Starting phenix.real_space_refine on Thu Feb 15 08:50:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5c_12025/02_2024/7b5c_12025.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5c_12025/02_2024/7b5c_12025.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5c_12025/02_2024/7b5c_12025.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5c_12025/02_2024/7b5c_12025.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5c_12025/02_2024/7b5c_12025.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5c_12025/02_2024/7b5c_12025.pdb" } resolution = 3.7 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= 0.004 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 Ca 4 9.91 5 S 74 5.16 5 C 7684 2.51 5 N 1936 2.21 5 O 2072 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 127": "NH1" <-> "NH2" Residue "A PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 236": "OD1" <-> "OD2" Residue "A PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 287": "OD1" <-> "OD2" Residue "A ASP 291": "OD1" <-> "OD2" Residue "A ARG 298": "NH1" <-> "NH2" Residue "A TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 405": "OD1" <-> "OD2" Residue "A PHE 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 439": "OD1" <-> "OD2" Residue "A GLU 447": "OE1" <-> "OE2" Residue "A ASP 452": "OD1" <-> "OD2" Residue "A GLU 457": "OE1" <-> "OE2" Residue "A GLU 459": "OE1" <-> "OE2" Residue "A TYR 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 535": "NH1" <-> "NH2" Residue "A GLU 555": "OE1" <-> "OE2" Residue "A GLU 573": "OE1" <-> "OE2" Residue "A GLU 578": "OE1" <-> "OE2" Residue "A TYR 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 688": "OE1" <-> "OE2" Residue "A PHE 710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 716": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 747": "NH1" <-> "NH2" Residue "A PHE 785": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 795": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 840": "OD1" <-> "OD2" Residue "A PHE 867": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 881": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 127": "NH1" <-> "NH2" Residue "B PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 236": "OD1" <-> "OD2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 287": "OD1" <-> "OD2" Residue "B ASP 291": "OD1" <-> "OD2" Residue "B ARG 298": "NH1" <-> "NH2" Residue "B TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 405": "OD1" <-> "OD2" Residue "B PHE 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 439": "OD1" <-> "OD2" Residue "B GLU 447": "OE1" <-> "OE2" Residue "B ASP 452": "OD1" <-> "OD2" Residue "B GLU 457": "OE1" <-> "OE2" Residue "B GLU 459": "OE1" <-> "OE2" Residue "B TYR 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 535": "NH1" <-> "NH2" Residue "B GLU 555": "OE1" <-> "OE2" Residue "B GLU 573": "OE1" <-> "OE2" Residue "B GLU 578": "OE1" <-> "OE2" Residue "B TYR 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 688": "OE1" <-> "OE2" Residue "B PHE 710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 716": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 747": "NH1" <-> "NH2" Residue "B PHE 785": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 795": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 840": "OD1" <-> "OD2" Residue "B PHE 867": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 881": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11770 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5883 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 31, 'TRANS': 686} Chain breaks: 4 Chain: "B" Number of atoms: 5883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5883 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 31, 'TRANS': 686} Chain breaks: 4 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.35, per 1000 atoms: 0.54 Number of scatterers: 11770 At special positions: 0 Unit cell: (116.38, 112.332, 114.356, 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) Ca 