Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 29 13:52:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d46_27176/04_2023/8d46_27176.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d46_27176/04_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_27176/04_2023/8d46_27176.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d46_27176/04_2023/8d46_27176.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d46_27176/04_2023/8d46_27176.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d46_27176/04_2023/8d46_27176.pdb" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.050 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 13.66, per 1000 atoms: 0.45 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: 27.95 Conformation dependent library (CDL) restraints added in 2.6 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: 0.98 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: 11.82 Time building geometry restraints manager: 28.36 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: 10597 17.94 - 35.87: 1137 35.87 - 53.81: 256 53.81 - 71.75: 65 71.75 - 89.68: 27 Dihedral angle restraints: 12082 sinusoidal: 5570 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 12079 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: 1.310 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: 8.720 Check model and map are aligned: 0.420 Set scattering table: 0.240 Process input model: 97.340 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.090 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:12.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.020 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 2.603 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: 2.0606 time to fit residues: 565.8116 Evaluate side-chains 208 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 175 time to evaluate : 2.637 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 32 residues processed: 1 average time/residue: 2.5731 time to fit residues: 6.3102 ------------------------------------------------------------------------------- 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: 0.2980 chunk 99 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 113 optimal weight: 0.4980 chunk 176 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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: 0.7222 moved from start: 0.0667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 15436 Z= 0.206 Angle : 0.534 5.065 20890 Z= 0.287 Chirality : 0.042 0.139 2304 Planarity : 0.005 0.085 2704 Dihedral : 4.724 28.505 2088 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.75 % Favored : 96.20 % Rotamer Outliers : 4.21 % 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: -0.50 (0.19), residues: 1948 helix: 0.77 (0.18), residues: 842 sheet: -1.19 (0.26), residues: 382 loop : -1.02 (0.24), residues: 724 *********************** 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 257 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 189 time to evaluate : 2.382 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: 68 outliers final: 49 residues processed: 241 average time/residue: 1.9633 time to fit residues: 547.8272 Evaluate side-chains 228 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 179 time to evaluate : 2.506 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 37 residues processed: 12 average time/residue: 0.7635 time to fit residues: 15.8686 ------------------------------------------------------------------------------- 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: 0.5980 chunk 146 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 176 optimal weight: 5.9990 chunk 190 optimal weight: 3.9990 chunk 157 optimal weight: 0.9980 chunk 175 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 474 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.0926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.080 15436 Z= 0.220 Angle : 0.522 5.013 20890 Z= 0.279 Chirality : 0.042 0.140 2304 Planarity : 0.004 0.082 2704 Dihedral : 4.775 31.364 2088 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.16 % Favored : 95.79 % Rotamer Outliers : 3.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.19), residues: 1948 helix: 0.89 (0.18), residues: 840 sheet: -1.15 (0.27), residues: 372 loop : -1.09 (0.23), residues: 736 *********************** 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 : 2.742 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: 46 residues processed: 235 average time/residue: 2.0610 time to fit residues: 558.1705 Evaluate side-chains 219 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 173 time to evaluate : 2.500 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 38 residues processed: 8 average time/residue: 0.6004 time to fit residues: 10.1889 ------------------------------------------------------------------------------- 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: 5.9990 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: 1.9990 chunk 177 optimal weight: 7.9990 chunk 187 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 167 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.1136 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= 0.281 Angle : 0.542 5.236 20890 Z= 0.291 Chirality : 0.043 0.140 2304 Planarity : 0.005 0.081 2704 Dihedral : 4.908 33.386 2088 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.47 % Favored : 95.48 % Rotamer Outliers : 4.15 % 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: 0.78 (0.18), residues: 840 sheet: -1.25 (0.27), residues: 372 loop : -1.18 (0.23), residues: 736 *********************** 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 251 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 184 time to evaluate : 2.503 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: 67 outliers final: 49 residues processed: 238 average time/residue: 1.9147 time to fit residues: 528.8883 Evaluate side-chains 225 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 176 time to evaluate : 2.620 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 39 residues processed: 10 average time/residue: 0.9576 time to fit residues: 15.8928 ------------------------------------------------------------------------------- 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: 3.9990 chunk 139 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 168 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 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: 0.7291 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.061 15436 Z= 0.377 Angle : 0.589 5.851 20890 Z= 0.320 Chirality : 0.045 0.141 2304 Planarity : 0.005 0.083 2704 Dihedral : 5.154 34.927 2088 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.34 % Favored : 94.61 % Rotamer Outliers : 4.46 % 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: -0.90 (0.19), residues: 1948 helix: 0.40 (0.18), residues: 844 sheet: -1.26 (0.28), residues: 348 loop : -1.31 (0.22), residues: 756 *********************** 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 251 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 179 time to evaluate : 2.706 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: 72 outliers final: 56 residues processed: 239 average time/residue: 1.9618 time to fit residues: 545.8599 Evaluate side-chains 231 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 175 time to evaluate : 2.550 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 47 residues processed: 9 average time/residue: 0.6003 time to fit residues: 11.3487 ------------------------------------------------------------------------------- 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: 7.9990 chunk 37 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 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: 0.0050 chunk 62 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.2002 ------------------------------------------------------------------------------- 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 