Starting phenix.real_space_refine on Sun Apr 14 01:57:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d46_27176/04_2024/8d46_27176.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d46_27176/04_2024/8d46_27176.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d46_27176/04_2024/8d46_27176.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d46_27176/04_2024/8d46_27176.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d46_27176/04_2024/8d46_27176.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d46_27176/04_2024/8d46_27176.pdb" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 76 5.16 5 C 9640 2.51 5 N 2556 2.21 5 O 2838 1.98 5 H 15096 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 28": "OE1" <-> "OE2" Residue "A GLU 46": "OE1" <-> "OE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A GLU 480": "OE1" <-> "OE2" Residue "A GLU 488": "OE1" <-> "OE2" Residue "C GLU 48": "OE1" <-> "OE2" Residue "C GLU 318": "OE1" <-> "OE2" Residue "C GLU 349": "OE1" <-> "OE2" Residue "C GLU 364": "OE1" <-> "OE2" Residue "C GLU 369": "OE1" <-> "OE2" Residue "C GLU 399": "OE1" <-> "OE2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D GLU 48": "OE1" <-> "OE2" Residue "D ASP 122": "OD1" <-> "OD2" Residue "D GLU 269": "OE1" <-> "OE2" Residue "D GLU 325": "OE1" <-> "OE2" Residue "D GLU 359": "OE1" <-> "OE2" Residue "D GLU 369": "OE1" <-> "OE2" Residue "D GLU 399": "OE1" <-> "OE2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B GLU 46": "OE1" <-> "OE2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B GLU 318": "OE1" <-> "OE2" Residue "B GLU 480": "OE1" <-> "OE2" Residue "B GLU 488": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 30206 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 7486 Classifications: {'peptide': 485} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 462} Chain: "C" Number of atoms: 7616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 7616 Classifications: {'peptide': 493} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 469} Chain: "D" Number of atoms: 7618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 7618 Classifications: {'peptide': 493} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 469} Chain: "B" Number of atoms: 7486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 7486 Classifications: {'peptide': 485} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 462} Time building chain proxies: 13.04, per 1000 atoms: 0.43 Number of scatterers: 30206 At special positions: 0 Unit cell: (105.93, 112.35, 100.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 76 16.00 O 2838 8.00 N 2556 7.00 C 9640 6.00 H 15096 1.00 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: 26.27 Conformation dependent library (CDL) restraints added in 3.0 seconds 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3536 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 19 sheets defined 44.4% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.43 Creating SS restraints... Processing helix chain 'A' and resid 56 through 71 Processing helix chain 'A' and resid 81 through 99 Processing helix chain 'A' and resid 99 through 112 Processing helix chain 'A' and resid 114 through 121 removed outlier: 3.610A pdb=" N ASN A 121 " --> pdb=" O ASN A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 136 Processing helix chain 'A' and resid 171 through 187 Proline residue: A 182 - end of helix Processing helix chain 'A' and resid 199 through 213 Processing helix chain 'A' and resid 228 through 236 Processing helix chain 'A' and resid 247 through 261 Processing helix chain 'A' and resid 283 through 297 removed outlier: 3.601A pdb=" N VAL A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 301 Processing helix chain 'A' and resid 312 through 330 removed outlier: 4.469A pdb=" N ASP A 317 " --> pdb=" O GLU A 313 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N GLU A 318 " --> pdb=" O SER A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 364 Processing helix chain 'A' and resid 394 through 399 removed outlier: 3.525A pdb=" N LYS A 398 " --> pdb=" O MET A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 422 Processing helix chain 'A' and resid 436 through 447 Processing helix chain 'A' and resid 479 through 483 Processing helix chain 'C' and resid 56 through 71 removed outlier: 3.718A pdb=" N ALA C 66 " --> pdb=" O LYS C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 80 Processing helix chain 'C' and resid 81 through 99 Processing helix chain 'C' and resid 99 through 112 Processing helix chain 'C' and resid 114 through 121 Processing helix chain 'C' and resid 121 through 137 Processing helix chain 'C' and resid 171 through 186 Proline residue: C 182 - end of helix Processing helix chain 'C' and resid 199 through 213 removed outlier: 3.654A pdb=" N LEU C 203 " --> pdb=" O PRO C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 236 Processing helix chain 'C' and resid 247 through 261 Processing helix chain 'C' and resid 283 through 297 Processing helix chain 'C' and resid 315 through 329 removed outlier: 3.737A pdb=" N GLU C 325 " --> pdb=" O ARG C 321 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS C 329 " --> pdb=" O GLU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 365 Processing helix chain 'C' and resid 394 through 398 Processing helix chain 'C' and resid 413 through 423 Processing helix chain 'C' and resid 437 through 447 removed outlier: 3.688A pdb=" N ILE