4 19.99 S 74 16.00 O 2072 8.00 N 1936 7.00 C 7684 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 395 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 836 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 386 " distance=2.03 Simple disulfide: pdb=" SG CYS A 625 " - pdb=" SG CYS A 630 " distance=2.04 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 395 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 836 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 386 " distance=2.03 Simple disulfide: pdb=" SG CYS B 625 " - pdb=" SG CYS B 630 " distance=2.04 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: 4.73 Conformation dependent library (CDL) restraints added in 2.3 seconds 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2752 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 4 sheets defined 63.4% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 166 through 181 Proline residue: A 177 - end of helix Processing helix chain 'A' and resid 205 through 211 Processing helix chain 'A' and resid 242 through 257 Processing helix chain 'A' and resid 268 through 275 Processing helix chain 'A' and resid 296 through 305 Processing helix chain 'A' and resid 307 through 311 removed outlier: 3.597A pdb=" N PHE A 311 " --> pdb=" O TYR A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 325 Processing helix chain 'A' and resid 325 through 360 Proline residue: A 344 - end of helix Processing helix chain 'A' and resid 363 through 368 removed outlier: 4.247A pdb=" N MET A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 393 Processing helix chain 'A' and resid 394 through 405 removed outlier: 4.045A pdb=" N ALA A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU A 403 " --> pdb=" O ARG A 399 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE A 404 " --> pdb=" O ALA A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 438 removed outlier: 4.081A pdb=" N VAL A 410 " --> pdb=" O ASN A 406 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE A 411 " --> pdb=" O PRO A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 466 Processing helix chain 'A' and resid 490 through 519 Processing helix chain 'A' and resid 536 through 568 removed outlier: 3.747A pdb=" N ALA A 540 " --> pdb=" O VAL A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 601 Proline residue: A 595 - end of helix Processing helix chain 'A' and resid 617 through 619 No H-bonds generated for 'chain 'A' and resid 617 through 619' Processing helix chain 'A' and resid 630 through 644 Processing helix chain 'A' and resid 648 through 667 Proline residue: A 658 - end of helix Processing helix chain 'A' and resid 685 through 690 Processing helix chain 'A' and resid 699 through 716 removed outlier: 4.078A pdb=" N PHE A 716 " --> pdb=" O PHE A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 744 removed outlier: 3.501A pdb=" N PHE A 726 " --> pdb=" O LEU A 722 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ARG A 736 " --> pdb=" O ILE A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 782 removed outlier: 4.114A pdb=" N VAL A 772 " --> pdb=" O GLY A 768 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ILE A 773 " --> pdb=" O LYS A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 795 Processing helix chain 'A' and resid 803 through 809 Processing helix chain 'A' and resid 813 through 817 removed outlier: 4.115A pdb=" N PHE A 817 " --> pdb=" O VAL A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 886 removed outlier: 3.922A pdb=" N TRP A 858 " --> pdb=" O SER A 854 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE A 886 " --> pdb=" O VAL A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 909 Processing helix chain 'B' and resid 166 through 181 Proline residue: B 177 - end of helix Processing helix chain 'B' and resid 205 through 211 Processing helix chain 'B' and resid 242 through 257 Processing helix chain 'B' and resid 268 through 275 Processing helix chain 