Mar 16 10:36:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ipq_35640/03_2024/8ipq_35640.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ipq_35640/03_2024/8ipq_35640.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ipq_35640/03_2024/8ipq_35640.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ipq_35640/03_2024/8ipq_35640.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ipq_35640/03_2024/8ipq_35640.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ipq_35640/03_2024/8ipq_35640.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.060 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 9180 2.51 5 N 2608 2.21 5 O 2610 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 226": "OE1" <-> "OE2" Residue "B GLU 286": "OE1" <-> "OE2" Residue "B GLU 503": "OE1" <-> "OE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A GLU 210": "OE1" <-> "OE2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "A PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 226": "OE1" <-> "OE2" Residue "C GLU 286": "OE1" <-> "OE2" Residue "C GLU 503": "OE1" <-> "OE2" Residue "D GLU 191": "OE1" <-> "OE2" Residue "D GLU 210": "OE1" <-> "OE2" Residue "D GLU 292": "OE1" <-> "OE2" Residue "D PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14456 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3679 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 31, 'TRANS': 473} Chain breaks: 1 Chain: "A" Number of atoms: 3549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3549 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 29, 'TRANS': 463} Chain breaks: 1 Chain: "C" Number of atoms: 3679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3679 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 31, 'TRANS': 473} Chain breaks: 1 Chain: "D" Number of atoms: 3549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3549 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 29, 'TRANS': 463} Chain breaks: 1 Time building chain proxies: 7.68, per 1000 atoms: 0.53 Number of scatterers: 14456 At special positions: 0 Unit cell: (89.024, 137.28, 188.032, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 2610 8.00 N 2608 7.00 C 9180 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=0, symmetry=0 Time building additional restraints: 6.28 Conformation dependent library (CDL) restraints added in 3.0 seconds 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3644 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 8 sheets defined 70.6% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'B' and resid -5 through 24 removed outlier: 3.584A pdb=" N SER B 10 " --> pdb=" O CYS B 6 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN B 24 " --> pdb=" O GLY B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 80 removed outlier: 3.603A pdb=" N GLY B 38 " --> pdb=" O ASP B 34 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU B 39 " --> pdb=" O TRP B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 98 removed outlier: 3.908A pdb=" N LEU B 87 " --> pdb=" O SER B 83 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA B 89 " --> pdb=" O ARG B 85 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ASP B 92 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N SER B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 104 No H-bonds generated for 'chain 'B' and resid 102 through 104' Processing helix chain 'B' and resid 105 through 112 removed outlier: 3.731A pdb=" N TYR B 112 " --> pdb=" O TYR B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 134 removed outlier: 3.802A pdb=" N THR B 123 " --> pdb=" O ALA B 119 " (cutoff:3.500A) Proline residue: B 124 - end of helix Processing helix chain 'B' and resid 134 through 145 removed outlier: 3.623A pdb=" N ALA B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 159 Processing helix chain 'B' and resid 161 through 183 removed outlier: 3.657A pdb=" N ALA B 165 " --> pdb=" O GLU B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 189 removed outlier: 3.684A pdb=" N ALA B 189 " --> pdb=" O PRO B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 219 removed outlier: 3.594A pdb=" N ILE B 200 " --> pdb=" O SER B 196 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA B 201 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU B 202 " --> pdb=" O GLN B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 245 removed outlier: 4.126A pdb=" N VAL B 233 " --> pdb=" O ALA B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 276 Proline residue: B 262 - end of helix Proline residue: B 267 - end of helix removed outlier: 4.311A pdb=" N HIS B 276 " --> pdb=" O GLY B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 290 Processing helix chain 'B' and resid 335 through 344 Processing helix chain 'B' and resid 362 through 364 No H-bonds generated for 'chain 'B' and resid 362 through 364' Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.712A pdb=" N GLY B 371 " --> pdb=" O SER B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 391 Processing helix chain 'B' and resid 399 through 408 Processing helix chain 'B' and resid 409 through 416 removed outlier: 3.585A pdb=" N GLU B 415 " --> pdb=" O GLU B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 446 removed outlier: 3.679A pdb=" N GLY B 446 " --> pdb=" O VAL B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 479 Processing helix chain 'B' and resid 489 through 494 Processing helix chain 'A' and resid 7 through 16 Processing helix chain 'A' and resid 20 through 54 removed outlier: 3.877A pdb=" N PHE A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 27 " --> pdb=" O ARG A 23 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN A 54 " --> pdb=" O THR A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 105 removed outlier: 4.225A pdb=" N VAL A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 126 Processing helix chain 'A' and resid 126 through 135 removed outlier: 3.588A pdb=" N ASP A 130 " --> pdb=" O GLY A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 161 removed