C 441 " --> pdb=" O ILE C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 485 removed outlier: 3.634A pdb=" N GLU C 485 " --> pdb=" O TYR C 481 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 71 removed outlier: 3.729A pdb=" N ALA D 66 " --> pdb=" O LYS D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 80 Processing helix chain 'D' and resid 81 through 99 Processing helix chain 'D' and resid 99 through 112 Processing helix chain 'D' and resid 114 through 121 Processing helix chain 'D' and resid 121 through 137 Processing helix chain 'D' and resid 171 through 187 Proline residue: D 182 - end of helix Processing helix chain 'D' and resid 199 through 213 removed outlier: 3.654A pdb=" N LEU D 203 " --> pdb=" O PRO D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 236 Processing helix chain 'D' and resid 247 through 261 Processing helix chain 'D' and resid 283 through 297 Processing helix chain 'D' and resid 315 through 329 removed outlier: 3.505A pdb=" N LYS D 329 " --> pdb=" O GLU D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 365 Processing helix chain 'D' and resid 394 through 398 Processing helix chain 'D' and resid 413 through 422 Processing helix chain 'D' and resid 437 through 447 removed outlier: 3.683A pdb=" N ILE D 441 " --> pdb=" O ILE D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 486 Processing helix chain 'B' and resid 56 through 71 Processing helix chain 'B' and resid 81 through 99 Processing helix chain 'B' and resid 99 through 112 Processing helix chain 'B' and resid 114 through 121 removed outlier: 3.610A pdb=" N ASN B 121 " --> pdb=" O ASN B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 136 Processing helix chain 'B' and resid 171 through 187 Proline residue: B 182 - end of helix Processing helix chain 'B' and resid 199 through 213 Processing helix chain 'B' and resid 228 through 236 Processing helix chain 'B' and resid 247 through 261 Processing helix chain 'B' and resid 283 through 297 removed outlier: 3.602A pdb=" N VAL B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 301 Processing helix chain 'B' and resid 312 through 330 removed outlier: 4.469A pdb=" N ASP B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N GLU B 318 " --> pdb=" O SER B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 364 Processing helix chain 'B' and resid 394 through 399 removed outlier: 3.524A pdb=" N LYS B 398 " --> pdb=" O MET B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 422 Processing helix chain 'B' and resid 436 through 447 Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 25 Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 41 removed outlier: 4.361A pdb=" N CYS A 50 " --> pdb=" O VAL A 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 144 through 145 removed outlier: 4.221A pdb=" N THR A 153 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N VAL B 452 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N THR A 491 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N VAL B 454 " --> pdb=" O THR A 491 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N THR A 493 " --> pdb=" O VAL B 454 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 219 through 221 removed outlier: 6.216A pdb=" N VAL A 190 " --> pdb=" O ASN A 220 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N CYS A 163 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LYS A 193 " --> pdb=" O CYS A 163 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N GLN A 165 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL A 242 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N GLU A 269 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N PHE A 244 " --> pdb=" O GLU A 269 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 308 through 311 removed outlier: 4.123A pdb=" N THR B 153 " --> pdb=" O ILE B 145 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 385 through 386 removed outlier: 7.300A pdb=" N THR A 385 " --> pdb=" O GLN A 406 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 23 through 25 Processing sheet with id=AA8, first strand: chain 'C' and resid 37 through 41 removed outlier: 5.663A pdb=" N PHE C 38 " --> pdb=" O GLN C 51 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLN C 51 " --> pdb=" O PHE C 38 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL C 40 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 144 through 145 removed outlier: 4.325A pdb=" N THR C 153 " --> pdb=" O ILE C 145 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N VAL D 452 " --> pdb=" O VAL C 489 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N THR C 491 " --> pdb=" O VAL D 452 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N VAL D 454 " --> pdb=" O THR C 491 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N THR C 493 " --> pdb=" O VAL D 454 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ALA D 430 " --> pdb=" O TRP D 453 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N SER D 274 " --> pdb=" O ALA D 306 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N SER D 307 " --> pdb=" O GLN D 407 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N MET D 409 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ILE D 309 " --> pdb=" O MET D 409 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N PHE D 411 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N VAL D 311 " --> pdb=" O PHE D 411 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LYS D 