'B' and resid 296 through 305 Processing helix chain 'B' and resid 307 through 311 removed outlier: 3.597A pdb=" N PHE B 311 " --> pdb=" O TYR B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 325 Processing helix chain 'B' and resid 325 through 360 Proline residue: B 344 - end of helix Processing helix chain 'B' and resid 363 through 368 removed outlier: 4.248A pdb=" N MET B 367 " --> pdb=" O ASN B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 393 Processing helix chain 'B' and resid 394 through 405 removed outlier: 4.044A pdb=" N ALA B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU B 403 " --> pdb=" O ARG B 399 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE B 404 " --> pdb=" O ALA B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 438 removed outlier: 4.080A pdb=" N VAL B 410 " --> pdb=" O ASN B 406 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE B 411 " --> pdb=" O PRO B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 466 Processing helix chain 'B' and resid 490 through 519 Processing helix chain 'B' and resid 536 through 568 removed outlier: 3.747A pdb=" N ALA B 540 " --> pdb=" O VAL B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 601 Proline residue: B 595 - end of helix Processing helix chain 'B' and resid 617 through 619 No H-bonds generated for 'chain 'B' and resid 617 through 619' Processing helix chain 'B' and resid 630 through 644 Processing helix chain 'B' and resid 648 through 667 Proline residue: B 658 - end of helix Processing helix chain 'B' and resid 685 through 690 Processing helix chain 'B' and resid 699 through 716 removed outlier: 4.078A pdb=" N PHE B 716 " --> pdb=" O PHE B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 744 removed outlier: 3.501A pdb=" N PHE B 726 " --> pdb=" O LEU B 722 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ARG B 736 " --> pdb=" O ILE B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 782 removed outlier: 4.113A pdb=" N VAL B 772 " --> pdb=" O GLY B 768 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE B 773 " --> pdb=" O LYS B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 795 Processing helix chain 'B' and resid 803 through 809 Processing helix chain 'B' and resid 813 through 817 removed outlier: 4.116A pdb=" N PHE B 817 " --> pdb=" O VAL B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 886 removed outlier: 3.921A pdb=" N TRP B 858 " --> pdb=" O SER B 854 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE B 886 " --> pdb=" O VAL B 882 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 909 Processing sheet with id=AA1, first strand: chain 'A' and resid 217 through 218 Processing sheet with id=AA2, first strand: chain 'A' and resid 615 through 616 removed outlier: 3.514A pdb=" N ILE A 616 " --> pdb=" O PHE A 620 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE A 620 " --> pdb=" O ILE A 616 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 217 through 218 Processing sheet with id=AA4, first strand: chain 'B' and resid 615 through 616 removed outlier: 3.514A pdb=" N ILE B 616 " --> pdb=" O PHE B 620 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE B 620 " --> pdb=" O ILE B 616 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 642 hydrogen bonds defined for protein. 1902 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: 3.23 Time building geometry restraints manager: 5.