outlier: 3.732A pdb=" N VAL A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE A 160 " --> pdb=" O VAL A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 193 Proline residue: A 180 - end of helix removed outlier: 3.538A pdb=" N THR A 192 " --> pdb=" O HIS A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.849A pdb=" N ASP A 202 " --> pdb=" O ARG A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 218 removed outlier: 4.095A pdb=" N SER A 218 " --> pdb=" O GLU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 244 removed outlier: 4.137A pdb=" N HIS A 231 " --> pdb=" O THR A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 270 removed outlier: 4.341A pdb=" N VAL A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA A 249 " --> pdb=" O PRO A 245 " (cutoff:3.500A) Proline residue: A 253 - end of helix removed outlier: 3.648A pdb=" N ALA A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 286 Processing helix chain 'A' and resid 287 through 290 Processing helix chain 'A' and resid 293 through 297 Processing helix chain 'A' and resid 299 through 317 removed outlier: 3.679A pdb=" N LEU A 317 " --> pdb=" O ARG A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 363 Processing helix chain 'A' and resid 385 through 391 Processing helix chain 'A' and resid 398 through 410 Processing helix chain 'A' and resid 411 through 417 Processing helix chain 'A' and resid 420 through 424 removed outlier: 3.783A pdb=" N THR A 424 " --> pdb=" O GLY A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 433 removed outlier: 3.538A pdb=" N ALA A 431 " --> pdb=" O GLY A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 449 Processing helix chain 'A' and resid 467 through 477 Processing helix chain 'C' and resid -4 through 24 removed outlier: 3.584A pdb=" N SER C 10 " --> pdb=" O CYS C 6 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN C 24 " --> pdb=" O GLY C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 80 removed outlier: 3.604A pdb=" N GLY C 38 " --> pdb=" O ASP C 34 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU C 39 " --> pdb=" O TRP C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 98 removed outlier: 3.908A pdb=" N LEU C 87 " --> pdb=" O SER C 83 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA C 89 " --> pdb=" O ARG C 85 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ASP C 92 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N SER C 93 " --> pdb=" O ALA C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 104 No H-bonds generated for 'chain 'C' and resid 102 through 104' Processing helix chain 'C' and resid 105 through 112 removed outlier: 3.731A pdb=" N TYR C 112 " --> pdb=" O TYR C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 134 removed outlier: 3.802A pdb=" N THR C 123 " --> pdb=" O ALA C 119 " (cutoff:3.500A) Proline residue: C 124 - end of helix Processing helix chain 'C' and resid 134 through 145 removed outlier: 3.622A pdb=" N ALA C 138 " --> pdb=" O ASP C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 159 Processing helix chain 'C' and resid 161 through 183 removed outlier: 3.657A pdb=" N ALA C 165 " --> pdb=" O GLU C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 189 removed outlier: 3.684A pdb=" N ALA C 189 " --> pdb=" O PRO C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 219 removed outlier: 3.594A pdb=" N ILE C 200 " --> pdb=" O SER C 196 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA C 201 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU C 202 " --> pdb=" O GLN C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 245 removed outlier: 4.125A pdb=" N VAL C 233 " --> pdb=" O ALA C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 276 Proline residue: C 262 - end of helix Proline residue: C 267 - end of helix removed outlier: 4.310A pdb=" N HIS C 276 " --> pdb=" O GLY C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 290 Processing helix chain 'C' and resid 335 through 344 Processing helix chain 'C' and resid 362 through 364 No H-bonds generated for 'chain 'C' and resid 362 through 364' Processing helix chain 'C' and resid 365 through 371 removed outlier: 3.713A pdb=" N GLY C 371 " --> pdb=" O SER C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 399 through 408 Processing helix chain 'C' and resid 409 through 416 removed outlier: 3.585A pdb=" N GLU C 415 " --> pdb=" O GLU C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 446 removed outlier: 3.680A pdb=" N GLY C 446 " --> pdb=" O VAL C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 479 Processing helix chain 'C' and resid 489 through 494 Processing helix chain 'D' and resid 7 through 16 Processing helix chain 'D' and resid 20 through 54 removed outlier: 3.877A pdb=" N PHE D 24 " --> pdb=" O ARG D 20 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA D 27 " --> pdb=" O ARG D 23 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN D 54 " --> pdb=" O THR D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 105 removed outlier: 4.225A pdb=" N VAL D 63 " --> pdb=" O LEU D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 126 Processing helix chain 'D' and resid 126 through 135 removed outlier: 3.588A pdb=" N ASP D 130 " --> pdb=" O GLY D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 161 removed outlier: 3.732A pdb=" N VAL D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE D 157 " --> pdb=" O ALA D 153 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE D 160 " --> pdb=" O VAL D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 193 Proline residue: D 180 - end of helix removed outlier: 3.538A pdb=" N THR D 192 " --> pdb=" O HIS D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.849A pdb=" N ASP D 202 " --> pdb=" O ARG D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 218 removed outlier: 4.095A pdb=" N SER D 218 " --> pdb=" O GLU D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 244 removed outlier: 4.137A pdb=" N HIS D 231 " --> pdb=" O THR D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 