410 " --> pdb=" O ASN D 389 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL D 386 " --> pdb=" O GLU D 369 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 219 through 221 removed outlier: 6.623A pdb=" N CYS C 163 " --> pdb=" O VAL C 191 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LYS C 193 " --> pdb=" O CYS C 163 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLN C 165 " --> pdb=" O LYS C 193 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 367 through 368 removed outlier: 6.654A pdb=" N LYS C 410 " --> pdb=" O ASN C 389 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N SER C 307 " --> pdb=" O GLN C 407 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N MET C 409 " --> pdb=" O SER C 307 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ILE C 309 " --> pdb=" O MET C 409 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N PHE C 411 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N VAL C 311 " --> pdb=" O PHE C 411 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N SER C 274 " --> pdb=" O ALA C 306 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ALA C 430 " --> pdb=" O TRP C 453 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N THR D 153 " --> pdb=" O ILE D 145 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 23 through 25 Processing sheet with id=AB4, first strand: chain 'D' and resid 37 through 41 removed outlier: 5.632A pdb=" N PHE D 38 " --> pdb=" O GLN D 51 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLN D 51 " --> pdb=" O PHE D 38 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL D 40 " --> pdb=" O LEU D 49 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 219 through 221 removed outlier: 6.608A pdb=" N CYS D 163 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N LYS D 193 " --> pdb=" O CYS D 163 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLN D 165 " --> pdb=" O LYS D 193 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 374 through 375 removed outlier: 4.182A pdb=" N PHE D 381 " --> pdb=" O TRP D 375 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 23 through 25 Processing sheet with id=AB8, first strand: chain 'B' and resid 37 through 41 removed outlier: 4.360A pdb=" N CYS B 50 " --> pdb=" O VAL B 40 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 219 through 221 removed outlier: 6.216A pdb=" N VAL B 190 " --> pdb=" O ASN B 220 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N CYS B 163 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LYS B 193 " --> pdb=" O CYS B 163 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N GLN B 165 " --> pdb=" O LYS B 193 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL B 242 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N GLU B 269 " --> pdb=" O VAL B 242 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N PHE B 244 " --> pdb=" O GLU B 269 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 385 through 386 removed outlier: 7.300A pdb=" N THR B 385 " --> pdb=" O GLN B 406 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 721 hydrogen bonds defined for protein. 2094 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: 11.65 Time building geometry restraints manager: 27.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 15052 1.01 - 1.21: 54 1.21 - 1.41: 6269 1.41 - 1.61: 9049 1.61 - 1.81: 108 Bond restraints: 30532 Sorted by residual: bond pdb=" SG CYS A 303 " pdb=" HG CYS A 303 " ideal model delta sigma weight residual 1.200 1.340 -0.140 2.00e-02 2.50e+03 4.87e+01 bond pdb=" SG CYS A 276 " pdb=" HG CYS A 276 " ideal model delta sigma weight residual 1.200 1.339 -0.139 2.00e-02 2.50e+03 4.85e+01 bond pdb=" SG CYS B 303 " pdb=" HG CYS B 303 " ideal model delta sigma weight residual 1.200 1.338 -0.138 2.00e-02 2.50e+03 4.79e+01 bond pdb=" SG CYS B 456 " pdb=" HG CYS B 456 " ideal model delta sigma weight residual 1.200 1.338 -0.138 2.00e-02 2.50e+03 4.74e+01 bond pdb=" SG CYS A 456 " pdb=" HG CYS A 456 " ideal model delta sigma weight residual 1.200 1.337 -0.137 2.00e-02 2.50e+03 4.71e+01 ... (remaining 30527 not shown) Histogram of bond angle deviations from ideal: 98.46 - 105.61: 381 105.61 - 112.77: 35769 112.77 - 119.93: 8417 119.93 - 127.09: 10573 127.09 - 134.24: 191 Bond angle restraints: 55331 Sorted by residual: angle pdb=" N ILE D 140 " pdb=" CA ILE D 140 " pdb=" C ILE D 140 " ideal model delta sigma weight residual 108.89 100.23 8.66 1.32e+00 5.74e-01 4.31e+01 angle pdb=" N THR C 144 " pdb=" CA THR C 144 " pdb=" C THR C 144 " ideal model delta sigma weight residual 108.73 98.46 10.27 1.63e+00 3.76e-01 3.97e+01 angle pdb=" N ILE C 140 " pdb=" CA ILE C 140 " pdb=" C ILE C 140 " ideal model delta sigma weight residual 108.89 100.66 8.23 1.32e+00 5.74e-01 3.89e+01 angle pdb=" N THR D 144 " pdb=" CA THR D 144 " pdb=" C THR D 144 " ideal model delta sigma weight residual 108.73 98.70 10.03 1.63e+00 3.76e-01 3.79e+01 angle pdb=" N LYS A 273 " pdb=" CA LYS A 273 " pdb=" C LYS A 273 " ideal model delta sigma weight residual 108.20 99.05 9.15 1.71e+00 3.42e-01 2.86e+01 ... (remaining 55326 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 12444 17.94 - 35.87: 1294 35.87 - 53.81: 437 53.81 - 71.75: 131 71.75 - 89.68: 27 Dihedral angle restraints: 14333 sinusoidal: 7821 harmonic: 6512 Sorted by residual: dihedral pdb=" CA PRO A 168 " pdb=" C PRO A 168 " pdb=" N TRP A 169 " pdb=" CA TRP A 169 " ideal model delta harmonic sigma weight residual -180.00 -153.04 -26.96 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA PRO B 168 " pdb=" C PRO B 168 " pdb=" N TRP B 169 " pdb=" CA TRP B 169 " ideal model delta harmonic sigma weight residual 180.00 -153.09 -26.91 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" C THR C 14 " pdb=" N THR C 14 " pdb=" CA THR C 14 " pdb=" CB THR C 14 " ideal model delta harmonic sigma weight residual -122.00 -132.71 10.71 0 2.50e+00 1.60e-01 1.84e+01 ... (remaining 14330 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2014 0.071 - 0.143: 269 0.143 - 0.214: 13 0.214 - 0.286: 6 0.286 - 0.357: 2 Chirality restraints: 2304 Sorted by residual: chirality pdb=" CA THR C 14 " pdb=" N THR C 14 " pdb=" C THR C 14 " pdb=" CB THR C 14 " both_signs ideal model delta sigma weight residual False 2.53 2.17 0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CA VAL C 11 " pdb=" N VAL C 11 " pdb=" C VAL C 11 " pdb=" CB VAL C 11 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CA LYS B 273 " pdb=" N LYS B 273 " pdb=" C LYS B 273 " pdb=" CB LYS B 273 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 2301 not shown) Planarity restraints: 4566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 121 " 0.308 2.00e-02 2.50e+03 4.13e-01 2.55e+03 pdb=" CG ASN D 121 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN D 121 " -0.308 2.00e-02 2.50e+03 pdb=" ND2 ASN D 121 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN D 121 " 0.657 2.00e-02 2.50e+03 pdb="HD22 ASN D 121 " -0.633 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 262 " 0.305 2.00e-02 2.50e+03 3.58e-01 1.93e+03 pdb=" CG ASN A 262 " -0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN A 262 " -0.301 2.00e-02 2.50e+03 pdb=" ND2 ASN A 262 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN A 262 " -0.537 2.00e-02 2.50e+03 pdb="HD22 ASN A 262 " 0.547 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 262 " -0.261 2.00e-02 2.50e+03 2.82e-01 1.19e+03 pdb=" CG ASN B 262 " 0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN B 262 " 0.259 2.00e-02 2.50e+03 pdb=" ND2 ASN B 262 " -0.004 2.00e-02 2.50e+03 pdb="HD21 ASN B 262 " 0.411 2.00e-02 2.50e+03 pdb="HD22 ASN B 262 " -0.414 2.00e-02 2.50e+03 ... (remaining 4563 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 1313 2.16 - 2.77: 60542 2.77 - 3.38: 90865 3.38 - 3.99: 120960 3.99 - 4.60: 190489 Nonbonded interactions: 464169 Sorted by model distance: nonbonded pdb=" HG1 THR D 442 " pdb=" HG SER B 497 " model vdw 1.554 2.100 nonbonded pdb=" O VAL C 489 " pdb="HH21 ARG D 476 " model vdw 1.615 1.850 nonbonded pdb=" H SER C 501 " pdb=" O ARG B 78 " model vdw 1.617 1.850 nonbonded pdb=" O ARG A 78 " pdb=" H SER D 501 " model vdw 1.618 1.850 nonbonded pdb="HH21 ARG C 476 " pdb=" O VAL D 489 " model vdw 1.625 1.850 ... (remaining 464164 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' and (resid 17 through 124 or (resid 125 and (name N or name CA or nam \ e C or name O or name H )) or resid 126 through 501)) selection = (chain 'B' and (resid 17 through 124 or (resid 125 and (name N or name CA or nam \ e C or name O or name H )) or resid 126 through 501)) selection = (chain 'C' and ((resid 17 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB3 o \ r name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name H \ Z1 or name HZ2 or name HZ3)) or resid 18 through 501)) selection = (chain 'D' and ((resid 17 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB3 o \ r name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name H \ Z1 or name HZ2 or name HZ3)) or resid 18 through 124 or (resid 125 and (name N o \ r name CA or name C or name O or name H )) or resid 126 through 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 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: 0.380 Extract box with map and model: 7.420 Check model and map are aligned: 0.440 Set scattering table: 0.260 Process input model: 95.540 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.100 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:10.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 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 0.042 15436 Z= 0.275 Angle : 0.772 10.272 20890 Z= 0.479 Chirality : 0.048 0.357 2304 Planarity : 0.005 0.092 2704 Dihedral : 17.106 89.682 5678 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.97 % Allowed : 22.40 % Favored : 74.63 % 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: -0.83 (0.20), residues: 1948 helix: 0.29 (0.18), residues: 838 sheet: -1.30 (0.28), residues: 362 loop : -0.96 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 375 HIS 0.014 0.001 HIS C 484 PHE 0.011 0.001 PHE D 483 TYR 0.018 0.002 TYR D 351 ARG 0.008 0.001 ARG B 476 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 198 time to evaluate : 2.476 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: A 65 LYS cc_start: 0.5511 (mmpt) cc_final: 0.5266 (mmpt) REVERT: C 46 GLU cc_start: 0.7724 (mp0) cc_final: 0.7213 (mp0) REVERT: D 348 LYS cc_start: 0.8274 (mttt) cc_final: 0.7602 (mmtt) REVERT: B 65 LYS cc_start: 0.5489 (mmpt) cc_final: 0.5245 (mmpt) outliers start: 48 outliers final: 33 residues processed: 239 average time/residue: 2.1213 time to fit residues: 582.9720 Evaluate side-chains 208 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 175 time to evaluate : 2.