Starting phenix.real_space_refine on Thu Mar 14 17:12:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exs_28661/03_2024/8exs_28661.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exs_28661/03_2024/8exs_28661.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exs_28661/03_2024/8exs_28661.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exs_28661/03_2024/8exs_28661.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exs_28661/03_2024/8exs_28661.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exs_28661/03_2024/8exs_28661.pdb" } resolution = 4.3 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= 0.003 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 Zn 2 6.06 5 S 38 5.16 5 C 6118 2.51 5 N 1538 2.21 5 O 1624 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9320 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 556, 4659 Classifications: {'peptide': 556} Link IDs: {'PTRANS': 11, 'TRANS': 544} Chain breaks: 1 Chain: "B" Number of atoms: 4659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 556, 4659 Classifications: {'peptide': 556} Link IDs: {'PTRANS': 11, 'TRANS': 544} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.44, per 1000 atoms: 0.58 Number of scatterers: 9320 At special positions: 0 Unit cell: (90.015, 90.015, 122.844, 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) Zn 2 29.99 S 38 16.00 O 1624 8.00 N 1538 7.00 C 6118 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.61 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 201 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 205 " pdb=" ZN B 701 " pdb="ZN ZN B 701 " - pdb=" NE2 HIS B 201 " pdb="ZN ZN B 701 " - pdb=" NE2 HIS B 205 " 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2148 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 4 sheets defined 58.4% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 1 through 31 Processing helix chain 'A' and resid 35 through 38 Processing helix chain 'A' and resid 39 through 46 Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 99 through 134 removed outlier: 4.522A pdb=" N ILE A 105 " --> pdb=" O SER A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 152 removed outlier: 5.088A pdb=" N LYS A 145 " --> pdb=" O ASN A 141 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 146 " --> pdb=" O GLU A 142 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASN A 152 " --> pdb=" O THR A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 188 Processing helix chain 'A' and resid 193 through 208 Processing helix chain 'A' and resid 209 through 224 Processing helix chain 'A' and resid 228 through 252 Processing helix chain 'A' and resid 253 through 256 removed outlier: 6.117A pdb=" N ASN A 256 " --> pdb=" O ILE A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 253 through 256' Processing helix chain 'A' and resid 257 through 271 removed outlier: 3.632A pdb=" N VAL A 269 " --> pdb=" O ILE A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 300 Processing helix chain 'A' and resid 307 through 327 removed outlier: 4.298A pdb=" N LEU A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 352 through 357 Processing helix chain 'A' and resid 377 through 382 Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 391 through 402 Processing helix chain 'A' and resid 421 through 425 Processing helix chain 'A' and resid 429 through 436 Processing helix chain 'A' and resid 438 through 449 Processing helix chain 'A' and resid 450 through 461 removed outlier: 3.529A pdb=" N THR A 454 " --> pdb=" O PRO A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 497 Processing helix chain 'A' and resid 502 through 513 removed outlier: 3.616A pdb=" N SER A 512 " --> pdb=" O GLN A 508 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A 513 " --> pdb=" O LEU A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 579 Processing helix chain 'B' and resid 2 through 31 Processing helix chain 'B' and resid 35 through 38 Processing helix chain 'B' and resid 39 through 46 Processing helix chain 'B' and resid 47 through 51 Processing