270 removed outlier: 4.342A pdb=" N VAL D 248 " --> pdb=" O ALA D 244 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA D 249 " --> pdb=" O PRO D 245 " (cutoff:3.500A) Proline residue: D 253 - end of helix removed outlier: 3.648A pdb=" N ALA D 270 " --> pdb=" O ILE D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 286 Processing helix chain 'D' and resid 287 through 290 Processing helix chain 'D' and resid 293 through 297 Processing helix chain 'D' and resid 299 through 317 removed outlier: 3.678A pdb=" N LEU D 317 " --> pdb=" O ARG D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 363 Processing helix chain 'D' and resid 385 through 391 Processing helix chain 'D' and resid 398 through 410 Processing helix chain 'D' and resid 411 through 417 Processing helix chain 'D' and resid 420 through 424 removed outlier: 3.783A pdb=" N THR D 424 " --> pdb=" O GLY D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 433 removed outlier: 3.538A pdb=" N ALA D 431 " --> pdb=" O GLY D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 449 Processing helix chain 'D' and resid 467 through 477 Processing sheet with id=AA1, first strand: chain 'B' and resid 318 through 320 removed outlier: 3.549A pdb=" N LEU B 355 " --> pdb=" O GLU B 312 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 373 through 376 removed outlier: 3.518A pdb=" N LEU B 453 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL B 325 " --> pdb=" O HIS B 498 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N VAL B 500 " --> pdb=" O VAL B 325 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL B 327 " --> pdb=" O VAL B 500 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 385 through 386 Processing sheet with id=AA4, first strand: chain 'A' and resid 339 through 340 removed outlier: 3.503A pdb=" N LEU A 455 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 318 through 320 removed outlier: 3.549A pdb=" N LEU C 355 " --> pdb=" O GLU C 312 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 373 through 376 removed outlier: 3.518A pdb=" N LEU C 453 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL C 325 " --> pdb=" O HIS C 498 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N VAL C 500 " --> pdb=" O VAL C 325 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL C 327 " --> pdb=" O VAL C 500 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 385 through 386 Processing sheet with id=AA8, first strand: chain 'D' and resid 339 through 340 removed outlier: 3.504A pdb=" N LEU D 455 " --> pdb=" O ALA D 373 " (cutoff:3.500A) 994 hydrogen bonds defined for protein. 2922 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: 4.36 Time building geometry restraints manager: 6.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2978 1.33 - 1.45: 2963 1.45 - 1.58: 8661 1.58 - 1.70: 0 1.70 - 1.82: 98 Bond restraints: 14700 Sorted by residual: bond pdb=" C GLU C 294 " pdb=" N PRO C 295 " ideal model delta sigma weight residual 1.331 1.389 -0.057 1.20e-02 6.94e+03 2.30e+01 bond pdb=" C GLU B 294 " pdb=" N PRO B 295 " ideal model delta sigma weight residual 1.331 1.389 -0.057 1.20e-02 6.94e+03 2.29e+01 bond pdb=" CA GLU B 456 " pdb=" C GLU B 456 " ideal model delta sigma weight residual 1.524 1.570 -0.046 1.26e-02 6.30e+03 1.32e+01 bond pdb=" C GLU B 456 " pdb=" N PRO B 457 " ideal model delta sigma weight residual 1.336 1.380 -0.044 1.25e-02 6.40e+03 1.26e+01 bond pdb=" N PHE C 219 " pdb=" CA PHE C 219 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.26e-02 6.30e+03 7.37e+00 ... (remaining 14695 not shown) Histogram of bond angle deviations from ideal: 97.51 - 105.20: 394 105.20 - 112.90: 8479 112.90 - 120.59: 6369 120.59 - 128.29: 4737 128.29 - 135.98: 133 Bond angle restraints: 20112 Sorted by residual: angle pdb=" N LEU C 344 " pdb=" CA LEU C 344 " pdb=" C LEU C 344 " ideal model delta sigma weight residual 113.28 104.57 8.71 1.22e+00 6.72e-01 5.10e+01 angle pdb=" N LEU B 344 " pdb=" CA LEU B 344 " pdb=" C LEU B 344 " ideal model delta sigma weight residual 113.28 104.58 8.70 1.22e+00 6.72e-01 5.09e+01 angle pdb=" C PHE C 219 " pdb=" CA PHE C 219 " pdb=" CB PHE C 219 " ideal model delta sigma weight residual 110.56 101.08 9.48 1.69e+00 3.50e-01 3.15e+01 angle pdb=" N PRO C 295 " pdb=" CA PRO C 295 " pdb=" C PRO C 295 " ideal model delta sigma weight residual 111.03 119.55 -8.52 1.54e+00 4.22e-01 3.06e+01 angle pdb=" N PRO B 295 " pdb=" CA PRO B 295 " pdb=" C PRO B 295 " ideal model delta sigma weight residual 111.03 119.53 -8.50 1.54e+00 4.22e-01 3.05e+01 ... (remaining 20107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 7632 17.21 - 34.42: 942 34.42 - 51.63: 260 51.63 - 68.84: 20 68.84 - 86.05: 10 Dihedral angle restraints: 8864 sinusoidal: 3220 harmonic: 5644 Sorted by residual: dihedral pdb=" C THR B 299 " pdb=" N THR B 299 " pdb=" CA THR B 299 " pdb=" CB THR B 299 " ideal model delta harmonic sigma weight residual -122.00 -134.61 12.61 0 2.50e+00 1.60e-01 2.55e+01 dihedral pdb=" C THR C 299 " pdb=" N THR C 299 " pdb=" CA THR C 299 " pdb=" CB THR C 299 " ideal model delta harmonic sigma weight residual -122.00 -134.60 12.60 0 2.50e+00 1.60e-01 2.54e+01 dihedral pdb=" N THR B 299 " pdb=" C THR B 299 " pdb=" CA THR B 299 " pdb=" CB THR B 299 " ideal model delta harmonic sigma weight residual 123.40 135.58 -12.18 0 2.50e+00 1.60e-01 2.37e+01 ... (remaining 8861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 2414 0.099 - 0.198: 102 0.198 - 0.296: 2 0.296 - 0.395: 0 0.395 - 0.494: 2 Chirality restraints: 2520 Sorted by residual: chirality pdb=" CA THR B 299 " pdb=" N THR B 299 " pdb=" C THR B 299 " pdb=" CB THR B 299 " both_signs ideal model delta sigma weight residual False 2.53 2.03 0.49 2.00e-01 2.50e+01 6.10e+00 chirality pdb=" CA THR C 299 " pdb=" N THR C 299 " pdb=" C THR C 299 " pdb=" CB THR C 299 " both_signs ideal model delta sigma weight residual False 2.53 2.03 0.49 2.00e-01 2.50e+01 6.10e+00 chirality pdb=" CA PRO B 295 " pdb=" N PRO B 295 " pdb=" C PRO B 295 " pdb=" CB PRO B 295 