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 464 CYS Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 497 SER Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 497 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 4.9990 chunk 147 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 152 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 176 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 117 ASN D 121 ASN D 474 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.0631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15436 Z= 0.249 Angle : 0.552 5.357 20890 Z= 0.299 Chirality : 0.043 0.134 2304 Planarity : 0.005 0.086 2704 Dihedral : 6.963 82.078 2139 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.75 % Favored : 96.20 % Rotamer: Outliers : 3.71 % Allowed : 22.96 % Favored : 73.33 % 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: -0.64 (0.19), residues: 1948 helix: 0.62 (0.18), residues: 844 sheet: -1.24 (0.26), residues: 382 loop : -1.06 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 375 HIS 0.012 0.001 HIS C 484 PHE 0.015 0.002 PHE D 483 TYR 0.010 0.002 TYR A 330 ARG 0.003 0.000 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 187 time to evaluate : 2.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 ARG cc_start: 0.7880 (mtp-110) cc_final: 0.7598 (mtp85) REVERT: D 348 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7453 (mmtt) outliers start: 60 outliers final: 43 residues processed: 229 average time/residue: 2.0778 time to fit residues: 546.2676 Evaluate side-chains 221 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 177 time to evaluate : 2.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 330 TYR Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 464 CYS Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 330 TYR Chi-restraints excluded: chain D residue 348 LYS Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 464 CYS Chi-restraints excluded: chain D residue 484 HIS Chi-restraints excluded: chain D residue 491 THR Chi-restraints excluded: chain D residue 497 SER Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 170 ASN Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 497 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 97 optimal weight: 2.9990 chunk 54 optimal weight: 0.0570 chunk 146 optimal weight: 10.9990 chunk 119 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 176 optimal weight: 5.9990 chunk 190 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 overall best weight: 1.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 ASN D 117 ASN D 474 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 15436 Z= 0.289 Angle : 0.552 5.251 20890 Z= 0.298 Chirality : 0.043 0.138 2304 Planarity : 0.005 0.083 2704 Dihedral : 6.128 53.935 2122 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.31 % Favored : 95.64 % Rotamer: Outliers : 4.33 % Allowed : 22.59 % Favored : 73.08 % 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: -0.70 (0.19), residues: 1948 helix: 0.63 (0.18), residues: 840 sheet: -1.26 (0.27), residues: 372 loop : -1.19 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 169 HIS 0.012 0.002 HIS C 484 PHE 0.013 0.002 PHE A 24 TYR 0.011 0.002 TYR D 426 ARG 0.005 0.000 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 185 time to evaluate : 2.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.6626 (ttmt) REVERT: A 330 TYR cc_start: 0.4855 (OUTLIER) cc_final: 0.4645 (t80) REVERT: C 262 ASN cc_start: 0.7256 (OUTLIER) cc_final: 0.6713 (p0) REVERT: D 143 ARG cc_start: 0.8250 (mtt90) cc_final: 0.7779 (mtp85) REVERT: D 348 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7481 (mmtt) REVERT: D 484 HIS cc_start: 0.7376 (OUTLIER) cc_final: 0.6761 (p-80) REVERT: D 485 GLU cc_start: 0.7345 (mm-30) cc_final: 0.7079 (mm-30) REVERT: B 91 LYS cc_start: 0.7720 (OUTLIER) cc_final: 0.6610 (ttmt) outliers start: 70 outliers final: 46 residues processed: 234 average time/residue: 2.2164 time to fit residues: 604.4193 Evaluate side-chains 226 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 174 time to evaluate : 2.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 330 TYR Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 330 TYR Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 464 CYS Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 330 TYR Chi-restraints excluded: chain D residue 348 LYS Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 464 CYS Chi-restraints excluded: chain D residue 484 HIS Chi-restraints excluded: chain D residue 491 THR Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 170 ASN Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 497 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 174 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 177 optimal weight: 9.9990 chunk 187 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 167 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 ASN C 220 ASN C 334 ASN D 117 ASN D 220 ASN D 474 ASN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15436 Z= 0.274 Angle : 0.540 5.169 20890 Z= 0.291 Chirality : 0.043 0.134 2304 Planarity : 0.005 0.083 2704 Dihedral : 6.016 53.234 2119 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.77 % Favored : 95.17 % Rotamer: Outliers : 3.65 % Allowed : 22.96 % Favored : 73.39 % 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: -0.72 (0.19), residues: 1948 helix: 0.66 (0.18), residues: 840 sheet: -1.33 (0.26), residues: 372 loop : -1.23 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 375 HIS 0.010 0.002 HIS C 484 PHE 0.012 0.002 PHE A 24 TYR 0.010 0.002 TYR D 457 ARG 0.003 0.000 ARG D 143 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 179 time to evaluate : 2.