Starting phenix.real_space_refine on Fri Dec 15 03:18:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d46_27176/12_2023/8d46_27176.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d46_27176/12_2023/8d46_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_27176/12_2023/8d46_27176.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d46_27176/12_2023/8d46_27176.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d46_27176/12_2023/8d46_27176.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d46_27176/12_2023/8d46_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-1.21rc1-5172/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: 12.04, per 1000 atoms: 0.40 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: 22.96 Conformation dependent library (CDL) restraints added in 2.9 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: 2.22 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: 11.39 Time building geometry restraints manager: 23.95 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: 12221 17.94 - 35.87: 1215 35.87 - 53.81: 302 53.81 - 71.75: 65 71.75 - 89.68: 27 Dihedral angle restraints: 13830 sinusoidal: 7318 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 13827 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: 1.090 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: 0.420 Extract box with map and model: 7.460 Check model and map are aligned: 0.410 Set scattering table: 0.240 Process input model: 89.120 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:11.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.580 ------------------------------------------------------------------------------- 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 : 2.439 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 outliers start: 48 outliers final: 33 residues processed: 239 average time/residue: 2.0564 time to fit residues: 564.5491 Evaluate side-chains 208 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 175 time to evaluate : 2.342 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 32 residues processed: 1 average time/residue: 2.4525 time to fit residues: 5.7832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0980 chunk 99 optimal weight: 0.0870 chunk 78 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 176 optimal weight: 5.9990 overall best weight: 0.4960 ------------------------------------------------------------------------------- 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: 0.7198 moved from start: 0.0686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15436 Z= 0.165 Angle : 0.518 5.153 20890 Z= 0.278 Chirality : 0.042 0.140 2304 Planarity : 0.005 0.084 2704 Dihedral : 4.608 25.888 2088 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.54 % Favored : 96.41 % Rotamer: Outliers : 3.71 % Allowed : 22.52 % Favored : 73.76 % 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 (0.20), residues: 1948 helix: 0.93 (0.18), residues: 842 sheet: -1.12 (0.27), residues: 382 loop : -0.96 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 375 HIS 0.009 0.001 HIS C 484 PHE 0.016 0.001 PHE B 38 TYR 0.010 0.001 TYR B 154 ARG 0.003 0.000 ARG A 308 *********************** 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 : 2.187 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 outliers start: 60 outliers final: 43 residues processed: 237 average time/residue: 2.0277 time to fit residues: 554.4668 Evaluate side-chains 219 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 176 time to evaluate : 2.524 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 37 residues processed: 6 average time/residue: 0.8184 time to fit residues: 9.7472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 0.2980 chunk 146 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 176 optimal weight: 5.9990 chunk 190 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 117 ASN D 474 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.0929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 15436 Z= 0.267 Angle : 0.538 5.231 20890 Z= 0.291 Chirality : 0.043 0.149 2304 Planarity : 0.005 0.083 2704 Dihedral : 4.835 33.255 2088 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.41 % Favored : 95.53 % Rotamer: Outliers : 3.96 % Allowed : 22.52 % Favored : 73.51 % 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: -0.48 (0.19), residues: 1948 helix: 0.81 (0.18), residues: 842 sheet: -1.14 (0.27), residues: 372 loop : -1.09 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 169 HIS 0.012 0.002 HIS C 484 PHE 0.011 0.002 PHE D 483 TYR 0.011 0.002 TYR D 426 ARG 0.005 0.001 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 250 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 186 time to evaluate : 2.426 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 outliers start: 64 outliers final: 50 residues processed: 235 average time/residue: 2.0977 time to fit residues: 574.4996 Evaluate side-chains 224 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 174 time to evaluate : 2.467 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 39 residues processed: 11 average time/residue: 0.8744 time to fit residues: 17.3379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 174 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 177 optimal weight: 7.9990 chunk 187 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 167 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 117 ASN C 220 ASN D 117 ASN D 220 ASN D 474 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15436 Z= 0.284 Angle : 0.539 5.168 20890 Z= 0.292 Chirality : 0.043 0.140 2304 Planarity : 0.005 0.079 2704 Dihedral : 4.919 33.097 2088 