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 2517 not shown) Planarity restraints: 2588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 343 " 0.016 2.00e-02 2.50e+03 3.34e-02 1.12e+01 pdb=" C ILE B 343 " -0.058 2.00e-02 2.50e+03 pdb=" O ILE B 343 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU B 344 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 343 " -0.016 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C ILE C 343 " 0.058 2.00e-02 2.50e+03 pdb=" O ILE C 343 " -0.022 2.00e-02 2.50e+03 pdb=" N LEU C 344 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 126 " 0.044 5.00e-02 4.00e+02 6.69e-02 7.15e+00 pdb=" N PRO A 127 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 127 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 127 " 0.037 5.00e-02 4.00e+02 ... (remaining 2585 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1903 2.75 - 3.29: 14730 3.29 - 3.82: 25155 3.82 - 4.36: 26136 4.36 - 4.90: 46398 Nonbonded interactions: 114322 Sorted by model distance: nonbonded pdb=" O ALA B 182 " pdb=" OG SER A 118 " model vdw 2.209 2.440 nonbonded pdb=" O LEU B 393 " pdb=" NE ARG A 220 " model vdw 2.230 2.520 nonbonded pdb=" O LEU C 393 " pdb=" NE ARG D 220 " model vdw 2.231 2.520 nonbonded pdb=" OD1 ASP C 134 " pdb=" NH2 ARG C 243 " model vdw 2.243 2.520 nonbonded pdb=" OD1 ASP B 134 " pdb=" NH2 ARG B 243 " model vdw 2.243 2.520 ... (remaining 114317 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 'D' } ncs_group { reference = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.580 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: 7.580 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 40.900 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14700 Z= 0.261 Angle : 0.774 11.295 20112 Z= 0.393 Chirality : 0.045 0.494 2520 Planarity : 0.006 0.107 2588 Dihedral : 16.068 86.048 5220 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.17 % Favored : 92.73 % Rotamer: Outliers : 0.61 % Allowed : 28.28 % Favored : 71.11 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.20), residues: 1980 helix: 1.51 (0.15), residues: 1304 sheet: 0.16 (0.52), residues: 120 loop : -2.46 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 375 HIS 0.005 0.001 HIS A 211 PHE 0.016 0.001 PHE A 24 TYR 0.010 0.001 TYR B 133 ARG 0.002 0.000 ARG B 85 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 266 time to evaluate : 1.585 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: B -4 TYR cc_start: 0.5522 (OUTLIER) cc_final: 0.5067 (t80) REVERT: B 212 MET cc_start: 0.8675 (tpp) cc_final: 0.8415 (tpt) REVERT: A 355 MET cc_start: 0.7854 (ptp) cc_final: 0.7559 (ptp) REVERT: C 70 GLU cc_start: 0.7682 (tm-30) cc_final: 0.7245 (tm-30) REVERT: D 215 LEU cc_start: 0.9255 (tp) cc_final: 0.8884 (tp) REVERT: D 231 HIS cc_start: 0.7020 (m170) cc_final: 0.6574 (m170) REVERT: D 299 ASP cc_start: 0.8494 (p0) cc_final: 0.6445 (t70) REVERT: D 350 LYS cc_start: 0.5662 (mtpt) cc_final: 0.5346 (mptt) REVERT: D 351 THR cc_start: 0.7983 (m) cc_final: 0.7361 (p) REVERT: D 440 ARG cc_start: 0.9002 (mtt90) cc_final: 0.8723 (ttm170) REVERT: D 456 LEU cc_start: 0.8556 (mm) cc_final: 0.8349 (mt) outliers start: 9 outliers final: 1 residues processed: 273 average time/residue: 0.2998 time to fit residues: 113.7537 Evaluate side-chains 183 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 181 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue -4 TYR Chi-restraints excluded: chain A residue 135 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 chunk 83 optimal weight: 0.4980 chunk 51 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 60 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 14700 Z= 0.322 Angle : 0.749 10.734 20112 Z= 0.359 Chirality : 0.044 0.204 2520 Planarity : 0.006 0.074 2588 Dihedral : 4.477 50.147 2151 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.78 % Favored : 92.07 % Rotamer: Outliers : 6.22 % Allowed : 25.96 % Favored : 67.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.20), residues: 1980 helix: 1.47 (0.15), residues: 1310 sheet: -0.10 (0.50), residues: 122 loop : -2.50 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 370 HIS 0.006 0.001 HIS D 380 PHE 0.025 0.002 PHE C 409 TYR 0.019 0.002 TYR D 102 ARG 0.006 0.000 ARG B 405 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 180 time to evaluate : 1.800 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: B -4 TYR cc_start: 0.5717 (OUTLIER) cc_final: 0.5054 (t80) REVERT: A 211 HIS cc_start: 0.7162 (OUTLIER) cc_final: 0.6779 (t-170) REVERT: C 376 MET cc_start: 0.7676 (tmm) cc_final: 0.7449 (tmm) REVERT: C 390 ASN cc_start: 0.6618 (OUTLIER) cc_final: 0.6245 (m-40) REVERT: D 88 ASP cc_start: 0.8927 (OUTLIER) cc_final: 0.8370 (t70) REVERT: D 102 TYR cc_start: 0.8816 (t80) cc_final: 0.8600 (t80) REVERT: D 329 VAL cc_start: 0.1640 (OUTLIER) cc_final: 0.0486 (m) outliers start: 91 outliers final: 47 residues processed: 253 average time/residue: 0.2629 time to fit residues: 97.4197 Evaluate side-chains 204 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 152 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue -4 TYR Chi-restraints excluded: chain B residue 1 VAL Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 369 TRP Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 422 THR Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 488 HIS Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 211 HIS Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 329 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 99 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 149 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 49 optimal weight: 20.0000 chunk 180 optimal weight: 3.9990 chunk 194 optimal weight: 10.0000 chunk 160 optimal weight: 0.7980 chunk 178 optimal weight: 0.8980 chunk 61 optimal weight: 0.0370 chunk 144 optimal weight: 2.9990 overall best weight: 1.1260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14700 Z= 0.218 Angle : 0.691 10.355 20112 Z= 0.324 Chirality : 0.042 0.248 2520 Planarity : 0.005 0.073 2588 Dihedral : 4.376 52.351 2151 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.63 % Favored : 92.22 % Rotamer: Outliers : 3.76 % Allowed : 28.89 % Favored : 67.