helix chain 'B' and resid 99 through 134 removed outlier: 4.522A pdb=" N ILE B 105 " --> pdb=" O SER B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 152 removed outlier: 5.088A pdb=" N LYS B 145 " --> pdb=" O ASN B 141 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE B 146 " --> pdb=" O GLU B 142 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASN B 152 " --> pdb=" O THR B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 188 Processing helix chain 'B' and resid 193 through 208 Processing helix chain 'B' and resid 209 through 224 Processing helix chain 'B' and resid 228 through 252 Processing helix chain 'B' and resid 253 through 256 removed outlier: 6.117A pdb=" N ASN B 256 " --> pdb=" O ILE B 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 253 through 256' Processing helix chain 'B' and resid 257 through 271 removed outlier: 3.632A pdb=" N VAL B 269 " --> pdb=" O ILE B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 300 Processing helix chain 'B' and resid 307 through 327 removed outlier: 4.296A pdb=" N LEU B 311 " --> pdb=" O SER B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 337 Processing helix chain 'B' and resid 352 through 357 Processing helix chain 'B' and resid 377 through 382 Processing helix chain 'B' and resid 387 through 390 Processing helix chain 'B' and resid 391 through 402 Processing helix chain 'B' and resid 421 through 425 Processing helix chain 'B' and resid 429 through 436 Processing helix chain 'B' and resid 438 through 449 Processing helix chain 'B' and resid 450 through 461 removed outlier: 3.531A pdb=" N THR B 454 " --> pdb=" O PRO B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 497 Processing helix chain 'B' and resid 502 through 513 removed outlier: 3.617A pdb=" N SER B 512 " --> pdb=" O GLN B 508 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU B 513 " --> pdb=" O LEU B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 579 Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 164 removed outlier: 6.597A pdb=" N VAL A 160 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ILE A 182 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ARG A 162 " --> pdb=" O ILE A 182 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 346 through 350 removed outlier: 6.898A pdb=" N ASP A 346 " --> pdb=" O TYR A 373 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N ILE A 375 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLN A 348 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLY A 530 " --> pdb=" O ASN A 537 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N GLY A 539 " --> pdb=" O GLY A 528 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLY A 528 " --> pdb=" O GLY A 539 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE A 541 " --> pdb=" O LYS A 526 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LYS A 526 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLY A 543 " --> pdb=" O TYR A 524 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N TYR A 524 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL A 545 " --> pdb=" O GLU A 522 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLU A 522 " --> pdb=" O VAL A 545 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N TYR A 521 " --> pdb=" O LYS A 517 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LYS A 517 " --> pdb=" O TYR A 521 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU A 523 " --> pdb=" O ILE A 515 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 160 through 164 removed outlier: 6.596A pdb=" N VAL B 160 " --> pdb=" O ILE B 180 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ILE B 182 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ARG B 162 " --> pdb=" O ILE B 182 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 346 through 350 removed outlier: 6.897A pdb=" N ASP B 346 " --> pdb=" O TYR B 373 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ILE B 375 " --> pdb=" O ASP B 346 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLN B 348 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLY B 530 " --> pdb=" O ASN B 537 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N GLY B 539 " --> pdb=" O GLY B 528 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLY B 528 " --> pdb=" O GLY B 539 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE B 541 " --> pdb=" O LYS B 526 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LYS B 526 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLY B 543 " --> pdb=" O TYR B 524 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N TYR B 524 " --> pdb=" O GLY B 543 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL B 545 " --> pdb=" O GLU B 522 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLU B 522 " --> pdb=" O VAL B 545 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TYR B 521 " --> pdb=" O LYS B 517 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LYS B 517 " --> pdb=" O TYR B 521 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU B 523 " --> pdb=" O ILE B 515 " (cutoff:3.500A) 489 hydrogen bonds defined for protein. 1401 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: 2.73 Time building geometry restraints manager: 3.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1464 1.30 - 1.43: 2855 1.43 - 1.57: 5100 1.57 - 1.70: 57 1.70 - 1.84: 70 Bond restraints: 9546 Sorted by residual: bond pdb=" CB HIS A 201 " pdb=" CG HIS A 201 " ideal model delta sigma weight residual 1.497 1.388 0.109 1.40e-02 5.10e+03 6.08e+01 bond pdb=" CB HIS B 201 " pdb=" CG HIS B 201 " ideal model delta sigma weight residual 1.497 1.389 0.108 1.40e-02 5.10e+03 6.00e+01 bond pdb=" CB PHE B 501 " pdb=" CG PHE B 501 " ideal model delta sigma weight residual 1.502 1.380 0.122 2.30e-02 1.89e+03 2.84e+01 bond pdb=" CB PHE A 501 " pdb=" CG PHE A 501 " ideal model delta sigma weight residual 1.502 1.381 0.121 2.30e-02 1.89e+03 2.78e+01 bond pdb=" CB HIS A 549 " pdb=" CG HIS A 549 " ideal model delta sigma weight residual 1.497 1.562 -0.065 1.40e-02 5.10e+03 2.17e+01 ... (remaining 9541 not shown) Histogram of bond angle deviations from ideal: 100.17 - 106.97: 322 106.97 - 113.77: 4913 113.77 - 120.57: 4431 120.57 - 127.37: 3096 127.37 - 134.17: 94 Bond angle restraints: 12856 Sorted by residual: angle pdb=" C SER A 386 " pdb=" N PRO A 387 " pdb=" CA PRO A 387 " ideal model delta sigma weight residual 119.56 128.94 -9.38 1.02e+00 9.61e-01 8.46e+01 angle pdb=" C SER B 386 " pdb=" N PRO B 387 " pdb=" CA PRO B 387 " ideal model delta sigma weight residual 119.56 128.84 -9.28 1.02e+00 9.61e-01 8.29e+01 angle pdb=" N ILE A 222 " pdb=" CA ILE A 222 " pdb=" C ILE A 222 " ideal model delta sigma weight residual 111.45 103.71 7.74 9.30e-01 1.16e+00 6.93e+01 angle pdb=" N ILE B 222 " pdb=" CA ILE B 222 " pdb=" C ILE B 222 " ideal model delta sigma weight residual 111.45 103.78 7.67 9.30e-01 1.16e+00 6.81e+01 angle pdb=" N TYR A 521 " pdb=" CA TYR A 521 " pdb=" C TYR A 521 " ideal model delta sigma weight residual 108.60 120.52 -11.92 1.46e+00 4.69e-01 6.67e+01 ... (remaining 12851 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.28: 5462 16.28 - 32.57: 183 32.57 - 48.85: 37 48.85 - 65.13: 20 65.13 - 81.41: 6 Dihedral angle restraints: 5708 sinusoidal: 2376 harmonic: 3332 Sorted by residual: dihedral pdb=" C ASN A 406 " pdb=" N ASN A 406 " pdb=" CA ASN A 406 " pdb=" CB ASN A 406 " ideal model delta harmonic sigma weight residual -122.60 -132.18 9.58 0 2.50e+00 1.60e-01 1.47e+01 dihedral pdb=" C ASN B 406 " pdb=" N ASN B 406 " pdb=" CA ASN B 406 " pdb=" CB ASN B 406 " ideal model delta harmonic sigma weight residual -122.60 -132.11 9.51 0 2.50e+00 1.60e-01 1.45e+01 dihedral pdb=" CA GLU A 202 " pdb=" CB GLU A 202 " pdb=" CG GLU A 202 " pdb=" CD GLU A 202 " ideal model delta sinusoidal sigma weight residual 60.00 4.59 55.41 3 1.50e+01 4.44e-03 9.35e+00 ... (remaining 5705 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 765 0.076 - 0.153: 463 0.153 - 0.229: 148 0.229 - 0.305: 10 0.305 - 0.381: 8 Chirality restraints: 1394 Sorted by residual: chirality pdb=" CA PHE A 220 " pdb=" N PHE A 220 " pdb=" C