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.57 % Favored : 95.38 % Rotamer: Outliers : 4.02 % Allowed : 22.40 % Favored : 73.58 % 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: -0.59 (0.19), residues: 1948 helix: 0.74 (0.18), residues: 842 sheet: -1.22 (0.27), residues: 372 loop : -1.15 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 375 HIS 0.011 0.001 HIS C 484 PHE 0.013 0.002 PHE A 24 TYR 0.011 0.002 TYR D 426 ARG 0.003 0.000 ARG A 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 245 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 180 time to evaluate : 2.605 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 outliers start: 65 outliers final: 47 residues processed: 233 average time/residue: 1.9528 time to fit residues: 527.8614 Evaluate side-chains 224 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 177 time to evaluate : 2.431 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 38 residues processed: 9 average time/residue: 1.0529 time to fit residues: 15.4387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 160 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 95 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 15436 Z= 0.374 Angle : 0.583 5.873 20890 Z= 0.318 Chirality : 0.045 0.145 2304 Planarity : 0.005 0.085 2704 Dihedral : 5.145 35.092 2088 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.29 % Favored : 94.66 % Rotamer: Outliers : 4.39 % Allowed : 22.52 % 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: -0.85 (0.19), residues: 1948 helix: 0.42 (0.18), residues: 842 sheet: -1.23 (0.28), residues: 348 loop : -1.25 (0.23), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 136 HIS 0.010 0.002 HIS C 484 PHE 0.015 0.002 PHE B 402 TYR 0.014 0.002 TYR D 457 ARG 0.004 0.001 ARG B 156 *********************** 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 253 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 182 time to evaluate : 2.263 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 outliers start: 71 outliers final: 55 residues processed: 241 average time/residue: 1.9106 time to fit residues: 535.3031 Evaluate side-chains 228 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 173 time to evaluate : 2.483 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 46 residues processed: 9 average time/residue: 0.6358 time to fit residues: 11.5241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 110 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 chunk 187 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- 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 C 220 ASN C 334 ASN D 117 ASN D 220 ASN D 474 ASN D 498 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15436 Z= 0.251 Angle : 0.536 5.086 20890 Z= 0.289 Chirality : 0.042 0.138 2304 Planarity : 0.005 0.080 2704 Dihedral : 4.992 32.375 2088 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.72 % Favored : 95.23 % Rotamer: Outliers : 4.02 % Allowed : 23.21 % 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: -0.67 (0.19), residues: 1948 helix: 0.62 (0.18), residues: 842 sheet: -1.20 (0.28), residues: 348 loop : -1.18 (0.23), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 375 HIS 0.010 0.001 HIS D 484 PHE 0.013 0.002 PHE A 402 TYR 0.011 0.002 TYR D 330 ARG 0.004 0.000 ARG C 143 *********************** 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 242 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 177 time to evaluate : 2.202 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 outliers start: 65 outliers final: 55 residues processed: 231 average time/residue: 1.9424 time to fit residues: 522.0152 Evaluate side-chains 227 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 172 time to evaluate : 2.265 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 47 residues processed: 8 average time/residue: 0.6792 time to fit residues: 10.9193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0870 chunk 106 optimal weight: 1.9990 chunk 137 optimal weight: 0.5980 chunk 158 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 113 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 19 GLN D 117 ASN D 474 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.1422 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= 0.192 Angle : 0.508 5.392 20890 Z= 0.271 Chirality : 0.042 0.133 2304 Planarity : 0.004 0.086 2704 Dihedral : 4.771 30.170 2088 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.21 % Favored : 95.74 % Rotamer: Outliers : 4.08 % Allowed : 23.21 % 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: -0.42 (0.20), residues: 1948 helix: 0.91 (0.18), residues: 844 sheet: -1.23 (0.27), residues: 372 loop : -1.05 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 375 HIS 0.011 0.001 HIS D 484 PHE 0.012 0.001 PHE A 24 TYR 0.012 0.001 TYR D 351 ARG 0.004 0.000 ARG A 143 *********************** 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 243 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 177 time to evaluate : 2.274 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 outliers start: 66 outliers final: 52 residues processed: 240 average time/residue: 1.8857 time to fit residues: 526.6488 Evaluate side-chains 228 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 176 time to evaluate : 2.524 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 51 residues processed: 1 average time/residue: 0.3412 time to fit residues: 3.7200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 74 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 118 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 146 optimal weight: 10.0000 chunk 170 optimal weight: 0.0870 chunk 179 optimal weight: 3.9990 overall best weight: 0.