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.20), residues: 1980 helix: 1.58 (0.15), residues: 1308 sheet: -0.20 (0.50), residues: 122 loop : -2.50 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP C 370 HIS 0.005 0.001 HIS D 380 PHE 0.016 0.001 PHE D 24 TYR 0.016 0.002 TYR C 108 ARG 0.005 0.000 ARG D 216 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 166 time to evaluate : 1.598 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: B -4 TYR cc_start: 0.5565 (OUTLIER) cc_final: 0.4984 (t80) REVERT: B 376 MET cc_start: 0.7977 (tmm) cc_final: 0.7699 (tmm) REVERT: A 211 HIS cc_start: 0.7086 (OUTLIER) cc_final: 0.6635 (t-170) REVERT: C 336 LYS cc_start: 0.6808 (mttp) cc_final: 0.6410 (mttt) REVERT: C 369 TRP cc_start: 0.6833 (t60) cc_final: 0.6599 (t60) REVERT: C 390 ASN cc_start: 0.6680 (OUTLIER) cc_final: 0.6363 (t0) REVERT: C 409 PHE cc_start: 0.7707 (t80) cc_final: 0.7397 (t80) REVERT: D 329 VAL cc_start: 0.0823 (OUTLIER) cc_final: 0.0615 (m) REVERT: D 353 MET cc_start: 0.8098 (mmm) cc_final: 0.7883 (mmp) REVERT: D 355 MET cc_start: 0.7220 (OUTLIER) cc_final: 0.6851 (ppp) REVERT: D 359 ASP cc_start: 0.8893 (t70) cc_final: 0.8355 (m-30) outliers start: 55 outliers final: 31 residues processed: 213 average time/residue: 0.2455 time to fit residues: 77.8468 Evaluate side-chains 189 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 153 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue -4 TYR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 422 THR Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 211 HIS Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 313 ARG Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 355 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 0.8980 chunk 135 optimal weight: 4.9990 chunk 93 optimal weight: 20.0000 chunk 19 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 180 optimal weight: 7.9990 chunk 191 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 chunk 171 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 389 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14700 Z= 0.288 Angle : 0.714 12.650 20112 Z= 0.338 Chirality : 0.043 0.239 2520 Planarity : 0.006 0.081 2588 Dihedral : 4.426 55.933 2151 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.53 % Favored : 92.32 % Rotamer: Outliers : 6.08 % Allowed : 28.01 % Favored : 65.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.20), residues: 1980 helix: 1.43 (0.15), residues: 1324 sheet: -0.40 (0.50), residues: 122 loop : -2.54 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 370 HIS 0.007 0.001 HIS D 211 PHE 0.023 0.001 PHE C 55 TYR 0.019 0.002 TYR D 102 ARG 0.012 0.000 ARG C 372 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 153 time to evaluate : 1.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B -4 TYR cc_start: 0.5615 (OUTLIER) cc_final: 0.4988 (t80) REVERT: B 113 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8457 (mp) REVERT: B 133 TYR cc_start: 0.8300 (m-80) cc_final: 0.7184 (m-80) REVERT: A 82 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8500 (tm-30) REVERT: A 426 LEU cc_start: 0.7480 (tt) cc_final: 0.7042 (pp) REVERT: C 212 MET cc_start: 0.8760 (mmm) cc_final: 0.8452 (mmm) REVERT: C 390 ASN cc_start: 0.6608 (OUTLIER) cc_final: 0.6270 (t0) REVERT: D 182 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7557 (tp) REVERT: D 215 LEU cc_start: 0.9147 (mt) cc_final: 0.8806 (tp) REVERT: D 353 MET cc_start: 0.8213 (mmm) cc_final: 0.7823 (mmp) REVERT: D 355 MET cc_start: 0.7292 (OUTLIER) cc_final: 0.7068 (ppp) REVERT: D 380 HIS cc_start: 0.6957 (t70) cc_final: 0.6521 (t70) outliers start: 89 outliers final: 62 residues processed: 228 average time/residue: 0.2367 time to fit residues: 81.8885 Evaluate side-chains 212 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 144 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue -4 TYR Chi-restraints excluded: chain B residue 1 VAL Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 369 TRP Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 422 THR Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 211 HIS Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 504 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 159 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 142 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 171 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN C 435 GLN ** C 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14700 Z= 0.267 Angle : 0.694 13.199 20112 Z= 0.326 Chirality : 0.042 0.145 2520 Planarity : 0.005 0.084 2588 Dihedral : 4.410 59.541 2151 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.58 % Favored : 92.27 % Rotamer: Outliers : 6.01 % Allowed : 28.89 % Favored : 65.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.20), residues: 1980 helix: 1.39 (0.14), residues: 1324 sheet: -0.39 (0.51), residues: 112 loop : -2.52 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 370 HIS 0.007 0.001 HIS D 211 PHE 0.019 0.001 PHE D 24 TYR 0.018 0.002 TYR D 102 ARG 0.005 0.000 ARG B 436 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 152 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B -4 TYR cc_start: 0.5516 (OUTLIER) cc_final: 0.5029 (t80) REVERT: B 113 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8472 (mp) REVERT: B 133 TYR cc_start: 0.8335 (m-80) cc_final: 0.7030 (m-80) REVERT: B 376 MET cc_start: 0.8032 (tmm) cc_final: 0.7513 (tmm) REVERT: B 460 HIS cc_start: 0.3829 (OUTLIER) cc_final: 0.2925 (m170) REVERT: A 82 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8514 (tm-30) REVERT: A 426 LEU cc_start: 0.7697 (tt) cc_final: 0.7197 (pp) REVERT: C 74 GLN cc_start: 0.7733 (mm110) cc_final: 0.7532 (mm110) REVERT: C 157 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8236 (mt) REVERT: C 250 THR cc_start: 0.7865 (OUTLIER) cc_final: 0.7563 (p) REVERT: C 390 ASN cc_start: 0.6519 (OUTLIER) cc_final: 0.6030 (m-40) REVERT: C 409 PHE cc_start: 0.7841 (t80) cc_final: 0.7515 (t80) REVERT: D 88 ASP cc_start: 0.8970 (OUTLIER) cc_final: 0.8288 (t70) REVERT: D 115 ARG cc_start: 0.7631 (mtm-85) cc_final: 0.7280 (ptp-170) REVERT: D 182 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7614 (tp) REVERT: D 215 LEU cc_start: 0.9155 (mt) cc_final: 0.8832 (tp) REVERT: D 353 MET cc_start: 0.8166 (mmm) cc_final: 0.7926 (mmm) REVERT: D 355 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.7224 (ppp) REVERT: D 362 ASN cc_start: 0.8518 (m-40) cc_final: 0.7797 (t0) REVERT: D 380 HIS cc_start: 0.6997 (t70) cc_final: 0.6596 (t70) outliers start: 88 outliers final: 63 residues processed: 226 average time/residue: 0.2378 time to fit residues: 81.6896 Evaluate side-chains 218 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 145 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue -4 TYR Chi-restraints excluded: chain B residue 1 VAL Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 369 TRP Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 460 HIS Chi-restraints excluded: chain B residue 488 HIS Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 422 THR Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain D residue 60 ASP Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 211 HIS Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 504 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 64 optimal weight: 0.9980 chunk 172 optimal weight: 5.9990 chunk 37 optimal weight: 0.0270 chunk 112 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 191 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN ** C 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN D 200 GLN D 470 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14700 Z= 0.200 Angle : 0.673 11.064 20112 Z= 0.312 Chirality : 0.041 0.318 2520 Planarity : 0.005 0.076 2588 Dihedral : 4.307 59.333 2151 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.68 % Favored : 92.12 % Rotamer: Outliers : 5.40 % Allowed : 29.71 % Favored : 64.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.20), residues: 1980 helix: 1.55 (0.15), residues: 1312 sheet: -0.60 (0.49), residues: 122 loop : -2.40 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 375 HIS 0.007 0.001 HIS D 211 PHE 0.019 0.001 PHE D 24 TYR 0.019 0.002 TYR D 102 ARG 0.007 0.000 ARG D 469 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 150 time to evaluate : 1.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B -4 TYR cc_start: 0.5526 (OUTLIER) cc_final: 0.4940 (t80) REVERT: B 113 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8438 (mp) REVERT: B 376 MET cc_start: 0.8076 (tmm) cc_final: 0.7871 (tmm) REVERT: B 460 HIS cc_start: 0.3774 (OUTLIER) cc_final: 0.2848 (m170) REVERT: A 82 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8492 (tm-30) REVERT: C 157 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8366 (mp) REVERT: C 390 ASN cc_start: 0.6397 (OUTLIER) cc_final: 0.6004 (m-40) REVERT: D 88 ASP cc_start: 0.8988 (OUTLIER) cc_final: 0.8300 (t70) REVERT: D 115 ARG cc_start: 0.7593 (mtm-85) cc_final: 0.7362 (ptp90) REVERT: D 182 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7617 (tp) REVERT: D 215 LEU cc_start: 0.9159 (mt) cc_final: 0.8783 (tp) REVERT: D 353 MET cc_start: 0.8092 (mmm) cc_final: 0.7756 (mmm) REVERT: D 355 MET cc_start: 0.7487 (OUTLIER) cc_final: 0.7226 (ppp) REVERT: D 362 ASN cc_start: 0.8512 (m-40) cc_final: 0.7760 (t0) REVERT: D 380 HIS cc_start: 0.7039 (t70) cc_final: 0.6628 (t70) outliers start: 79 outliers final: 56 residues processed: 218 average time/residue: 0.2200 time to fit residues: 74.1765 Evaluate side-chains 209 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 144 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue -4 TYR Chi-restraints excluded: chain B residue 1 VAL Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 460 HIS Chi-restraints excluded: chain B residue 488 HIS Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 422 THR Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 60 ASP Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 211 HIS Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 504 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 139 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 chunk 161 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 190 optimal weight: 20.0000 chunk 119 optimal weight: 0.5980 chunk 116 optimal weight: 0.8980 chunk 88 optimal weight: 0.0020 overall best weight: 1.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 437 GLN ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 470 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14700 Z= 0.217 Angle : 0.683 10.856 20112 Z= 0.316 Chirality : 0.041 0.195 2520 Planarity : 0.005 0.079 2588 Dihedral : 4.281 58.188 2151 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.37 % Favored : 92.42 % Rotamer: Outliers : 5.60 % Allowed : 29.78 % Favored : 64.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.20), residues: 1980 helix: 1.58 (0.15), residues: 1310 sheet: -0.46 (0.51), residues: 112 loop : -2.39 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 375 HIS 0.007 0.001 HIS D 211 PHE 0.018 0.001 PHE D 24 TYR 0.021 0.002 TYR D 102 ARG 0.003 0.000 ARG D 439 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 145 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B -4 TYR cc_start: 0.5585 (OUTLIER) cc_final: 0.4933 (t80) REVERT: B 39 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8650 (mp) REVERT: B 113 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8492 (mp) REVERT: B 376 MET cc_start: 0.8099 (tmm) cc_final: 0.7839 (tmm) REVERT: B 460 HIS cc_start: 0.3812 (OUTLIER) cc_final: 0.2812 (m170) REVERT: A 82 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8488 (tm-30) REVERT: C 157 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8388 (mp) REVERT: C 250 THR cc_start: 0.7800 (OUTLIER) cc_final: 