PHE A 220 " pdb=" CB PHE A 220 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.64e+00 chirality pdb=" CA PHE B 220 " pdb=" N PHE B 220 " pdb=" C PHE B 220 " pdb=" CB PHE B 220 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" CA ILE B 515 " pdb=" N ILE B 515 " pdb=" C ILE B 515 " pdb=" CB ILE B 515 " both_signs ideal model delta sigma weight residual False 2.43 2.80 -0.37 2.00e-01 2.50e+01 3.37e+00 ... (remaining 1391 not shown) Planarity restraints: 1576 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 419 " 0.062 2.00e-02 2.50e+03 3.23e-02 2.09e+01 pdb=" CG TYR A 419 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR A 419 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR A 419 " -0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR A 419 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR A 419 " -0.015 2.00e-02 2.50e+03 pdb=" CZ TYR A 419 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 419 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 419 " -0.061 2.00e-02 2.50e+03 3.20e-02 2.05e+01 pdb=" CG TYR B 419 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR B 419 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR B 419 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR B 419 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR B 419 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR B 419 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 419 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 540 " 0.056 2.00e-02 2.50e+03 2.68e-02 1.79e+01 pdb=" CG TRP B 540 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TRP B 540 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP B 540 " -0.025 2.00e-02 2.50e+03 pdb=" NE1 TRP B 540 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP B 540 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 540 " -0.029 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 540 " 0.035 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 540 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP B 540 " 0.022 2.00e-02 2.50e+03 ... (remaining 1573 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.36: 16 2.36 - 2.99: 5681 2.99 - 3.63: 14464 3.63 - 4.26: 24287 4.26 - 4.90: 37307 Nonbonded interactions: 81755 Sorted by model distance: nonbonded pdb=" CB ASP A 422 " pdb=" CB ASP B 422 " model vdw 1.722 3.840 nonbonded pdb=" O ALA A 91 " pdb=" CZ PHE B 421 " model vdw 1.923 3.340 nonbonded pdb=" CZ PHE A 421 " pdb=" O ALA B 91 " model vdw 1.924 3.340 nonbonded pdb=" OE2 GLU B 242 " pdb="ZN ZN B 701 " model vdw 2.099 2.230 nonbonded pdb=" OE2 GLU A 242 " pdb="ZN ZN A 701 " model vdw 2.099 2.230 ... (remaining 81750 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.330 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: 0.010 Extract box with map and model: 2.200 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 30.150 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5053 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 : 0.020 0.122 9546 Z= 1.281 Angle : 1.722 11.922 12856 Z= 1.186 Chirality : 0.099 0.381 1394 Planarity : 0.009 0.041 1576 Dihedral : 10.181 81.415 3560 Min Nonbonded Distance : 1.722 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.58 % Allowed : 0.77 % Favored : 98.65 % 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: 0.10 (0.23), residues: 1104 helix: 0.31 (0.19), residues: 594 sheet: 0.08 (0.47), residues: 124 loop : -0.07 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.008 TRP B 540 HIS 0.010 0.002 HIS A 205 PHE 0.047 0.006 PHE A 274 TYR 0.062 0.010 TYR A 419 ARG 0.003 0.001 ARG B 384 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 341 time to evaluate : 0.935 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: A 173 PHE cc_start: 0.4322 (m-80) cc_final: 0.3598 (m-80) REVERT: A 316 ILE cc_start: 0.7263 (tp) cc_final: 0.6910 (tp) REVERT: A 320 LEU cc_start: 0.8007 (mt) cc_final: 0.7510 (tp) REVERT: A 412 MET cc_start: 0.2881 (tpp) cc_final: 0.1904 (tpp) REVERT: A 434 MET cc_start: 0.4727 (tpp) cc_final: 0.4362 (tpp) REVERT: B 173 PHE cc_start: 0.4309 (m-80) cc_final: 0.3592 (m-80) REVERT: B 316 ILE cc_start: 0.7205 (tp) cc_final: 0.6845 (tp) REVERT: B 320 LEU cc_start: 0.8018 (mt) cc_final: 0.7504 (tp) REVERT: B 412 MET cc_start: 0.3080 (tpp) cc_final: 0.2131 (tpp) REVERT: B 434 MET cc_start: 0.4728 (tpp) cc_final: 0.4340 (tpp) outliers start: 6 outliers final: 2 residues processed: 343 average time/residue: 0.2321 time to fit residues: 108.7896 Evaluate side-chains 202 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 200 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 ASN A 252 ASN A 297 ASN A 409 ASN ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN B 252 ASN B 297 ASN B 409 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5024 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9546 Z= 0.212 Angle : 0.619 5.966 12856 Z= 0.356 Chirality : 0.044 0.177 1394 Planarity : 0.004 0.031 1576 Dihedral : 4.815 20.452 1212 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.62 % Favored : 96.20 % Rotamer: Outliers : 0.39 % Allowed : 2.02 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.25), residues: 1104 helix: 1.28 (0.20), residues: 588 sheet: 0.23 (0.49), residues: 128 loop : -0.27 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 424 HIS 0.003 0.001 HIS A 403 PHE 0.028 0.002 PHE B 22 TYR 0.024 0.002 TYR A 203 ARG 0.003 0.001 ARG A 23 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 288 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 PHE cc_start: 0.4544 (m-80) cc_final: 0.4221 (m-80) REVERT: A 195 LEU cc_start: 0.6943 (mm) cc_final: 0.6485 (mm) REVERT: A 237 ILE cc_start: 0.8826 (mt) cc_final: 0.8605 (mt) REVERT: A 310 ILE cc_start: 0.7586 (mt) cc_final: 0.6640 (tt) REVERT: A 322 MET cc_start: 0.5818 (ttp) cc_final: 0.5410 (ttp) REVERT: A 434 MET cc_start: 0.4066 (tpp) cc_final: 0.3652 (tpp) REVERT: A 499 ASN cc_start: 0.6942 (p0) cc_final: 0.6722 (p0) REVERT: B 173 PHE cc_start: 0.4535 (m-80) cc_final: 0.4202 (m-80) REVERT: B 195 LEU cc_start: 0.6937 (mm) cc_final: 0.6513 (mm) REVERT: B 237 ILE cc_start: 0.8825 (mt) cc_final: 0.8590 (mt) REVERT: B 310 ILE cc_start: 0.7586 (mt) cc_final: 0.6672 (tt) REVERT: B 322 MET cc_start: 0.5876 (ttp) cc_final: 0.5460 (ttp) REVERT: B 434 MET cc_start: 0.4062 (tpp) cc_final: 0.3582 (tpp) outliers start: 4 outliers final: 2 residues processed: 292 average time/residue: 0.1902 time to fit residues: 80.0885 Evaluate side-chains 231 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 229 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 chunk 100 optimal weight: 20.0000 chunk 108 optimal weight: 0.4980 chunk 89 optimal weight: 2.9990 chunk 99 optimal weight: 0.3980 chunk 34 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 ASN A 327 GLN A 428 GLN ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5051 moved from start: 0.4420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9546 Z= 0.169 Angle : 0.531 5.196 12856 Z= 0.302 Chirality : 0.042 0.159 1394 Planarity : 0.003 0.025 1576 Dihedral : 4.520 16.771 1212 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.10 % Allowed : 1.54 % Favored : 98.36 % 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: 1.02 (0.25), residues: 1104 helix: 1.48 (0.21), residues: 584 sheet: 0.23 (0.49), residues: 126 loop : -0.29 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 424 HIS 0.003 0.001 HIS B 282 PHE 0.024 0.002 PHE B 22 TYR 0.032 0.002 TYR B 391 ARG 0.002 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 257 time to evaluate : 1.031 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: A 173 PHE cc_start: 0.4548 (m-80) cc_final: 0.4151 (m-80) REVERT: A 181 LEU cc_start: 0.7707 (tp) cc_final: 0.7450 (tp) REVERT: A 195 LEU cc_start: 0.6997 (mm) cc_final: 0.6594 (mm) REVERT: A 237 ILE cc_start: 0.8852 (mt) cc_final: 0.8538 (mt) REVERT: A 499 ASN cc_start: 0.6958 (p0) cc_final: 0.6581 (p0) REVERT: B 173 PHE cc_start: 0.4536 (m-80) cc_final: 0.4124 (m-80) REVERT: B 181 LEU cc_start: 0.7721 (tp) cc_final: 0.7416 (tp) REVERT: B 195 LEU cc_start: 0.6834 (mm) cc_final: 0.6160 (mm) REVERT: B 237 ILE cc_start: 0.8885 (mt) cc_final: 0.8551 (mt) outliers start: 1 outliers final: 1 residues processed: 258 average time/residue: 0.1785 time to fit residues: 66.3501 Evaluate side-chains 202 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 201 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 67 optimal weight: 0.0270 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 8.9990 chunk 52 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 overall best weight: 1.7644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 ASN ** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 GLN ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 252 ASN ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5170 moved from start: 0.5103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9546 Z= 0.226 Angle : 0.574 7.474 12856 Z= 0.320 Chirality : 0.043 0.178 1394 Planarity : 0.004 0.031 1576 Dihedral : 4.574 15.800 1212 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % 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 (0.25), residues: 1104 helix: 1.24 (0.20), residues: 588 sheet: 0.26 (0.49), residues: 126 loop : -0.63 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 475 HIS 0.006 0.001 HIS A 231 PHE 0.031 0.002 PHE A 491 TYR 0.018 0.002 TYR B 441 ARG 0.003 0.000 ARG A 247 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 253 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.8099 (mt) cc_final: 0.7886 (mp) REVERT: A 173 PHE cc_start: 0.4931 (m-80) cc_final: 0.4362 (m-80) REVERT: A 181 LEU cc_start: 0.7733 (tp) cc_final: 0.7483 (tp) REVERT: A 195 LEU cc_start: 0.7023 (mm) cc_final: 0.6641 (mm) REVERT: A 434 MET cc_start: 0.4073 (tpp) cc_final: 0.3561 (tpp) REVERT: A 499 ASN cc_start: 0.6875 (p0) cc_final: 0.6345 (p0) REVERT: B 195 LEU cc_start: 0.7157 (mm) cc_final: 0.6657 (mm) REVERT: B 434 MET cc_start: 0.4131 (tpp) cc_final: 0.3617 (tpp) outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.1834 time to fit residues: 67.0726 Evaluate side-chains 189 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 79 optimal weight: 0.0030 chunk 43 optimal weight: 7.9990 chunk 90 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 54 optimal weight: 0.5980 chunk 95 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 GLN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 GLN B 428 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5104 moved from start: 0.5594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9546 Z= 0.150 Angle : 0.523 8.909 12856 Z= 0.289 Chirality : 0.041 0.152 1394 Planarity : 0.003 0.033 1576 Dihedral : 4.366 14.741 1212 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % 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: 0.88 (0.25), residues: 1104 helix: 1.35 (0.20), residues: 592 sheet: 0.37 (0.49), residues: 126 loop : -0.46 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 424 HIS 0.003 0.001 HIS A 205 PHE 0.031 0.002 PHE A 22 TYR 0.020 0.001 TYR B 203 ARG 0.003 0.000 ARG B 247 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 253 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 PHE cc_start: 0.4658 (m-80) cc_final: 0.4158 (m-80) REVERT: A 181 LEU cc_start: 0.7821 (tp) cc_final: 0.7424 (tp) REVERT: A 195 LEU cc_start: 0.6982 (mm) cc_final: 0.6542 (mm) REVERT: A 499 ASN cc_start: 0.6685 (p0) cc_final: 0.6296 (p0) REVERT: B 195 LEU cc_start: 0.7044 (mm) cc_final: 0.6418 (mm) outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.1840 time to fit residues: 67.2022 Evaluate side-chains 190 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 106 optimal weight: 20.0000 chunk 88 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 102 optimal weight: 9.