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3642 1.35 - 1.47: 3075 1.47 - 1.59: 5225 1.59 - 1.71: 0 1.71 - 1.83: 122 Bond restraints: 12064 Sorted by residual: bond pdb=" C MET A 378 " pdb=" N CYS A 379 " ideal model delta sigma weight residual 1.333 1.292 0.041 1.59e-02 3.96e+03 6.55e+00 bond pdb=" C MET B 378 " pdb=" N CYS B 379 " ideal model delta sigma weight residual 1.333 1.292 0.040 1.59e-02 3.96e+03 6.48e+00 bond pdb=" C SER A 527 " pdb=" N PRO A 528 " ideal model delta sigma weight residual 1.334 1.371 -0.037 2.34e-02 1.83e+03 2.50e+00 bond pdb=" CA ILE A 343 " pdb=" C ILE A 343 " ideal model delta sigma weight residual 1.523 1.538 -0.014 9.20e-03 1.18e+04 2.48e+00 bond pdb=" CA ILE B 343 " pdb=" C ILE B 343 " ideal model delta sigma weight residual 1.523 1.537 -0.014 9.20e-03 1.18e+04 2.43e+00 ... (remaining 12059 not shown) Histogram of bond angle deviations from ideal: 100.06 - 106.85: 357 106.85 - 113.64: 6420 113.64 - 120.43: 5165 120.43 - 127.22: 4248 127.22 - 134.00: 130 Bond angle restraints: 16320 Sorted by residual: angle pdb=" N VAL B 536 " pdb=" CA VAL B 536 " pdb=" C VAL B 536 " ideal model delta sigma weight residual 113.53 106.75 6.78 9.80e-01 1.04e+00 4.79e+01 angle pdb=" N VAL A 536 " pdb=" CA VAL A 536 " pdb=" C VAL A 536 " ideal model delta sigma weight residual 113.53 106.75 6.78 9.80e-01 1.04e+00 4.79e+01 angle pdb=" C THR B 235 " pdb=" N ASP B 236 " pdb=" CA ASP B 236 " ideal model delta sigma weight residual 121.54 129.35 -7.81 1.91e+00 2.74e-01 1.67e+01 angle pdb=" C THR A 235 " pdb=" N ASP A 236 " pdb=" CA ASP A 236 " ideal model delta sigma weight residual 121.54 129.34 -7.80 1.91e+00 2.74e-01 1.67e+01 angle pdb=" CA LEU B 722 " pdb=" CB LEU B 722 " pdb=" CG LEU B 722 " ideal model delta sigma weight residual 116.30 129.53 -13.23 3.50e+00 8.16e-02 1.43e+01 ... (remaining 16315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 6340 17.88 - 35.77: 720 35.77 - 53.65: 130 53.65 - 71.54: 18 71.54 - 89.42: 10 Dihedral angle restraints: 7218 sinusoidal: 2966 harmonic: 4252 Sorted by residual: dihedral pdb=" CB CYS A 382 " pdb=" SG CYS A 382 " pdb=" SG CYS A 386 " pdb=" CB CYS A 386 " ideal model delta sinusoidal sigma weight residual 93.00 47.69 45.31 1 1.00e+01 1.00e-02 2.85e+01 dihedral pdb=" CB CYS B 382 " pdb=" SG CYS B 382 " pdb=" SG CYS B 386 " pdb=" CB CYS B 386 " ideal model delta sinusoidal sigma weight residual 93.00 47.70 45.30 1 1.00e+01 1.00e-02 2.85e+01 dihedral pdb=" CA CYS A 370 " pdb=" C CYS A 370 " pdb=" N ASP A 371 " pdb=" CA ASP A 371 " ideal model delta harmonic sigma weight residual 180.00 154.90 25.10 0 5.00e+00 4.00e-02 2.52e+01 ... (remaining 7215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1301 0.051 - 0.103: 388 0.103 - 0.154: 89 0.154 - 0.206: 14 0.206 - 0.257: 4 Chirality restraints: 1796 Sorted by residual: chirality pdb=" CB VAL B 310 " pdb=" CA VAL B 310 " pdb=" CG1 VAL B 310 " pdb=" CG2 VAL B 310 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB VAL A 310 " pdb=" CA VAL A 310 " pdb=" CG1 VAL A 310 " pdb=" CG2 VAL A 310 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CB VAL B 569 " pdb=" CA VAL B 569 " pdb=" CG1 VAL B 569 " pdb=" CG2 VAL B 569 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 1793 not shown) Planarity restraints: 2044 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 203 " -0.055 5.00e-02 4.00e+02 8.18e-02 1.07e+01 pdb=" N PRO B 204 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO B 204 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 204 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 203 " 0.054 5.00e-02 4.00e+02 8.17e-02 1.07e+01 pdb=" N PRO A 204 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO A 204 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 204 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 723 " 0.051 5.00e-02 4.00e+02 7.65e-02 9.37e+00 pdb=" N PRO A 724 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 724 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 724 " 0.043 5.00e-02 4.00e+02 ... (remaining 2041 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2381 2.77 - 3.30: 11383 3.30 - 3.84: 19670 3.84 - 4.37: 21569 4.37 - 4.90: 37092 Nonbonded interactions: 92095 Sorted by model distance: nonbonded pdb=" O LYS A 740 " pdb=" OG1 THR A 744 " model vdw 2.239 2.440 nonbonded pdb=" O LYS B 740 " pdb=" OG1 THR B 744 " model vdw 2.239 2.440 nonbonded pdb=" O ALA A 600 " pdb=" OG1 THR A 782 " model vdw 2.242 2.440 nonbonded pdb=" O ALA B 600 " pdb=" OG1 THR B 782 " model vdw 2.242 2.440 nonbonded pdb=" OH TYR A 791 " pdb=" O HIS A 802 " model vdw 2.257 2.440 ... (remaining 92090 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: 1.190 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: 4.240 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 33.510 Find NCS groups from input model: 0.580 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:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 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 : 0.005 0.048 12064 Z= 0.318 Angle : 0.857 13.232 16320 Z= 0.486 Chirality : 0.052 0.257 1796 Planarity : 0.008 0.082 2044 Dihedral : 15.211 89.423 4442 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.78 % Allowed : 8.75 % Favored : 90.47 % 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: -3.64 (0.18), residues: 1416 helix: -1.58 (0.15), residues: 838 sheet: -2.47 (0.87), residues: 32 loop : -3.72 (0.20), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 427 HIS 0.007 0.001 HIS A 402 PHE 0.019 0.002 PHE B 589 TYR 0.018 0.002 TYR A 222 ARG 0.011 0.000 ARG B 321 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 250 time to evaluate : 1.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 PHE cc_start: 0.5415 (t80) cc_final: 0.5122 (t80) REVERT: A 446 GLU cc_start: 0.5564 (OUTLIER) cc_final: 0.5343 (mm-30) REVERT: A 524 MET cc_start: 0.2653 (ptt) cc_final: 0.1590 (ttt) REVERT: A 560 ILE cc_start: 0.8464 (tp) cc_final: 0.8245 (tt) REVERT: B 341 MET cc_start: 0.7809 (mmm) cc_final: 0.7602 (mmm) REVERT: B 351 ILE cc_start: 0.8798 (tp) cc_final: 0.8465 (pt) REVERT: B 418 LEU cc_start: 0.8079 (tt) cc_final: 0.7479 (mp) REVERT: B 446 GLU cc_start: 0.5953 (OUTLIER) cc_final: 0.5631 (mm-30) REVERT: B 515 ARG cc_start: 0.6786 (tpm170) cc_final: 0.6103 (ttt180) REVERT: B 524 MET cc_start: 0.2614 (ptt) cc_final: 0.1569 (ttt) REVERT: B 666 TYR cc_start: 0.3989 (t80) cc_final: 0.3436 (m-80) outliers start: 10 outliers final: 1 residues processed: 258 average time/residue: 0.3305 time to fit residues: 112.4635 Evaluate side-chains 164 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 161 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 446 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 43 optimal weight: 0.4980 chunk 67 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 128 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN A 340 GLN ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 GLN A 709 GLN A 775 ASN B 215 GLN B 431 GLN B 709 GLN B 775 ASN B 895 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 12064 Z= 0.227 Angle : 0.629 9.953 16320 Z= 0.329 Chirality : 0.042 0.155 1796 Planarity : 0.006 0.077 2044 Dihedral : 5.965 69.543 1591 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 3.36 % Allowed : 14.84 % Favored : 81.80 % 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: -2.23 (0.21), residues: 1416 helix: -0.22 (0.17), residues: 838 sheet: -2.15 (0.91), residues: 32 loop : -3.54 (0.22), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 427 HIS 0.009 0.001 HIS B 402 PHE 0.027 0.002 PHE B 617 TYR 0.017 0.002 TYR A 251 ARG 0.007 0.001 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 184 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 381 LEU cc_start: 0.7085 (OUTLIER) cc_final: 0.6587 (pp) REVERT: A 446 GLU cc_start: 0.5761 (OUTLIER) cc_final: 0.5470 (mm-30) REVERT: A 491 PHE cc_start: 0.4977 (t80) cc_final: 0.4741 (t80) REVERT: A 524 MET cc_start: 0.2429 (ptt) cc_final: 0.1420 (ttt) REVERT: A 560 ILE cc_start: 0.8593 (tp) cc_final: 0.8276 (tt) REVERT: A 904 MET cc_start: 0.6411 (mtp) cc_final: 0.5749 (mtp) REVERT: B 381 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.6762 (pp) REVERT: B 418 LEU cc_start: 0.8153 (tt) cc_final: 0.7578 (mp) REVERT: B 446 GLU cc_start: 0.5870 (OUTLIER) cc_final: 0.5510 (mm-30) REVERT: B 515 ARG cc_start: 0.6812 (tpm170) cc_final: 0.6227 (ttt180) REVERT: B 524 MET cc_start: 0.2504 (ptt) cc_final: 0.1477 (ttt) REVERT: B 560 ILE cc_start: 0.8630 (tp) cc_final: 0.8307 (tt) REVERT: B 666 TYR cc_start: 0.3968 (t80) cc_final: 0.3350 (m-80) outliers start: 43 outliers final: 16 residues processed: 216 average time/residue: 0.2522 time to fit residues: 76.1139 Evaluate side-chains 181 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 161 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 849 HIS Chi-restraints excluded: chain A residue 883 ASP Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 382 CYS Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 431 GLN Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 709 GLN Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 849 HIS Chi-restraints excluded: chain B residue 883 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 10.0000 chunk 40 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 129 optimal weight: 0.8980 chunk 139 optimal weight: 0.9980 chunk 115 optimal weight: 0.0070 chunk 128 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 ASN ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 GLN B 709 GLN B 775 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12064 Z= 0.167 Angle : 0.610 10.286 16320 Z= 0.311 Chirality : 0.040 0.148 1796 Planarity : 0.005 0.077 2044 Dihedral : 5.778 70.480 1590 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.19 % Allowed : 17.81 % Favored : 80.00 % 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: -1.48 (0.21), residues: 1416 helix: 0.46 (0.18), residues: 840 sheet: -2.08 (0.90), residues: 32 loop : -3.36 (0.22), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 427 HIS 0.007 0.001 HIS B 402 PHE 0.027 0.001 PHE A 617 TYR 0.025 0.001 TYR A 251 ARG 0.004 0.000 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 183 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 MET cc_start: 0.7950 (tpp) cc_final: 0.7573 (ttt) REVERT: A 418 LEU cc_start: 0.8040 (tt) cc_final: 0.7748 (mp) REVERT: A 491 PHE cc_start: 0.5036 (t80) cc_final: 0.4776 (t80) REVERT: A 524 MET cc_start: 0.2290 (ptt) cc_final: 0.1488 (ttt) REVERT: A 560 ILE cc_start: 0.8593 (tp) cc_final: 0.8255 (tt) REVERT: B 277 TYR cc_start: 0.5901 (m-80) cc_final: 0.4716 (m-80) REVERT: B 418 LEU cc_start: 0.7992 (tt) cc_final: 0.7577 (mp) REVERT: B 446 GLU cc_start: 0.5824 (OUTLIER) cc_final: 0.5466 (mm-30) REVERT: B 515 ARG cc_start: 0.6635 (tpm170) cc_final: 0.6121 (ttt180) REVERT: B 524 MET cc_start: 0.2370 (ptt) cc_final: 0.1527 (ttt) REVERT: B 560 ILE cc_start: 0.8611 (tp) cc_final: 0.8252 (tt) REVERT: B 666 TYR cc_start: 0.3903 (t80) cc_final: 0.3288 (m-80) outliers start: 28 outliers final: 12 residues processed: 205 average time/residue: 0.2441 time to fit residues: 70.7550 Evaluate side-chains 175 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 162 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 849 HIS Chi-restraints excluded: chain A residue 883 ASP Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 849 HIS Chi-restraints excluded: chain B residue 883 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 61 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 GLN ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 ASN ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 775 ASN B 895 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12064 Z= 0.189 Angle : 0.594 9.888 16320 Z= 0.304 Chirality : 0.041 0.151 1796 Planarity : 0.005 0.075 2044 Dihedral : 5.261 71.023 1587 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 2.50 % Allowed : 18.91 % Favored : 78.59 % 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: -1.17 (0.22), residues: 1416 helix: 0.72 (0.18), residues: 840 sheet: -2.00 (0.90), residues: 32 loop : -3.25 (0.23), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 427 HIS 0.008 0.001 HIS B 402 PHE 0.020 0.001 PHE A 696 TYR 0.024 0.001 TYR A 251 ARG 0.005 0.000 ARG A 125 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 180 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 LEU cc_start: 0.8063 (tt) cc_final: 0.7773 (mp) REVERT: A 491 PHE