0.7557 (p) REVERT: C 390 ASN cc_start: 0.6353 (OUTLIER) cc_final: 0.5679 (m110) REVERT: D 88 ASP cc_start: 0.9001 (OUTLIER) cc_final: 0.8296 (t70) REVERT: D 182 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7614 (tp) REVERT: D 215 LEU cc_start: 0.9164 (mt) cc_final: 0.8785 (tp) REVERT: D 353 MET cc_start: 0.8013 (mmm) cc_final: 0.7712 (mmm) REVERT: D 355 MET cc_start: 0.7545 (OUTLIER) cc_final: 0.7249 (ppp) REVERT: D 362 ASN cc_start: 0.8499 (m-40) cc_final: 0.7810 (t0) REVERT: D 380 HIS cc_start: 0.6954 (t70) cc_final: 0.6561 (t70) outliers start: 82 outliers final: 64 residues processed: 216 average time/residue: 0.2330 time to fit residues: 77.5578 Evaluate side-chains 217 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 142 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue -4 TYR Chi-restraints excluded: chain B residue 1 VAL Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 460 HIS Chi-restraints excluded: chain B residue 488 HIS Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 422 THR Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 60 ASP Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 211 HIS Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 313 ARG Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 506 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 118 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 121 optimal weight: 0.9990 chunk 130 optimal weight: 20.0000 chunk 94 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 150 optimal weight: 4.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 GLN A 54 GLN ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 287 GLN D 470 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 14700 Z= 0.372 Angle : 0.762 11.156 20112 Z= 0.363 Chirality : 0.044 0.282 2520 Planarity : 0.006 0.087 2588 Dihedral : 4.459 53.160 2151 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.68 % Favored : 92.17 % Rotamer: Outliers : 6.49 % Allowed : 29.23 % Favored : 64.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.20), residues: 1980 helix: 1.32 (0.15), residues: 1314 sheet: -0.47 (0.52), residues: 112 loop : -2.43 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 375 HIS 0.006 0.001 HIS A 211 PHE 0.022 0.002 PHE C 55 TYR 0.021 0.003 TYR C 108 ARG 0.014 0.001 ARG C 58 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 145 time to evaluate : 1.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B -4 TYR cc_start: 0.5771 (OUTLIER) cc_final: 0.5034 (t80) REVERT: B 39 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8588 (mp) REVERT: B 113 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8578 (mp) REVERT: B 133 TYR cc_start: 0.8520 (m-80) cc_final: 0.7243 (m-80) REVERT: B 376 MET cc_start: 0.8154 (tmm) cc_final: 0.7881 (tmm) REVERT: B 460 HIS cc_start: 0.3760 (OUTLIER) cc_final: 0.2585 (m170) REVERT: A 355 MET cc_start: 0.8100 (ptp) cc_final: 0.7861 (ptp) REVERT: A 499 PHE cc_start: 0.5617 (OUTLIER) cc_final: 0.4817 (t80) REVERT: C 147 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8225 (mp) REVERT: C 157 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8273 (mt) REVERT: C 250 THR cc_start: 0.8053 (OUTLIER) cc_final: 0.7831 (p) REVERT: C 375 TRP cc_start: 0.7424 (t-100) cc_final: 0.6868 (t-100) REVERT: D 88 ASP cc_start: 0.8929 (OUTLIER) cc_final: 0.8275 (t70) REVERT: D 118 SER cc_start: 0.7436 (p) cc_final: 0.7166 (p) REVERT: D 182 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7718 (tp) REVERT: D 215 LEU cc_start: 0.9185 (mt) cc_final: 0.8760 (tp) REVERT: D 355 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.7325 (ppp) REVERT: D 362 ASN cc_start: 0.8590 (m-40) cc_final: 0.7855 (t0) REVERT: D 380 HIS cc_start: 0.6994 (t70) cc_final: 0.6624 (t-90) outliers start: 95 outliers final: 63 residues processed: 231 average time/residue: 0.2332 time to fit residues: 83.3890 Evaluate side-chains 217 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 143 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue -4 TYR Chi-restraints excluded: chain B residue 1 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 460 HIS Chi-restraints excluded: chain B residue 488 HIS Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 499 PHE Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 422 THR Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 60 ASP Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 211 HIS Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 506 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 0.7980 chunk 182 optimal weight: 5.9990 chunk 166 optimal weight: 0.9980 chunk 177 optimal weight: 3.9990 chunk 107 optimal weight: 0.0470 chunk 77 optimal weight: 2.9990 chunk 139 optimal weight: 7.9990 chunk 54 optimal weight: 0.5980 chunk 160 optimal weight: 0.8980 chunk 168 optimal weight: 20.0000 chunk 116 optimal weight: 3.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 GLN A 54 GLN A 82 GLN ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN D 470 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14700 Z= 0.196 Angle : 0.704 13.050 20112 Z= 0.322 Chirality : 0.041 0.275 2520 Planarity : 0.005 0.081 2588 Dihedral : 4.298 52.733 2151 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.32 % Favored : 92.47 % Rotamer: Outliers : 4.10 % Allowed : 31.49 % Favored : 64.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.20), residues: 1980 helix: 1.51 (0.15), residues: 1306 sheet: -0.29 (0.55), residues: 100 loop : -2.36 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 375 HIS 0.006 0.001 HIS A 211 PHE 0.020 0.001 PHE D 24 TYR 0.020 0.002 TYR D 102 ARG 0.009 0.000 ARG C 58 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 146 time to evaluate : 1.