Starting phenix.real_space_refine on Tue Feb 13 21:33:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avv_15684/02_2024/8avv_15684_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avv_15684/02_2024/8avv_15684.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avv_15684/02_2024/8avv_15684.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avv_15684/02_2024/8avv_15684.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avv_15684/02_2024/8avv_15684_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avv_15684/02_2024/8avv_15684_updated.pdb" } resolution = 3.4 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= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 4958 2.51 5 N 1378 2.21 5 O 1436 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 26": "NH1" <-> "NH2" Residue "A ARG 70": "NH1" <-> "NH2" Residue "A GLU 125": "OE1" <-> "OE2" Residue "A GLU 148": "OE1" <-> "OE2" Residue "A GLU 185": "OE1" <-> "OE2" Residue "A ARG 192": "NH1" <-> "NH2" Residue "A ARG 222": "NH1" <-> "NH2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A ARG 254": "NH1" <-> "NH2" Residue "A TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ARG 310": "NH1" <-> "NH2" Residue "A GLU 333": "OE1" <-> "OE2" Residue "A ARG 337": "NH1" <-> "NH2" Residue "A ARG 375": "NH1" <-> "NH2" Residue "A GLU 381": "OE1" <-> "OE2" Residue "A GLU 432": "OE1" <-> "OE2" Residue "A ARG 442": "NH1" <-> "NH2" Residue "A GLU 444": "OE1" <-> "OE2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A GLU 475": "OE1" <-> "OE2" Residue "A ARG 477": "NH1" <-> "NH2" Residue "A GLU 489": "OE1" <-> "OE2" Residue "A GLU 490": "OE1" <-> "OE2" Residue "A ARG 495": "NH1" <-> "NH2" Residue "B ARG 26": "NH1" <-> "NH2" Residue "B ARG 70": "NH1" <-> "NH2" Residue "B GLU 125": "OE1" <-> "OE2" Residue "B GLU 148": "OE1" <-> "OE2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "B ARG 192": "NH1" <-> "NH2" Residue "B ARG 222": "NH1" <-> "NH2" Residue "B ARG 228": "NH1" <-> "NH2" Residue "B ARG 254": "NH1" <-> "NH2" Residue "B TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 265": "NH1" <-> "NH2" Residue "B ARG 310": "NH1" <-> "NH2" Residue "B GLU 333": "OE1" <-> "OE2" Residue "B ARG 337": "NH1" <-> "NH2" Residue "B ARG 375": "NH1" <-> "NH2" Residue "B GLU 432": "OE1" <-> "OE2" Residue "B ARG 442": "NH1" <-> "NH2" Residue "B GLU 444": "OE1" <-> "OE2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "B GLU 475": "OE1" <-> "OE2" Residue "B ARG 477": "NH1" <-> "NH2" Residue "B GLU 489": "OE1" <-> "OE2" Residue "B GLU 490": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7794 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3849 Classifications: {'peptide': 504} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 463} Chain breaks: 2 Chain: "B" Number of atoms: 3859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3859 Classifications: {'peptide': 506} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 465} Chain breaks: 1 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'LBV': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'LBV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.54, per 1000 atoms: 0.58 Number of scatterers: 7794 At special positions: 0 Unit cell: (93.0636, 98.2338, 115.468, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 1436 8.00 N 1378 7.00 C 4958 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: 2.90 Conformation dependent library (CDL) restraints added in 1.4 seconds 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1856 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 8 sheets defined 31.3% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'A' and resid 58 through 62 Processing helix chain 'A' and resid 66 through 69 No H-bonds generated for 'chain 'A' and resid 66 through 69' Processing helix chain 'A' and resid 74 through 77 No H-bonds generated for 'chain 'A' and resid 74 through 77' Processing helix chain 'A' and resid 82 through 88 removed outlier: 3.645A pdb=" N ALA A 87 " --> pdb=" O PRO A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 147 Processing helix chain 'A' and resid 156 through 168 removed outlier: 3.518A pdb=" N THR A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 215 Processing helix chain 'A' and resid 258 through 266 removed outlier: 3.520A pdb=" N GLN A 262 " --> pdb=" O PRO A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 329 removed outlier: 3.619A pdb=" N THR A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N THR A 304 " --> pdb=" O ASP A 300 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 314 " --> pdb=" O ARG A 310 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLN A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL A 318 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN A 329 " --> pdb=" O ALA A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 341 removed outlier: 3.753A