cc_start: 0.5116 (t80) cc_final: 0.4866 (t80) REVERT: A 515 ARG cc_start: 0.6542 (tpm170) cc_final: 0.5933 (ttt180) REVERT: A 524 MET cc_start: 0.2156 (ptt) cc_final: 0.1478 (ttt) REVERT: A 560 ILE cc_start: 0.8589 (tp) cc_final: 0.8239 (tt) REVERT: B 381 LEU cc_start: 0.6881 (OUTLIER) cc_final: 0.6585 (pp) REVERT: B 418 LEU cc_start: 0.8024 (tt) cc_final: 0.7625 (mp) REVERT: B 515 ARG cc_start: 0.6525 (tpm170) cc_final: 0.6094 (ttt180) REVERT: B 524 MET cc_start: 0.2301 (ptt) cc_final: 0.1540 (ttt) REVERT: B 560 ILE cc_start: 0.8602 (tp) cc_final: 0.8232 (tt) REVERT: B 666 TYR cc_start: 0.3895 (t80) cc_final: 0.3313 (m-80) REVERT: B 840 ASP cc_start: 0.7017 (t70) cc_final: 0.6803 (t0) outliers start: 32 outliers final: 17 residues processed: 207 average time/residue: 0.2652 time to fit residues: 77.7430 Evaluate side-chains 176 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 158 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 849 HIS Chi-restraints excluded: chain A residue 883 ASP Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 849 HIS Chi-restraints excluded: chain B residue 883 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 102 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 123 optimal weight: 0.9990 chunk 34 optimal weight: 20.0000 chunk 46 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 ASN B 195 ASN ** B 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12064 Z= 0.322 Angle : 0.666 9.656 16320 Z= 0.345 Chirality : 0.044 0.153 1796 Planarity : 0.005 0.073 2044 Dihedral : 5.012 19.103 1584 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 3.36 % Allowed : 19.77 % Favored : 76.88 % 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: -1.27 (0.22), residues: 1416 helix: 0.60 (0.18), residues: 836 sheet: -1.95 (0.90), residues: 32 loop : -3.19 (0.23), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 427 HIS 0.008 0.001 HIS A 402 PHE 0.022 0.002 PHE A 617 TYR 0.028 0.002 TYR B 251 ARG 0.007 0.001 ARG A 125 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 173 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 ASP cc_start: 0.1330 (OUTLIER) cc_final: -0.0483 (t70) REVERT: A 176 MET cc_start: 0.8126 (tpp) cc_final: 0.7846 (ttt) REVERT: A 515 ARG cc_start: 0.6783 (tpm170) cc_final: 0.6074 (ttt180) REVERT: A 524 MET cc_start: 0.2365 (ptt) cc_final: 0.1569 (ttt) REVERT: A 560 ILE cc_start: 0.8612 (tp) cc_final: 0.8261 (tt) REVERT: B 118 ASP cc_start: 0.1658 (OUTLIER) cc_final: -0.0146 (t70) REVERT: B 381 LEU cc_start: 0.7302 (OUTLIER) cc_final: 0.6764 (pp) REVERT: B 391 MET cc_start: 0.8131 (tpt) cc_final: 0.7896 (tpt) REVERT: B 515 ARG cc_start: 0.6683 (tpm170) cc_final: 0.6146 (ttt180) REVERT: B 524 MET cc_start: 0.2681 (ptt) cc_final: 0.1538 (ttt) REVERT: B 560 ILE cc_start: 0.8613 (tp) cc_final: 0.8255 (tt) REVERT: B 666 TYR cc_start: 0.4060 (t80) cc_final: 0.3391 (m-80) outliers start: 43 outliers final: 26 residues processed: 204 average time/residue: 0.2659 time to fit residues: 75.2366 Evaluate side-chains 184 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 155 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 849 HIS Chi-restraints excluded: chain A residue 883 ASP Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 849 HIS Chi-restraints excluded: chain B residue 883 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 137 optimal weight: 0.6980 chunk 114 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 11 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 132 optimal weight: 4.