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B -4 TYR cc_start: 0.5532 (OUTLIER) cc_final: 0.5001 (t80) REVERT: B 39 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8609 (mp) REVERT: B 376 MET cc_start: 0.8086 (tmm) cc_final: 0.7623 (tmm) REVERT: B 460 HIS cc_start: 0.3795 (OUTLIER) cc_final: 0.2658 (m170) REVERT: A 305 MET cc_start: 0.8030 (mmm) cc_final: 0.7622 (mmt) REVERT: A 355 MET cc_start: 0.8101 (ptp) cc_final: 0.7865 (ptp) REVERT: A 499 PHE cc_start: 0.5643 (OUTLIER) cc_final: 0.4918 (t80) REVERT: C 157 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8415 (mp) REVERT: C 250 THR cc_start: 0.7726 (OUTLIER) cc_final: 0.7474 (p) REVERT: C 375 TRP cc_start: 0.7313 (t-100) cc_final: 0.6706 (t-100) REVERT: D 88 ASP cc_start: 0.9005 (OUTLIER) cc_final: 0.8389 (t0) REVERT: D 118 SER cc_start: 0.7512 (p) cc_final: 0.6933 (t) REVERT: D 182 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7691 (tp) REVERT: D 215 LEU cc_start: 0.9162 (mt) cc_final: 0.8747 (tp) REVERT: D 355 MET cc_start: 0.7523 (OUTLIER) cc_final: 0.7248 (ppp) REVERT: D 362 ASN cc_start: 0.8566 (m-40) cc_final: 0.7880 (t0) REVERT: D 380 HIS cc_start: 0.6968 (t70) cc_final: 0.6580 (t70) outliers start: 60 outliers final: 43 residues processed: 198 average time/residue: 0.2386 time to fit residues: 71.9086 Evaluate side-chains 192 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 140 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue -4 TYR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 460 HIS Chi-restraints excluded: chain B residue 488 HIS Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 499 PHE Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 422 THR Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 211 HIS Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 313 ARG Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 506 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 188 optimal weight: 20.0000 chunk 114 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 130 optimal weight: 20.0000 chunk 197 optimal weight: 0.6980 chunk 181 optimal weight: 6.9990 chunk 157 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 121 optimal weight: 0.9990 chunk 96 optimal weight: 8.9990 chunk 124 optimal weight: 0.5980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 470 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14700 Z= 0.216 Angle : 0.720 13.923 20112 Z= 0.327 Chirality : 0.042 0.276 2520 Planarity : 0.005 0.081 2588 Dihedral : 4.278 51.317 2151 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.37 % Favored : 92.42 % Rotamer: Outliers : 3.89 % Allowed : 31.76 % Favored : 64.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.20), residues: 1980 helix: 1.52 (0.15), residues: 1306 sheet: -0.25 (0.56), residues: 100 loop : -2.34 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 375 HIS 0.006 0.001 HIS A 211 PHE 0.027 0.001 PHE C 409 TYR 0.020 0.002 TYR C 108 ARG 0.012 0.000 ARG C 86 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 146 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B -4 TYR cc_start: 0.5535 (OUTLIER) cc_final: 0.5104 (t80) REVERT: B 133 TYR cc_start: 0.8371 (m-80) cc_final: 0.6951 (m-80) REVERT: B 376 MET cc_start: 0.8093 (tmm) cc_final: 0.7584 (tmm) REVERT: B 460 HIS cc_start: 0.3685 (OUTLIER) cc_final: 0.2423 (m170) REVERT: B 502 MET cc_start: 0.3221 (mmp) cc_final: 0.1636 (ttt) REVERT: A 355 MET cc_start: 0.8069 (ptp) cc_final: 0.7835 (ptp) REVERT: A 407 ASP cc_start: 0.9177 (OUTLIER) cc_final: 0.8936 (p0) REVERT: A 499 PHE cc_start: 0.5594 (OUTLIER) cc_final: 0.4835 (t80) REVERT: C 70 GLU cc_start: 0.7251 (mm-30) cc_final: 0.6801 (tp30) REVERT: C 157 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8467 (mp) REVERT: C 250 THR cc_start: 0.7630 (OUTLIER) cc_final: 0.7376 (p) REVERT: C 375 TRP cc_start: 0.7320 (t-100) cc_final: 0.6797 (t-100) REVERT: D 88 ASP cc_start: 0.9010 (OUTLIER) cc_final: 0.8412 (t0) REVERT: D 118 SER cc_start: 0.7508 (p) cc_final: 0.6942 (t) REVERT: D 182 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7679 (tp) REVERT: D 362 ASN cc_start: 0.8595 (m-40) cc_final: 0.8017 (t0) REVERT: D 380 HIS cc_start: 0.6985 (t70) cc_final: 0.6599 (t70) outliers start: 57 outliers final: 44 residues processed: 197 average time/residue: 0.2323 time to fit residues: 69.9060 Evaluate side-chains 193 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 141 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue -4 TYR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 460 HIS Chi-restraints excluded: chain B residue 488 HIS Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 499 PHE Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 422 THR Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 60 ASP Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 211 HIS Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 506 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 0.5980 chunk 48 optimal weight: 40.0000 chunk 144 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 43 optimal weight: 10.0000 chunk 157 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 19 optimal weight: 0.0570 chunk 28 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 370 GLN D 470 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.178079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.105916 restraints weight = 24512.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.108255 restraints weight = 13273.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.107726 restraints weight = 8108.800| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14700 Z= 0.191 Angle : 0.714 14.251 20112 Z= 0.323 Chirality : 0.042 0.266 2520 Planarity : 0.005 0.080 2588 Dihedral : 4.192 50.470 2151 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.42 % Favored : 92.37 % Rotamer: Outliers : 3.62 % Allowed : 32.10 % Favored : 64.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.20), residues: 1980 helix: 1.57 (0.15), residues: 1308 sheet: -0.19 (0.56), residues: 100 loop : -2.42 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 375 HIS 0.007 0.001 HIS D 211 PHE 0.020 0.001 PHE D 24 TYR 0.019 0.002 TYR C 108 ARG 0.007 0.000 ARG C 58 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2918.83 seconds wall clock time: 53 minutes 4.68 seconds (3184.68 seconds total)