pdb=" N VAL A 338 " --> pdb=" O HIS A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 351 No H-bonds generated for 'chain 'A' and resid 348 through 351' Processing helix chain 'A' and resid 385 through 397 removed outlier: 3.769A pdb=" N ASP A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR A 397 " --> pdb=" O ALA A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 411 No H-bonds generated for 'chain 'A' and resid 408 through 411' Processing helix chain 'A' and resid 413 through 415 No H-bonds generated for 'chain 'A' and resid 413 through 415' Processing helix chain 'A' and resid 456 through 459 removed outlier: 3.867A pdb=" N ALA A 459 " --> pdb=" O PRO A 456 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 456 through 459' Processing helix chain 'A' and resid 485 through 518 removed outlier: 3.578A pdb=" N ASP A 493 " --> pdb=" O GLU A 489 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 494 " --> pdb=" O GLU A 490 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP A 496 " --> pdb=" O GLN A 492 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR A 497 " --> pdb=" O ASP A 493 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A 502 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLY A 503 " --> pdb=" O THR A 499 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N GLU A 504 " --> pdb=" O GLY A 500 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG A 505 " --> pdb=" O ALA A 501 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP A 511 " --> pdb=" O SER A 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 62 Processing helix chain 'B' and resid 66 through 69 No H-bonds generated for 'chain 'B' and resid 66 through 69' Processing helix chain 'B' and resid 74 through 77 No H-bonds generated for 'chain 'B' and resid 74 through 77' Processing helix chain 'B' and resid 82 through 88 removed outlier: 3.643A pdb=" N ALA B 87 " --> pdb=" O PRO B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 147 Processing helix chain 'B' and resid 156 through 168 removed outlier: 3.525A pdb=" N THR B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 215 Processing helix chain 'B' and resid 258 through 266 removed outlier: 3.518A pdb=" N GLN B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 329 removed outlier: 3.617A pdb=" N THR B 303 " --> pdb=" O PRO B 299 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N THR B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 314 " --> pdb=" O ARG B 310 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLN B 317 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 318 " --> pdb=" O LEU B 314 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA B 325 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN B 329 " --> pdb=" O ALA B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 341 removed outlier: 3.746A pdb=" N VAL B 338 " --> pdb=" O HIS B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 351 No H-bonds generated for 'chain 'B' and resid 348 through 351' Processing helix chain 'B' and resid 385 through 397 removed outlier: 3.773A pdb=" N ASP B 389 " --> pdb=" O ALA B 385 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N THR B 397 " --> pdb=" O ALA B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 411 No H-bonds generated for 'chain 'B' and resid 408 through 411' Processing helix chain 'B' and resid 413 through 415 No H-bonds generated for 'chain 'B' and resid 413 through 415' Processing helix chain 'B' and resid 456 through 459 removed outlier: 3.868A pdb=" N ALA B 459 " --> pdb=" O PRO B 456 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 456 through 459' Processing helix chain 'B' and resid 485 through 518 removed outlier: 3.570A pdb=" N ASP B 493 " --> pdb=" O GLU B 489 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B 494 " --> pdb=" O GLU B 490 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP B 496 " --> pdb=" O GLN B 492 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR B 497 " --> pdb=" O ASP B 493 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU B 502 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLY B 503 " --> pdb=" O THR B 499 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N GLU B 504 " --> pdb=" O GLY B 500 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG B 505 " --> pdb=" O ALA B 501 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP B 511 " --> pdb=" O SER B 507 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 99 through 103 removed outlier: 6.220A pdb=" N ASP A 45 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL A 51 " --> pdb=" O ASP A 45 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 184 through 191 removed outlier: 6.962A pdb=" N LEU A 175 " --> pdb=" O ILE A 187 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLU A 189 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL A 173 