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.6638 (ttmt) REVERT: C 262 ASN cc_start: 0.7518 (OUTLIER) cc_final: 0.6974 (p0) REVERT: D 97 GLU cc_start: 0.7941 (tt0) cc_final: 0.7698 (tt0) REVERT: D 348 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7475 (mmtt) REVERT: D 484 HIS cc_start: 0.7506 (OUTLIER) cc_final: 0.7019 (p-80) REVERT: D 485 GLU cc_start: 0.7277 (mm-30) cc_final: 0.6912 (mm-30) REVERT: B 65 LYS cc_start: 0.5414 (mmpt) cc_final: 0.5160 (mmpt) REVERT: B 91 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.6629 (ttmt) outliers start: 59 outliers final: 45 residues processed: 223 average time/residue: 2.2052 time to fit residues: 562.5573 Evaluate side-chains 224 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 174 time to evaluate : 2.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 330 TYR Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 464 CYS Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 330 TYR Chi-restraints excluded: chain D residue 348 LYS Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 464 CYS Chi-restraints excluded: chain D residue 484 HIS Chi-restraints excluded: chain D residue 497 SER Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 170 ASN Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 497 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 156 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 160 optimal weight: 0.6980 chunk 129 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 168 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN C 220 ASN D 117 ASN D 220 ASN D 474 ASN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 15436 Z= 0.313 Angle : 0.557 8.307 20890 Z= 0.300 Chirality : 0.043 0.140 2304 Planarity : 0.005 0.083 2704 Dihedral : 6.051 52.868 2118 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.18 % Favored : 94.76 % Rotamer: Outliers : 4.52 % Allowed : 22.34 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.19), residues: 1948 helix: 0.58 (0.18), residues: 840 sheet: -1.21 (0.28), residues: 348 loop : -1.25 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 375 HIS 0.011 0.002 HIS C 484 PHE 0.013 0.002 PHE B 402 TYR 0.011 0.002 TYR C 457 ARG 0.003 0.000 ARG D 143 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 177 time to evaluate : 2.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.6650 (ttmt) REVERT: A 106 MET cc_start: 0.6048 (tmm) cc_final: 0.5753 (tmm) REVERT: D 97 GLU cc_start: 0.7975 (tt0) cc_final: 0.7737 (tt0) REVERT: D 284 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7072 (tp) REVERT: D 348 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7515 (mmtt) REVERT: D 484 HIS cc_start: 0.7579 (OUTLIER) cc_final: 0.7213 (p-80) REVERT: D 485 GLU cc_start: 0.7286 (mm-30) cc_final: 0.7041 (mm-30) REVERT: B 65 LYS cc_start: 0.5432 (mmpt) cc_final: 0.5178 (mmpt) REVERT: B 91 LYS cc_start: 0.7745 (OUTLIER) cc_final: 0.6648 (ttmt) REVERT: B 106 MET cc_start: 0.6048 (tmm) cc_final: 0.5750 (tmm) outliers start: 73 outliers final: 55 residues processed: 234 average time/residue: 2.0730 time to fit residues: 557.9947 Evaluate side-chains 231 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 171 time to evaluate : 2.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 330 TYR Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 484 HIS Chi-restraints excluded: chain C residue 491 THR Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 330 TYR Chi-restraints excluded: chain D residue 348 LYS Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 464 CYS Chi-restraints excluded: chain D residue 484 HIS Chi-restraints excluded: chain D residue 491 THR Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 170 ASN Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 497 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 63 optimal weight: 1.9990 chunk 168 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 110 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 187 optimal weight: 4.9990 chunk 155 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN C 117 ASN D 117 ASN D 220 ASN D 474 ASN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15436 Z= 0.228 Angle : 0.522 4.888 20890 Z= 0.280 Chirality : 0.042 0.136 2304 Planarity : 0.005 0.081 2704 Dihedral : 5.898 52.690 2117 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.31 % Favored : 95.64 % Rotamer: Outliers : 3.65 % Allowed : 23.45 % Favored : 72.90 % 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 (0.19), residues: 1948 helix: 0.77 (0.18), residues: 842 sheet: -1.20 (0.27), residues: 350 loop : -1.16 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 375 HIS 0.009 0.001 HIS C 484 PHE 0.012 0.001 PHE A 24 TYR 0.010 0.002 TYR D 20 ARG 0.002 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 176 time to evaluate : 2.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.6632 (ttmt) REVERT: A 106 MET cc_start: 0.6070 (tmm) cc_final: 0.5786 (tmm) REVERT: C 419 LYS cc_start: 0.7784 (OUTLIER) cc_final: 0.7139 (mmpt) REVERT: D 97 GLU cc_start: 0.7959 (tt0) cc_final: 0.7733 (tt0) REVERT: D 284 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.7075 (tp) REVERT: D 348 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7489 (mmtt) REVERT: D 484 HIS cc_start: 0.7538 (OUTLIER) cc_final: 0.7295 (p-80) REVERT: B 91 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.6629 (ttmt) REVERT: B 106 MET cc_start: 0.6105 (tmm) cc_final: 0.5824 (tmm) outliers start: 59 outliers final: 49 residues processed: 223 average time/residue: 2.1290 time to fit residues: 546.4725 Evaluate side-chains 224 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 169 time to evaluate : 2.