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 GLN ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 252 ASN ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 GLN ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5116 moved from start: 0.5858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9546 Z= 0.162 Angle : 0.546 8.464 12856 Z= 0.297 Chirality : 0.042 0.201 1394 Planarity : 0.003 0.039 1576 Dihedral : 4.405 15.601 1212 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.25), residues: 1104 helix: 1.28 (0.21), residues: 596 sheet: 0.49 (0.48), residues: 126 loop : -0.50 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 475 HIS 0.017 0.002 HIS B 95 PHE 0.030 0.002 PHE A 491 TYR 0.027 0.002 TYR B 337 ARG 0.003 0.000 ARG B 247 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 1.132 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: A 195 LEU cc_start: 0.7101 (mm) cc_final: 0.6427 (mm) REVERT: A 499 ASN cc_start: 0.6739 (p0) cc_final: 0.6276 (p0) REVERT: B 171 ILE cc_start: 0.8561 (mm) cc_final: 0.8275 (tp) REVERT: B 195 LEU cc_start: 0.6992 (mm) cc_final: 0.6551 (mm) REVERT: B 499 ASN cc_start: 0.6728 (p0) cc_final: 0.6354 (p0) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.1649 time to fit residues: 59.2083 Evaluate side-chains 184 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 89 optimal weight: 6.9990 chunk 59 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 ASN A 327 GLN ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 ASN B 95 HIS ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 GLN B 537 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5093 moved from start: 0.6140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9546 Z= 0.166 Angle : 0.555 8.121 12856 Z= 0.298 Chirality : 0.042 0.161 1394 Planarity : 0.003 0.040 1576 Dihedral : 4.321 16.051 1212 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % 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: 0.82 (0.25), residues: 1104 helix: 1.31 (0.21), residues: 584 sheet: 0.39 (0.48), residues: 130 loop : -0.47 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 540 HIS 0.013 0.001 HIS B 95 PHE 0.025 0.002 PHE A 217 TYR 0.018 0.001 TYR B 203 ARG 0.003 0.000 ARG B 247 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 249 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 ILE cc_start: 0.8598 (mm) cc_final: 0.8232 (tp) REVERT: A 434 MET cc_start: 0.3883 (tpp) cc_final: 0.3660 (tpp) REVERT: A 499 ASN cc_start: 0.6742 (p0) cc_final: 0.6351 (p0) REVERT: B 195 LEU cc_start: 0.7035 (mm) cc_final: 0.6619 (mm) REVERT: B 499 ASN cc_start: 0.6748 (p0) cc_final: 0.6505 (p0) outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.1694 time to fit residues: 62.6642 Evaluate side-chains 198 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 83 optimal weight: 0.2980 chunk 96 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 HIS ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 ASN A 327 GLN ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 GLN ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5110 moved from start: 0.6421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9546 Z= 0.176 Angle : 0.599 7.739 12856 Z= 0.322 Chirality : 0.043 0.231 1394 Planarity : 0.004 0.039 1576 Dihedral : 4.394 16.666 1212 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % 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: 0.81 (0.25), residues: 1104 helix: 1.27 (0.21), residues: 584 sheet: 0.67 (0.48), residues: 126 loop : -0.55 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 475 HIS 0.012 0.001 HIS A 95 PHE 0.043 0.002 PHE B 491 TYR 0.018 0.002 TYR B 203 ARG 0.003 0.000 ARG B 247 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.7756 (mp) cc_final: 0.7472 (mp) REVERT: A 95 HIS cc_start: 0.1678 (p90) cc_final: 0.1247 (p-80) REVERT: A 195 LEU cc_start: 0.7075 (mm) cc_final: 0.6620 (mm) REVERT: A 202 GLU cc_start: 0.6939 (mm-30) cc_final: 0.6648 (mm-30) REVERT: A 226 TYR cc_start: 0.6311 (p90) cc_final: 0.6107 (p90) REVERT: A 434 MET cc_start: 0.4028 (tpp) cc_final: 0.3785 (tpp) REVERT: A 499 ASN cc_start: 0.6746 (p0) cc_final: 0.6225 (p0) REVERT: B 151 PHE cc_start: 0.5473 (t80) cc_final: 0.5253 (t80) REVERT: B 195 LEU cc_start: 0.7022 (mm) cc_final: 0.6454 (mm) REVERT: B 499 ASN cc_start: 0.6783 (p0) cc_final: 0.6502 (p0) outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 