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N TRP A 284 " --> pdb=" O PHE A 178 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL A 277 " --> pdb=" O TRP A 284 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LEU A 286 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL A 275 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ALA A 288 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU A 273 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N HIS A 290 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N SER A 271 " --> pdb=" O HIS A 290 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 375 through 380 removed outlier: 3.528A pdb=" N PHE A 372 " --> pdb=" O ARG A 375 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 447 through 452 removed outlier: 3.818A pdb=" N LEU A 447 " --> pdb=" O LYS A 476 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 99 through 103 removed outlier: 6.227A pdb=" N ASP B 45 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL B 51 " --> pdb=" O ASP B 45 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 184 through 191 removed outlier: 6.974A pdb=" N LEU B 175 " --> pdb=" O ILE B 187 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLU B 189 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL B 173 " --> pdb=" O GLU B 189 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N TRP B 284 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL B 277 " --> pdb=" O TRP B 284 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N LEU B 286 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL B 275 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ALA B 288 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU B 273 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N HIS B 290 " --> pdb=" O SER B 271 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N SER B 271 " --> pdb=" O HIS B 290 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 375 through 380 removed outlier: 3.529A pdb=" N PHE B 372 " --> pdb=" O ARG B 375 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 447 through 452 removed outlier: 3.811A pdb=" N LEU B 447 " --> pdb=" O LYS B 476 " (cutoff:3.500A) 270 hydrogen bonds defined for protein. 759 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: 2.20 Time building geometry restraints manager: 3.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1984 1.34 - 1.46: 2367 1.46 - 1.58: 3608 1.58 - 1.70: 0 1.70 - 1.82: 36 Bond restraints: 7995 Sorted by residual: bond pdb=" C2D LBV A1000 " pdb=" C3D LBV A1000 " ideal model delta sigma weight residual 1.358 1.435 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" C2D LBV B1000 " pdb=" C3D LBV B1000 " ideal model delta sigma weight residual 1.358 1.432 -0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C3A LBV B1000 " pdb=" C4A LBV B1000 " ideal model delta sigma weight residual 1.463 1.392 0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C4C LBV B1000 " pdb=" CHD LBV B1000 " ideal model delta sigma weight residual 1.428 1.360 0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" C4C LBV A1000 " pdb=" CHD LBV A1000 " ideal model delta sigma weight residual 1.428 1.363 0.065 2.00e-02 2.50e+03 1.05e+01 ... (remaining 7990 not shown) Histogram of bond angle deviations from ideal: 99.99 - 107.07: 436 107.07 - 114.16: 4373 114.16 - 121.25: 3515 121.25 - 128.34: 2533 128.34 - 135.43: 86 Bond angle restraints: 10943 Sorted by residual: angle pdb=" N LEU B 346 " pdb=" CA LEU B 346 " pdb=" C LEU B 346 " ideal model delta sigma weight residual 114.31 108.90 5.41 1.29e+00 6.01e-01 1.76e+01 angle pdb=" N LEU A 346 " pdb=" CA LEU A 346 " pdb=" C LEU A 346 " ideal model delta sigma weight residual 114.31 109.14 5.17 1.29e+00 6.01e-01 1.61e+01 angle pdb=" C LEU A 297 " pdb=" N PRO A 298 " pdb=" CA PRO A 298 " ideal model delta sigma weight residual 119.66 122.50 -2.84 7.20e-01 1.93e+00 1.56e+01 angle pdb=" C GLN B 398 " pdb=" CA GLN B 398 " pdb=" CB GLN B 398 " ideal model delta sigma weight residual 109.26 114.91 -5.65 1.47e+00 4.63e-01 1.48e+01 angle pdb=" C GLN A 398 " pdb=" CA GLN A 398 " pdb=" CB GLN A 398 " ideal model delta sigma weight residual 109.26 114.88 -5.62 1.47e+00 4.63e-01 1.46e+01 ... (remaining 10938 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.78: 4031 15.78 - 31.55: 464 31.55 - 47.32: 181 47.32 - 63.10: 54 63.10 - 78.87: 41 Dihedral angle restraints: 4771 sinusoidal: 1892 harmonic: 2879 Sorted by residual: dihedral pdb=" CA HIS B 219 " pdb=" C HIS B 219 " pdb=" N LEU B 220 " pdb=" CA LEU B 220 " ideal model delta harmonic sigma weight residual -180.00 -157.73 -22.27 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA HIS A 219 " pdb=" C HIS A 219 " pdb=" N LEU A 220 " pdb=" CA LEU A 220 " ideal model delta harmonic sigma weight residual -180.00 -157.74 -22.26 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA MET B 54 " pdb=" C MET B 54 " pdb=" N SER B 55 " pdb=" CA SER B 55 " ideal model delta harmonic sigma weight residual 180.00 159.38 20.62 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 4768 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 665 0.055 - 0.110: 337 0.110 - 0.165: 165 0.165 - 0.221: 55 0.221 - 0.276: 8 Chirality restraints: 1230 Sorted by residual: chirality pdb=" CA ARG B 337 " pdb=" N ARG B 337 " pdb=" C ARG B 337 " pdb=" CB ARG B 337 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA ASN A 243 " pdb=" N ASN A 243 " pdb=" C ASN A 243 " pdb=" CB ASN A 243 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CA ASN B 243 " pdb=" N ASN B 243 " pdb=" C ASN B 243 " pdb=" CB ASN B 243 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 1227 not shown) Planarity restraints: 1437 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D LBV B1000 " 0.021 2.00e-02 2.50e+03 2.03e-01 9.27e+02 pdb=" C2D LBV B1000 " -0.088 2.00e-02 2.50e+03 pdb=" C3D LBV B1000 " 0.053 2.00e-02 2.50e+03 pdb=" C4D LBV B1000 " -0.071 2.00e-02 2.50e+03 pdb=" CAD LBV B1000 " 0.269 2.00e-02 2.50e+03 pdb=" CHD LBV B1000 " 0.362 2.00e-02 2.50e+03 pdb=" CMD LBV B1000 " -0.265 2.00e-02 2.50e+03 pdb=" N_D LBV B1000 " -0.285 2.00e-02 2.50e+03 pdb=" O_D LBV B1000 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D LBV A1000 " 0.024 2.00e-02 2.50e+03 1.68e-01 6.32e+02 pdb=" C2D LBV A1000 " 0.055 2.00e-02 2.50e+03 pdb=" C3D LBV A1000 " -0.003 2.00e-02 2.50e+03 pdb=" C4D LBV A1000 " 0.040 2.00e-02 2.50e+03 pdb=" CAD LBV A1000 " -0.101 2.00e-02 2.50e+03 pdb=" CHD LBV A1000 " -0.290 2.00e-02 2.50e+03 pdb=" CMD LBV A1000 " 0.089 2.00e-02 2.50e+03 pdb=" N_D LBV A1000 " 0.346 2.00e-02 2.50e+03 pdb=" O_D LBV A1000 " -0.159 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C LBV A1000 " 0.033 2.00e-02 2.50e+03 1.36e-01 4.17e+02 pdb=" C2C LBV A1000 " -0.009 2.00e-02 2.50e+03 pdb=" C3C LBV A1000 " 0.019 2.00e-02 2.50e+03 pdb=" C4C LBV A1000 " 0.011 2.00e-02 2.50e+03 pdb=" CAC LBV A1000 " -0.048 2.00e-02 2.50e+03 pdb=" CHC LBV A1000 " -0.148 2.00e-02 2.50e+03 pdb=" CHD LBV A1000 " -0.217 2.00e-02 2.50e+03 pdb=" CMC LBV A1000 " 0.058 2.00e-02 2.50e+03 pdb=" N_C LBV A1000 " 0.301 2.00e-02 2.50e+03 ... (remaining 1434 not shown) Histogram of nonbonded interaction distances: 2.58 - 3.04: 3465 3.04 - 3.51: 7769 3.51 - 3.97: 11999 3.97 - 4.44: 13714 4.44 - 4.90: 22341 Nonbonded interactions: 59288 Sorted by model distance: nonbonded pdb=" O ARG A 514 " pdb=" OG1 THR A 517 " model vdw 2.580 2.440 nonbonded pdb=" O ARG B 514 " pdb=" OG1 THR B 517 " model vdw 2.581 2.440 nonbonded pdb=" N ALA B 401 " pdb=" N LEU B 402 " model vdw 2.618 2.560 nonbonded pdb=" N HIS B 344 " pdb=" N SER B 345 " model vdw 2.619 2.560 nonbonded pdb=" OD2 ASP B 45 " pdb=" N SER B 48 " model vdw 2.620 2.520 ... (remaining 59283 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' and (resid 7 through 106 or resid 109 through 519 or resid 1000)) } 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: 7.650 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: 18.650 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 24.290 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.040 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 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 : 0.008 0.077 7995 Z= 0.520 Angle : 1.381 8.435 10943 Z= 0.921 Chirality : 0.081 0.276 1230 Planarity : 0.009 0.203 1437 Dihedral : 18.227 78.875 2915 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.70 % Favored : 95.10 % Rotamer: Outliers : 5.03 % Allowed : 12.94 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -3.08 (0.22), residues: 1000 helix: -3.09 (0.22), residues: 316 sheet: 0.12 (0.37), residues: 174 loop : -2.11 (0.22), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 412 HIS 0.008 0.002 HIS B 484 PHE 0.016 0.003 PHE A 170 TYR 0.016 0.002 TYR A 263 ARG 0.004 0.001 ARG B 154 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 132 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7002 (pm20) REVERT: A 148 GLU cc_start: 0.8703 (mt-10) cc_final: 0.7809 (mp0) REVERT: A 154 ARG cc_start: 0.8383 (ptt180) cc_final: 0.7959 (tpt-90) REVERT: A 218 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.7740 (tpt-90) REVERT: A 259 MET cc_start: 0.8754 (tpp) cc_final: 0.8541 (mmm) REVERT: A 261 MET cc_start: 0.7975 (mmm) cc_final: 0.7718 (mtt) REVERT: A 340 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7668 (tt) REVERT: A 408 LEU cc_start: 0.7990 (tp) cc_final: 0.7724 (tt) REVERT: A 493 ASP cc_start: 0.8287 (OUTLIER) cc_final: 0.8079 (m-30) REVERT: B 31 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8425 (pt) REVERT: B 261 MET cc_start: 0.8331 (mmm) cc_final: 0.8114 (mtp) REVERT: B 282 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7584 (mm-40) REVERT: B 317 GLN cc_start: 0.8582 (mt0) cc_final: 0.8308 (tt0) REVERT: B 363 MET cc_start: 0.8898 (mmt) cc_final: 0.8504 (mmt) REVERT: B 411 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8298 (tp) outliers start: 40 outliers final: 16 residues processed: 158 average time/residue: 0.2571 time to fit residues: 51.6964 Evaluate side-chains 100 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 78 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 218 ARG Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 282 GLN Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 349 HIS Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 508 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 40 optimal weight: 0.0870 chunk 78 optimal weight: 0.0980 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 58 optimal weight: 0.0980 chunk 90 optimal weight: 3.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 290 HIS A 349 HIS B 72 GLN B 290 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7995 Z= 0.179 Angle : 0.624 9.211 10943 Z= 0.310 Chirality : 0.041 0.157 1230 Planarity : 0.004 0.029 1437 Dihedral : 8.660 81.822 1178 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.50 % Favored : 98.30 % Rotamer: Outliers : 2.51 % Allowed : 17.59 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.50 (0.24), residues: 1000 helix: -1.36 (0.26), residues: 313 sheet: 0.48 (0.35), residues: 183 loop : -1.27 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 82 HIS 0.004 0.001 HIS A 334 PHE 0.009 0.001 PHE B 170 TYR 0.017 0.002 TYR A 307 ARG 0.004 0.000 ARG B 332 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 88 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7035 (pm20) REVERT: A 65 GLU cc_start: 0.8072 (pm20) cc_final: 0.7394 (pm20) REVERT: A 154 ARG cc_start: 0.8488 (ptt180) cc_final: 0.8031 (tpt-90) REVERT: A 218 ARG cc_start: 0.8692 (ttm-80) cc_final: 0.7786 (mmm160) REVERT: A 243 ASN cc_start: 0.7847 (t0) cc_final: 0.7646 (t0) REVERT: A 381 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7250 (mm-30) REVERT: A 408 LEU cc_start: 0.8109 (tp) cc_final: 0.7889 (tt) REVERT: B 154 ARG cc_start: 0.8748 (mmm-85) cc_final: 0.8461 (ttm-80) REVERT: B 222 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.8099 (pmm150) REVERT: B 282 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7662 (mm-40) REVERT: B 311 LEU cc_start: 0.7839 (mt) cc_final: 0.7551 (mt) outliers start: 20 outliers final: 10 residues processed: 106 average time/residue: 0.2470 time to fit residues: 34.0579 Evaluate side-chains 86 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 74 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 282 GLN Chi-restraints excluded: chain B residue 349 HIS Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 506 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 98 optimal weight: 0.4980 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 72 optimal weight: 0.0570 chunk 89 optimal weight: 1.9990 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 291 HIS B 349 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7995 Z= 0.217 Angle : 0.573 7.918 10943 Z= 0.278 Chirality : 0.042 0.181 1230 Planarity : 0.004 0.031 1437 Dihedral : 7.286 84.042 1150 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.01 % Allowed : 18.34 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.71 (0.25), residues: 1000 helix: -0.32 (0.29), residues: 309 sheet: 0.68 (0.36), residues: 183 loop : -0.95 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 82 HIS 0.006 0.001 HIS A 334 PHE 0.007 0.001 PHE A 170 TYR 0.021 0.002 TYR A 176 ARG 0.004 0.000 ARG B 191 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 76 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7036 (pm20) REVERT: A 65 GLU cc_start: 0.7997 (pm20) cc_final: 0.7325 (pm20) REVERT: A 154 ARG cc_start: 0.8489 (ptt180) cc_final: 0.8025 (tpt-90) REVERT: A 218 ARG cc_start: 0.8740 (ttm-80) cc_final: 0.7892 (mtp85) REVERT: A 222 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7855 (pmm150) REVERT: A 243 ASN cc_start: 0.7891 (t0) cc_final: 0.7612 (t0) REVERT: A 381 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7268 (mm-30) REVERT: A 404 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8560 (pp30) REVERT: B 154 ARG cc_start: 0.8795 (mmm-85) cc_final: 0.8475 (ttm-80) REVERT: B 282 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.7702 (mm-40) outliers start: 16 outliers final: 10 residues processed: 90 average time/residue: 0.2420 time to fit residues: 28.7008 Evaluate side-chains 80 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 67 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 404 GLN Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 282 GLN Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 506 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.0170 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 86 