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: 0.7261 moved from start: 0.1372 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= 0.233 Angle : 0.535 5.697 20890 Z= 0.287 Chirality : 0.042 0.138 2304 Planarity : 0.004 0.082 2704 Dihedral : 4.961 32.276 2088 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.41 % Favored : 95.53 % Rotamer Outliers : 4.27 % 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: -0.66 (0.19), residues: 1948 helix: 0.64 (0.18), residues: 842 sheet: -1.20 (0.28), residues: 348 loop : -1.19 (0.23), residues: 758 *********************** 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 248 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 179 time to evaluate : 2.496 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: 69 outliers final: 55 residues processed: 237 average time/residue: 1.9723 time to fit residues: 540.4994 Evaluate side-chains 228 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 173 time to evaluate : 2.516 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 49 residues processed: 6 average time/residue: 0.6827 time to fit residues: 8.7735 ------------------------------------------------------------------------------- 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: 0.5980 chunk 106 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 115 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: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN C 220 ASN D 474 ASN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 15436 Z= 0.251 Angle : 0.537 4.935 20890 Z= 0.287 Chirality : 0.042 0.132 2304 Planarity : 0.004 0.085 2704 Dihedral : 4.915 32.272 2088 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.88 % Favored : 95.07 % Rotamer Outliers : 3.96 % 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: -0.61 (0.19), residues: 1948 helix: 0.69 (0.18), residues: 844 sheet: -1.21 (0.28), residues: 350 loop : -1.15 (0.23), residues: 754 *********************** 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 239 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 175 time to evaluate : 2.576 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: 64 outliers final: 56 residues processed: 233 average time/residue: 1.9247 time to fit residues: 521.2836 Evaluate side-chains 231 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 175 time to evaluate : 2.659 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 52 residues processed: 4 average time/residue: 0.9207 time to fit residues: 8.1771 ------------------------------------------------------------------------------- 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: 0.9980 chunk 111 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 92 optimal weight: 0.3980 chunk 17 optimal weight: 3.9990 chunk 146 optimal weight: 10.0000 chunk 170 optimal weight: 4.9990 chunk 179 optimal weight: 5.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 ** 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: 0.7257 moved from start: 0.1481 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= 0.242 Angle : 0.530 4.827 20890 Z= 0.284 Chirality : 0.042 0.132 2304 Planarity : 0.004 0.083 2704 Dihedral : 4.876 31.923 2088 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.36 % Favored : 95.59 % Rotamer Outliers : 3.90 % 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: 0.73 (0.18), residues: 844 sheet: -1.20 (0.28), residues: 350 loop : -1.11 (0.23), residues: 754 *********************** 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 239 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 176 time to evaluate : 2.567 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: 63 outliers final: 56 residues processed: 232 average time/residue: 2.0069 time to fit residues: 542.1617 Evaluate side-chains 227 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 171 time to evaluate : 2.560 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 51 residues processed: 5 average time/residue: 0.3836 time to fit residues: 6.6926 ------------------------------------------------------------------------------- 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: 0.9980 chunk 174 optimal weight: 6.9990 chunk 179 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 164 optimal weight: 0.7980 chunk 173 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 423 ASN D 474 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 15436 Z= 0.256 Angle : 0.535 4.917 20890 Z= 0.286 Chirality : 0.043 0.133 2304 Planarity : 0.004 0.084 2704 Dihedral : 4.877 32.214 2088 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.77 % Favored : 95.17 % Rotamer Outliers : 3.71 % 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: -0.57 (0.19), residues: 1948 helix: 0.71 (0.18), residues: 846 sheet: -1.21 (0.28), residues: 350 loop : -1.10 (0.23), residues: 752 *********************** 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 229 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 169 time to evaluate : 2.282 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: 60 outliers final: 52 residues processed: 225 average time/residue: 1.9742 time to fit residues: 514.5867 Evaluate side-chains 217 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 165 time to evaluate : 2.522 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 50 residues processed: 2 average time/residue: 0.4144 time to fit residues: 4.5983 ------------------------------------------------------------------------------- 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: 0.1980 chunk 112 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 193 optimal weight: 2.9990 chunk 177 optimal weight: 10.0000 chunk 153 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 118 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7231 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 15436 Z= 0.173 Angle : 0.503 5.348 20890 Z= 0.267 Chirality : 0.042 0.133 2304 Planarity : 0.004 0.082 2704 Dihedral : 4.678 29.034 2088 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.64 % Favored : 96.30 % Rotamer Outliers : 3.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.20), residues: 1948 helix: 0.99 (0.18), residues: 846 sheet: -1.23 (0.27), residues: 372 loop : -0.98 (0.24), residues: 730 ********************** 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 234 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 180 time to evaluate : 2.739 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: 54 outliers final: 50 residues processed: 232 average time/residue: 2.0347 time to fit residues: 552.3656 Evaluate side-chains 221 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 171 time to evaluate : 2.557 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 50 residues processed: 0 time to fit residues: 3.2363 ------------------------------------------------------------------------------- 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: 8.9990 chunk 42 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 158 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 135 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.181908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.140375 restraints weight = 45269.269| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 1.80 r_work: 0.3535 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.1595 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= 0.223 Angle : 0.519 5.405 20890 Z= 0.276 Chirality : 0.042 0.132 2304 Planarity : 0.004 0.084 2704 Dihedral : 4.727 30.765 2088 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.31 % Favored : 95.64 % Rotamer Outliers : 3.40 % 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: -0.34 (0.20), residues: 1948 helix: 0.98 (0.18), residues: 846 sheet: -1.22 (0.27), residues: 372 loop : -1.00 (0.24), residues: 730 =============================================================================== Job complete usr+sys time: 9935.73 seconds wall clock time: 175 minutes 24.70 seconds (10524.70 seconds total)