0.1729 time to fit residues: 63.0151 Evaluate side-chains 185 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 89 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 ASN A 409 ASN ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 HIS ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 GLN B 327 GLN B 436 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5184 moved from start: 0.6587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9546 Z= 0.235 Angle : 0.643 9.729 12856 Z= 0.345 Chirality : 0.044 0.185 1394 Planarity : 0.004 0.044 1576 Dihedral : 4.502 17.285 1212 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % 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 (0.25), residues: 1104 helix: 1.07 (0.21), residues: 582 sheet: 0.29 (0.48), residues: 130 loop : -0.74 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 424 HIS 0.011 0.002 HIS B 95 PHE 0.031 0.002 PHE A 21 TYR 0.026 0.002 TYR A 32 ARG 0.003 0.000 ARG B 247 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 LEU cc_start: 0.7109 (mm) cc_final: 0.6712 (mm) REVERT: A 499 ASN cc_start: 0.6829 (p0) cc_final: 0.6369 (p0) REVERT: B 151 PHE cc_start: 0.5618 (t80) cc_final: 0.5363 (t80) REVERT: B 195 LEU cc_start: 0.6997 (mm) cc_final: 0.6575 (mm) REVERT: B 499 ASN cc_start: 0.6768 (p0) cc_final: 0.6477 (p0) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.1736 time to fit residues: 59.5404 Evaluate side-chains 169 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 9 optimal weight: 0.0270 chunk 67 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 HIS ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 ASN A 327 GLN A 436 ASN ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS B 227 ASN ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5142 moved from start: 0.6822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9546 Z= 0.183 Angle : 0.612 9.447 12856 Z= 0.326 Chirality : 0.043 0.161 1394 Planarity : 0.004 0.048 1576 Dihedral : 4.458 16.615 1212 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.25), residues: 1104 helix: 1.02 (0.21), residues: 582 sheet: 0.47 (0.47), residues: 126 loop : -0.66 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 110 HIS 0.010 0.001 HIS A 95 PHE 0.028 0.002 PHE B 21 TYR 0.021 0.002 TYR B 337 ARG 0.002 0.000 ARG B 247 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 LEU cc_start: 0.7058 (mm) cc_final: 0.6642 (mm) REVERT: A 499 ASN cc_start: 0.6813 (p0) cc_final: 0.6363 (p0) REVERT: B 151 PHE cc_start: 0.5565 (t80) cc_final: 0.5331 (t80) REVERT: B 499 ASN cc_start: 0.6733 (p0) cc_final: 0.6431 (p0) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.1790 time to fit residues: 62.0650 Evaluate side-chains 184 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 5.9990 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 76 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 ASN A 327 GLN A 436 ASN A 448 GLN B 95 HIS ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS B 327 GLN B 436 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.162454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.115284 restraints weight = 23053.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.118870 restraints weight = 14516.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.121304 restraints weight = 10464.419| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 moved from start: 0.7006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9546 Z= 0.172 Angle : 0.609 9.386 12856 Z= 0.323 Chirality : 0.043 0.185 1394 Planarity : 0.004 0.047 1576 Dihedral : 4.385 15.931 1212 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.25), residues: 1104 helix: 1.07 (0.21), residues: 582 sheet: 0.42 (0.47), residues: 126 loop : -0.69 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 39 HIS 0.011 0.001 HIS B 95 PHE 0.029 0.002 PHE B 21 TYR 0.026 0.002 TYR B 36 ARG 0.003 0.000 ARG A 194 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2157.84 seconds wall clock time: 39 minutes 57.75 seconds (2397.75 seconds total)