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.1822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 HIS A 317 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7995 Z= 0.281 Angle : 0.602 7.830 10943 Z= 0.290 Chirality : 0.043 0.214 1230 Planarity : 0.004 0.032 1437 Dihedral : 7.144 88.651 1142 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.52 % Allowed : 17.96 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 (0.26), residues: 1000 helix: -0.05 (0.30), residues: 312 sheet: 0.68 (0.36), residues: 183 loop : -0.85 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 82 HIS 0.007 0.001 HIS A 334 PHE 0.010 0.002 PHE B 469 TYR 0.015 0.002 TYR B 176 ARG 0.005 0.000 ARG B 191 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 74 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.8009 (mm-30) cc_final: 0.6952 (pm20) REVERT: A 65 GLU cc_start: 0.7924 (pm20) cc_final: 0.7336 (pm20) REVERT: A 154 ARG cc_start: 0.8504 (ptt180) cc_final: 0.7991 (tpt-90) REVERT: A 218 ARG cc_start: 0.8715 (ttm-80) cc_final: 0.7843 (mtp85) REVERT: A 222 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7494 (pmm150) REVERT: A 243 ASN cc_start: 0.7953 (t0) cc_final: 0.7676 (t0) REVERT: A 404 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8545 (pp30) REVERT: B 154 ARG cc_start: 0.8837 (mmm-85) cc_final: 0.8456 (ttm-80) REVERT: B 282 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.7820 (mm-40) REVERT: B 510 ARG cc_start: 0.7160 (OUTLIER) cc_final: 0.6427 (mtm110) outliers start: 28 outliers final: 14 residues processed: 98 average time/residue: 0.2685 time to fit residues: 33.7400 Evaluate side-chains 86 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 68 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 404 GLN Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 282 GLN Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 510 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7995 Z= 0.193 Angle : 0.539 7.732 10943 Z= 0.257 Chirality : 0.041 0.195 1230 Planarity : 0.004 0.030 1437 Dihedral : 6.784 89.064 1140 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.14 % Allowed : 19.10 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.23 (0.26), residues: 1000 helix: 0.26 (0.30), residues: 315 sheet: 0.90 (0.39), residues: 169 loop : -0.73 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 284 HIS 0.004 0.001 HIS B 38 PHE 0.006 0.001 PHE B 469 TYR 0.012 0.001 TYR B 176 ARG 0.005 0.000 ARG B 191 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 73 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7881 (mm-30) cc_final: 0.6961 (pm20) REVERT: A 154 ARG cc_start: 0.8459 (ptt180) cc_final: 0.7978 (tpt-90) REVERT: A 218 ARG cc_start: 0.8638 (ttm-80) cc_final: 0.7759 (mtp85) REVERT: A 222 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7474 (pmm150) REVERT: A 514 ARG cc_start: 0.8627 (tpp80) cc_final: 0.8343 (tpp-160) REVERT: B 24 CYS cc_start: 0.8029 (p) cc_final: 0.7129 (m) REVERT: B 154 ARG cc_start: 0.8777 (mmm-85) cc_final: 0.8379 (ttm-80) REVERT: B 282 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.7897 (mm-40) REVERT: B 510 ARG cc_start: 0.6985 (OUTLIER) cc_final: 0.6433 (mtm110) outliers start: 25 outliers final: 13 residues processed: 92 average time/residue: 0.2447 time to fit residues: 29.3043 Evaluate side-chains 84 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 68 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 282 GLN Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 510 ARG Chi-restraints excluded: chain B residue 511 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 8 optimal weight: 0.0970 chunk 32 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS B 317 GLN B 458 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7995 Z= 0.221 Angle : 0.549 7.963 10943 Z= 0.262 Chirality : 0.041 0.179 1230 Planarity : 0.004 0.031 1437 Dihedral : 6.756 89.538 1140 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.27 % Allowed : 19.35 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.08 (0.26), residues: 1000 helix: 0.37 (0.30), residues: 321 sheet: 1.00 (0.39), residues: 169 loop : -0.66 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 284 HIS 0.004 0.001 HIS B 38 PHE 0.006 0.001 PHE A 9 TYR 0.012 0.001 TYR B 176 ARG 0.007 0.000 ARG B 191 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 75 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7876 (mm-30) cc_final: 0.6941 (pm20) REVERT: A 65 GLU cc_start: 0.7749 (pm20) cc_final: 0.7212 (pm20) REVERT: A 154 ARG cc_start: 0.8473 (ptt180) cc_final: 0.7981 (tpt-90) REVERT: A 181 ASP cc_start: 0.7821 (t70) cc_final: 0.7513 (t0) REVERT: A 218 ARG cc_start: 0.8605 (ttm-80) cc_final: 0.7742 (mtp85) REVERT: A 222 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7446 (pmm150) REVERT: A 274 SER cc_start: 0.8586 (OUTLIER) cc_final: 0.8303 (p) REVERT: A 404 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8546 (pp30) REVERT: A 514 ARG cc_start: 0.8588 (tpp80) cc_final: 0.8307 (tpp-160) REVERT: B 31 ILE cc_start: 0.8886 (OUTLIER) cc_final: 0.8647 (pt) REVERT: B 154 ARG cc_start: 0.8795 (mmm-85) cc_final: 0.8391 (ttm-80) REVERT: B 282 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.7967 (mm-40) outliers start: 26 outliers final: 18 residues processed: 95 average time/residue: 0.2407 time to fit residues: 30.3017 Evaluate side-chains 96 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 73 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 404 GLN Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 282 GLN Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 511 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 58 optimal weight: 0.0010 chunk 44 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 chunk 38 optimal weight: 0.0980 chunk 57 optimal weight: 0.5980 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7995 Z= 0.228 Angle : 0.559 7.407 10943 Z= 0.264 Chirality : 0.041 0.157 1230 Planarity : 0.004 0.031 1437 Dihedral : 6.761 89.535 1140 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.39 % Allowed : 20.10 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.04 (0.26), residues: 1000 helix: 0.41 (0.30), residues: 321 sheet: 0.75 (0.38), residues: 179 loop : -0.55 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 284 HIS 0.005 0.001 HIS B 38 PHE 0.008 0.001 PHE B 9 TYR 0.013 0.001 TYR B 176 ARG 0.008 0.000 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 73 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7832 (mm-30) cc_final: 0.6896 (pm20) REVERT: A 65 GLU cc_start: 0.7738 (pm20) cc_final: 0.7199 (pm20) REVERT: A 154 ARG cc_start: 0.8483 (ptt180) cc_final: 0.7986 (tpt-90) REVERT: A 181 ASP cc_start: 0.7762 (t70) cc_final: 0.7461 (t0) REVERT: A 218 ARG cc_start: 0.8629 (ttm-80) cc_final: 0.7715 (mtp85) REVERT: A 222 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7540 (pmm150) REVERT: A 274 SER cc_start: 0.8594 (OUTLIER) cc_final: 0.8341 (p) REVERT: A 404 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8548 (pp30) REVERT: A 514 ARG cc_start: 0.8590 (tpp80) cc_final: 0.8340 (tpp-160) REVERT: B 154 ARG cc_start: 0.8806 (mmm-85) cc_final: 0.8389 (ttm-80) REVERT: B 510 ARG cc_start: 0.6978 (OUTLIER) cc_final: 0.6371 (mtm110) outliers start: 27 outliers final: 19 residues processed: 94 average time/residue: 0.2372 time to fit residues: 29.5053 Evaluate side-chains 92 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 69 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 404 GLN Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 282 GLN Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 510 ARG Chi-restraints excluded: chain B residue 511 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 89 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7995 Z= 0.220 Angle : 0.546 7.184 10943 Z= 0.261 Chirality : 0.041 0.179 1230 Planarity : 0.004 0.032 1437 Dihedral : 6.743 89.108 1140 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.52 % Allowed : 20.23 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.01 (0.26), residues: 1000 helix: 0.47 (0.30), residues: 321 sheet: 0.77 (0.38), residues: 179 loop : -0.52 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 394 HIS 0.005 0.001 HIS B 38 PHE 0.007 0.001 PHE B 9 TYR 0.012 0.001 TYR B 176 ARG 0.005 0.000 ARG B 191 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 75 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7864 (mm-30) cc_final: 0.6894 (pm20) REVERT: A 65 GLU cc_start: 0.7741 (pm20) cc_final: 0.7208 (pm20) REVERT: A 154 ARG cc_start: 0.8497 (ptt180) cc_final: 0.8001 (tpt-90) REVERT: A 181 ASP cc_start: 0.7761 (t70) cc_final: 0.7462 (t0) REVERT: A 218 ARG cc_start: 0.8610 (ttm-80) cc_final: 0.7704 (mtp85) REVERT: A 222 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7479 (pmm150) REVERT: A 274 SER cc_start: 0.8582 (OUTLIER) cc_final: 0.8319 (p) REVERT: A 404 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8554 (pp30) REVERT: A 514 ARG cc_start: 0.8653 (tpp80) cc_final: 0.8354 (tpp-160) REVERT: B 26 ARG cc_start: 0.6951 (mmm160) cc_final: 0.6693 (mmm160) REVERT: B 154 ARG cc_start: 0.8782 (mmm-85) cc_final: 0.8377 (ttm-80) REVERT: B 510 ARG cc_start: 0.6978 (OUTLIER) cc_final: 0.6338 (mtm110) outliers start: 28 outliers final: 20 residues processed: 98 average time/residue: 0.2595 time to fit residues: 32.8460 Evaluate side-chains 97 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 73 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 404 GLN Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 282 GLN Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 510 ARG Chi-restraints excluded: chain B residue 511 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7995 Z= 0.215 