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 330 TYR Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 419 LYS Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 464 CYS Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 330 TYR Chi-restraints excluded: chain D residue 348 LYS Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 464 CYS Chi-restraints excluded: chain D residue 484 HIS Chi-restraints excluded: chain D residue 491 THR Chi-restraints excluded: chain D residue 497 SER Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 170 ASN Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 497 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 180 optimal weight: 7.9990 chunk 21 optimal weight: 0.0980 chunk 106 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 186 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN C 19 GLN C 220 ASN D 474 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15436 Z= 0.170 Angle : 0.493 4.835 20890 Z= 0.263 Chirality : 0.041 0.134 2304 Planarity : 0.004 0.084 2704 Dihedral : 5.665 52.235 2117 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.95 % Favored : 96.00 % Rotamer: Outliers : 3.22 % Allowed : 24.13 % Favored : 72.65 % 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: 1948 helix: 1.06 (0.18), residues: 844 sheet: -1.23 (0.27), residues: 372 loop : -1.04 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 375 HIS 0.008 0.001 HIS D 484 PHE 0.017 0.001 PHE A 402 TYR 0.012 0.001 TYR C 351 ARG 0.002 0.000 ARG D 131 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 180 time to evaluate : 2.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 97 GLU cc_start: 0.7949 (tt0) cc_final: 0.7717 (tt0) REVERT: D 284 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7072 (tp) REVERT: D 322 ARG cc_start: 0.7672 (mtt-85) cc_final: 0.7397 (mtt-85) REVERT: D 348 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7452 (mmtt) outliers start: 52 outliers final: 35 residues processed: 225 average time/residue: 2.1226 time to fit residues: 547.3094 Evaluate side-chains 214 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 177 time to evaluate : 2.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 330 TYR Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 330 TYR Chi-restraints excluded: chain D residue 348 LYS Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 464 CYS Chi-restraints excluded: chain D residue 491 THR Chi-restraints excluded: chain D residue 497 SER Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 266 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 74 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 146 optimal weight: 10.0000 chunk 170 optimal weight: 7.9990 chunk 179 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 117 ASN D 117 ASN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 15436 Z= 0.325 Angle : 0.554 5.464 20890 Z= 0.299 Chirality : 0.043 0.132 2304 Planarity : 0.005 0.084 2704 Dihedral : 5.736 51.896 2110 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.08 % Favored : 94.87 % Rotamer: Outliers : 4.02 % Allowed : 23.33 % Favored : 72.65 % 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 (0.19), residues: 1948 helix: 0.73 (0.18), residues: 842 sheet: -1.17 (0.28), residues: 350 loop : -1.13 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 375 HIS 0.013 0.001 HIS C 484 PHE 0.016 0.002 PHE A 402 TYR 0.012 0.002 TYR D 426 ARG 0.003 0.000 ARG D 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 177 time to evaluate : 2.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 389 ASN cc_start: 0.7902 (OUTLIER) cc_final: 0.7463 (m-40) REVERT: D 97 GLU cc_start: 0.7979 (tt0) cc_final: 0.7751 (tt0) REVERT: D 284 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7112 (tp) REVERT: D 348 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7512 (mmtt) REVERT: B 90 TYR cc_start: 0.7850 (OUTLIER) cc_final: 0.7540 (m-80) REVERT: B 106 MET cc_start: 0.6222 (tmm) cc_final: 0.5976 (tmm) outliers start: 65 outliers final: 52 residues processed: 230 average time/residue: 2.1011 time to fit residues: 555.9356 Evaluate side-chains 230 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 174 time to evaluate : 2.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 330 TYR Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 389 ASN Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 464 CYS Chi-restraints excluded: chain C residue 484 HIS Chi-restraints excluded: chain C residue 491 THR Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 330 TYR Chi-restraints excluded: chain D residue 348 LYS Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 464 CYS Chi-restraints excluded: chain D residue 491 THR Chi-restraints excluded: chain D residue 497 SER Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 90 TYR Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 170 ASN Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 391 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 0.1980 chunk 174 optimal weight: 7.9990 chunk 179 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 