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 19 GLN D 474 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15436 Z= 0.182 Angle : 0.497 4.712 20890 Z= 0.266 Chirality : 0.042 0.134 2304 Planarity : 0.004 0.081 2704 Dihedral : 4.675 29.930 2088 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.00 % Favored : 95.94 % Rotamer: Outliers : 3.59 % Allowed : 23.89 % Favored : 72.52 % 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: 844 sheet: -1.17 (0.27), residues: 372 loop : -0.97 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 375 HIS 0.011 0.001 HIS D 484 PHE 0.013 0.001 PHE B 402 TYR 0.013 0.001 TYR C 351 ARG 0.004 0.000 ARG D 321 *********************** 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 241 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 183 time to evaluate : 2.391 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 outliers start: 58 outliers final: 48 residues processed: 237 average time/residue: 1.9612 time to fit residues: 538.6137 Evaluate side-chains 221 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 173 time to evaluate : 2.348 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 47 residues processed: 1 average time/residue: 0.3334 time to fit residues: 3.7056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 179 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 chunk 114 optimal weight: 0.5980 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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 D 117 ASN D 474 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 15436 Z= 0.307 Angle : 0.547 5.249 20890 Z= 0.295 Chirality : 0.043 0.133 2304 Planarity : 0.005 0.086 2704 Dihedral : 4.881 33.463 2088 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.03 % Favored : 94.92 % Rotamer: Outliers : 3.53 % Allowed : 23.76 % 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: -0.47 (0.19), residues: 1948 helix: 0.79 (0.18), residues: 846 sheet: -1.16 (0.28), residues: 350 loop : -1.05 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 375 HIS 0.011 0.002 HIS D 484 PHE 0.022 0.002 PHE B 402 TYR 0.013 0.002 TYR D 316 ARG 0.004 0.001 ARG D 131 *********************** 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 231 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 174 time to evaluate : 2.255 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 outliers start: 57 outliers final: 54 residues processed: 223 average time/residue: 2.0707 time to fit residues: 535.9999 Evaluate side-chains 226 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 172 time to evaluate : 2.216 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 47 residues processed: 7 average time/residue: 0.3813 time to fit residues: 7.8152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 184 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 chunk 128 optimal weight: 0.9980 chunk 193 optimal weight: 1.9990 chunk 177 optimal weight: 9.9990 chunk 153 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 118 optimal weight: 0.0970 chunk 94 optimal weight: 1.9990 chunk 122 optimal weight: 0.5980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 19 GLN D 117 ASN D 474 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15436 Z= 0.163 Angle : 0.498 5.276 20890 Z= 0.265 Chirality : 0.042 0.134 2304 Planarity : 0.004 0.079 2704 Dihedral : 4.640 28.416 2088 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.64 % Favored : 96.30 % Rotamer: Outliers : 3.16 % Allowed : 24.13 % 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: -0.16 (0.20), residues: 1948 helix: 1.13 (0.18), residues: 846 sheet: -1.13 (0.27), residues: 372 loop : -0.90 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 375 HIS 0.011 0.001 HIS D 484 PHE 0.015 0.001 PHE B 402 TYR 0.015 0.001 TYR C 90 ARG 0.003 0.000 ARG A 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 228 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 177 time to evaluate : 2.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 47 residues processed: 226 average time/residue: 1.9067 time to fit residues: 498.7951 Evaluate side-chains 222 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 175 time to evaluate : 2.280 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 47 residues processed: 0 time to fit residues: 2.7898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 141 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 158 optimal weight: 0.7980 chunk 19 optimal weight: 0.0370 chunk 28 optimal weight: 4.9990 chunk 135 optimal weight: 0.6980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 19 GLN D 474 ASN D 498 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.184200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.142270 restraints weight = 45169.224| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 1.83 r_work: 0.3546 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15436 Z= 0.165 Angle : 0.487 4.981 20890 Z= 0.259 Chirality : 0.041 0.132 2304 Planarity : 0.004 0.085 2704 Dihedral : 4.499 27.116 2088 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.06 % Favored : 95.89 % Rotamer: Outliers : 3.16 % Allowed : 24.20 % 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: 0.03 (0.20), residues: 1948 helix: 1.31 (0.18), residues: 846 sheet: -1.07 (0.27), residues: 372 loop : -0.83 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 375 HIS 0.011 0.001 HIS D 484 PHE 0.015 0.001 PHE B 402 TYR 0.019 0.001 TYR D 351 ARG 0.003 0.000 ARG A 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10264.63 seconds wall clock time: 188 minutes 27.70 seconds (11307.70 seconds total)