Angle : 0.555 7.153 10943 Z= 0.263 Chirality : 0.041 0.191 1230 Planarity : 0.004 0.056 1437 Dihedral : 6.736 89.055 1140 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.02 % Allowed : 20.98 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.06 (0.26), residues: 1000 helix: 0.56 (0.30), residues: 321 sheet: 0.77 (0.38), residues: 179 loop : -0.52 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 284 HIS 0.005 0.001 HIS B 38 PHE 0.008 0.001 PHE B 9 TYR 0.012 0.001 TYR B 176 ARG 0.015 0.000 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 75 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7875 (mm-30) cc_final: 0.6895 (pm20) REVERT: A 65 GLU cc_start: 0.7752 (pm20) cc_final: 0.7222 (pm20) REVERT: A 154 ARG cc_start: 0.8498 (ptt180) cc_final: 0.8012 (tpt-90) REVERT: A 181 ASP cc_start: 0.7764 (t70) cc_final: 0.7446 (t0) REVERT: A 222 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7551 (pmm150) REVERT: A 274 SER cc_start: 0.8576 (OUTLIER) cc_final: 0.8324 (p) REVERT: A 404 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8549 (pp30) REVERT: A 513 ASN cc_start: 0.8395 (t0) cc_final: 0.7941 (t0) REVERT: A 514 ARG cc_start: 0.8593 (tpp80) cc_final: 0.8314 (tpp-160) REVERT: B 154 ARG cc_start: 0.8771 (mmm-85) cc_final: 0.8371 (ttm-80) REVERT: B 510 ARG cc_start: 0.6979 (OUTLIER) cc_final: 0.6339 (mtm110) outliers start: 24 outliers final: 19 residues processed: 94 average time/residue: 0.2564 time to fit residues: 31.4923 Evaluate side-chains 98 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 75 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 404 GLN Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 282 GLN Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 510 ARG Chi-restraints excluded: chain B residue 511 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 84 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7995 Z= 0.176 Angle : 0.538 8.257 10943 Z= 0.256 Chirality : 0.041 0.213 1230 Planarity : 0.004 0.063 1437 Dihedral : 6.670 89.521 1140 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.89 % Allowed : 20.85 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.14 (0.26), residues: 1000 helix: 0.62 (0.30), residues: 321 sheet: 0.81 (0.39), residues: 179 loop : -0.47 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 284 HIS 0.004 0.001 HIS B 38 PHE 0.008 0.001 PHE B 9 TYR 0.011 0.001 TYR B 176 ARG 0.014 0.000 ARG B 213 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 78 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7877 (mm-30) cc_final: 0.6905 (pm20) REVERT: A 65 GLU cc_start: 0.7757 (pm20) cc_final: 0.7231 (pm20) REVERT: A 154 ARG cc_start: 0.8479 (ptt180) cc_final: 0.8006 (tpt-90) REVERT: A 181 ASP cc_start: 0.7777 (t70) cc_final: 0.7439 (t0) REVERT: A 218 ARG cc_start: 0.8605 (ttm-80) cc_final: 0.7686 (mtp85) REVERT: A 222 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7503 (pmm150) REVERT: A 274 SER cc_start: 0.8548 (OUTLIER) cc_final: 0.8298 (p) REVERT: A 404 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8544 (pp30) REVERT: A 513 ASN cc_start: 0.8402 (t0) cc_final: 0.7877 (t0) REVERT: A 514 ARG cc_start: 0.8508 (tpp80) cc_final: 0.7866 (mmt90) REVERT: B 26 ARG cc_start: 0.6933 (mmm160) cc_final: 0.6670 (mmm160) REVERT: B 154 ARG cc_start: 0.8757 (mmm-85) cc_final: 0.8494 (ttm-80) REVERT: B 510 ARG cc_start: 0.6998 (OUTLIER) cc_final: 0.6324 (mtm110) outliers start: 23 outliers final: 14 residues processed: 96 average time/residue: 0.2404 time to fit residues: 29.8899 Evaluate side-chains 91 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 73 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 404 GLN Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 282 GLN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 510 ARG Chi-restraints excluded: chain B residue 511 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 69 optimal weight: 0.0570 chunk 4 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.145185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.120024 restraints weight = 10625.413| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.89 r_work: 0.3127 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7995 Z= 0.205 Angle : 0.556 7.611 10943 Z= 0.262 Chirality : 0.041 0.200 1230 Planarity : 0.004 0.063 1437 Dihedral : 6.693 89.491 1140 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.39 % Allowed : 21.86 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.14 (0.26), residues: 1000 helix: 0.63 (0.30), residues: 321 sheet: 0.77 (0.39), residues: 179 loop : -0.45 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 284 HIS 0.005 0.001 HIS B 38 PHE 0.007 0.001 PHE A 9 TYR 0.011 0.001 TYR B 176 ARG 0.015 0.001 ARG B 213 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2057.49 seconds wall clock time: 37 minutes 53.10 seconds (2273.10 seconds total)