157 optimal weight: 1.9990 chunk 164 optimal weight: 0.7980 chunk 173 optimal weight: 0.9980 chunk 114 optimal weight: 0.0670 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 19 GLN C 220 ASN D 117 ASN D 220 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 15436 Z= 0.154 Angle : 0.495 4.488 20890 Z= 0.263 Chirality : 0.041 0.135 2304 Planarity : 0.004 0.082 2704 Dihedral : 5.503 51.773 2110 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.90 % Favored : 96.05 % Rotamer: Outliers : 2.72 % Allowed : 24.57 % Favored : 72.71 % 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: -0.25 (0.20), residues: 1948 helix: 1.07 (0.18), residues: 842 sheet: -1.17 (0.27), residues: 372 loop : -0.98 (0.24), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 375 HIS 0.008 0.001 HIS D 484 PHE 0.017 0.001 PHE B 402 TYR 0.010 0.001 TYR C 90 ARG 0.003 0.000 ARG C 143 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 179 time to evaluate : 2.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 389 ASN cc_start: 0.7827 (OUTLIER) cc_final: 0.7405 (m-40) REVERT: D 97 GLU cc_start: 0.7937 (tt0) cc_final: 0.7707 (tt0) REVERT: D 284 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.7070 (tp) REVERT: D 348 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7452 (mmtt) REVERT: B 90 TYR cc_start: 0.7790 (OUTLIER) cc_final: 0.7492 (m-80) outliers start: 44 outliers final: 31 residues processed: 216 average time/residue: 2.1281 time to fit residues: 529.3010 Evaluate side-chains 210 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 175 time to evaluate : 2.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 330 TYR Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 389 ASN Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 484 HIS Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 330 TYR Chi-restraints excluded: chain D residue 348 LYS Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 464 CYS Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 90 TYR Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 266 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 184 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 177 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 19 GLN C 117 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15436 Z= 0.234 Angle : 0.520 4.758 20890 Z= 0.277 Chirality : 0.042 0.130 2304 Planarity : 0.004 0.084 2704 Dihedral : 5.542 51.762 2108 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.67 % Favored : 95.28 % Rotamer: Outliers : 2.91 % Allowed : 24.32 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.19), residues: 1948 helix: 0.97 (0.18), residues: 844 sheet: -1.19 (0.27), residues: 372 loop : -0.99 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 375 HIS 0.012 0.001 HIS C 484 PHE 0.014 0.001 PHE A 483 TYR 0.014 0.002 TYR D 351 ARG 0.002 0.000 ARG C 143 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 177 time to evaluate : 2.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 389 ASN cc_start: 0.7847 (OUTLIER) cc_final: 0.7425 (m-40) REVERT: C 399 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7486 (tt0) REVERT: D 97 GLU cc_start: 0.7935 (tt0) cc_final: 0.7723 (tt0) REVERT: D 284 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7093 (tp) REVERT: D 348 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7484 (mmtt) REVERT: D 399 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7475 (tt0) REVERT: B 90 TYR cc_start: 0.7805 (OUTLIER) cc_final: 0.7560 (m-80) outliers start: 47 outliers final: 40 residues processed: 216 average time/residue: 2.1865 time to fit residues: 540.2467 Evaluate side-chains 217 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 173 time to evaluate : 2.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 330 TYR Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 389 ASN Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 484 HIS Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 330 TYR Chi-restraints excluded: chain D residue 348 LYS Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 464 CYS Chi-restraints excluded: chain D residue 497 SER Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 90 TYR Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 309 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 158 optimal weight: 1.9990 chunk 19 optimal weight: 0.0670 chunk 28 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 19 GLN C 117 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.182097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.140683 restraints weight = 45301.415| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.80 r_work: 0.3506 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15436 Z= 0.219 Angle : 0.517 6.186 20890 Z= 0.275 Chirality : 0.042 0.131 2304 Planarity : 0.004 0.082 2704 Dihedral : 5.532 51.746 2108 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.36 % Favored : 95.59 % Rotamer: Outliers : 2.97 % Allowed : 24.44 % Favored : 72.59 % 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: 1948 helix: 0.98 (0.18), residues: 844 sheet: -1.16 (0.27), residues: 372 loop : -0.97 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 375 HIS 0.010 0.001 HIS C 484 PHE 0.015 0.001 PHE A 402 TYR 0.010 0.001 TYR C 90 ARG 0.002 0.000 ARG A 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10169.87 seconds wall clock time: 181 minutes 10.40 seconds (10870.40 seconds total)