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 431 GLN ** B 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 775 ASN B 895 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12064 Z= 0.253 Angle : 0.647 9.887 16320 Z= 0.333 Chirality : 0.042 0.185 1796 Planarity : 0.005 0.073 2044 Dihedral : 5.065 28.770 1584 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 3.20 % Allowed : 21.41 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.22), residues: 1416 helix: 0.73 (0.18), residues: 836 sheet: -1.75 (0.93), residues: 32 loop : -3.07 (0.23), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 427 HIS 0.008 0.001 HIS B 402 PHE 0.018 0.001 PHE A 617 TYR 0.029 0.002 TYR B 251 ARG 0.011 0.000 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 174 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 515 ARG cc_start: 0.6595 (tpm170) cc_final: 0.6024 (ttt180) REVERT: A 524 MET cc_start: 0.2379 (ptt) cc_final: 0.1566 (ttt) REVERT: A 560 ILE cc_start: 0.8601 (tp) cc_final: 0.8243 (tt) REVERT: B 118 ASP cc_start: 0.1548 (OUTLIER) cc_final: -0.0260 (t70) REVERT: B 381 LEU cc_start: 0.6939 (OUTLIER) cc_final: 0.6725 (pp) REVERT: B 515 ARG cc_start: 0.6652 (tpm170) cc_final: 0.6091 (ttt180) REVERT: B 524 MET cc_start: 0.2667 (ptt) cc_final: 0.1519 (ttt) REVERT: B 560 ILE cc_start: 0.8611 (tp) cc_final: 0.8253 (tt) REVERT: B 666 TYR cc_start: 0.4040 (t80) cc_final: 0.3399 (m-80) outliers start: 41 outliers final: 28 residues processed: 203 average time/residue: 0.2616 time to fit residues: 74.5870 Evaluate side-chains 189 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 159 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 849 HIS Chi-restraints excluded: chain A residue 883 ASP Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 431 GLN Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 773 ILE Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 849 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 4.9990 chunk 78 optimal weight: 0.1980 chunk 100 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 115 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 136 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 775 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12064 Z= 0.222 Angle : 0.627 9.826 16320 Z= 0.322 Chirality : 0.041 0.151 1796 Planarity : 0.005 0.074 2044 Dihedral : 4.955 25.891 1584 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 2.89 % Allowed : 21.41 % Favored : 75.70 % 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 (0.22), residues: 1416 helix: 0.87 (0.18), residues: 836 sheet: -1.58 (0.95), residues: 32 loop : -2.95 (0.24), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 427 HIS 0.008 0.001 HIS B 402 PHE 0.017 0.001 PHE B 617 TYR 0.027 0.001 TYR B 251 ARG 0.012 0.000 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 173 time to evaluate : 1.323 Fit side-chains revert: symmetry clash REVERT: A 118 ASP cc_start: 0.1404 (OUTLIER) cc_final: -0.0201 (t70) REVERT: A 515 ARG cc_start: 0.6531 (tpm170) cc_final: 0.5988 (ttt180) REVERT: A 524 MET cc_start: 0.2423 (ptt) cc_final: 0.1629 (ttt) REVERT: A 560 ILE cc_start: 0.8596 (tp) cc_final: 0.8239 (tt) REVERT: A 755 LYS cc_start: 0.6842 (mptt) cc_final: 0.6573 (mmtt) REVERT: B 118 ASP cc_start: 0.1464 (OUTLIER) cc_final: -0.0306 (t70) REVERT: B 515 ARG cc_start: 0.6609 (tpm170) cc_final: 0.6099 (ttt180) REVERT: B 524 MET cc_start: 0.2613 (ptt) cc_final: 0.1535 (ttt) REVERT: B 560 ILE cc_start: 0.8655 (tp) cc_final: 0.8279 (tt) REVERT: B 666 TYR cc_start: 0.4018 (t80) cc_final: 0.3442 (m-80) outliers start: 37 outliers final: 24 residues processed: 202 average time/residue: 0.2507 time to fit residues: 71.4759 Evaluate side-chains 183 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 157 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 849 HIS Chi-restraints excluded: chain A residue 883 ASP Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 773 ILE Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 849 HIS Chi-restraints excluded: chain B residue 883 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 2.9990 chunk 81 optimal weight: 0.0010 chunk 41 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 107 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 chunk 131 optimal weight: 0.9980 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 775 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12064 Z= 0.180 Angle : 0.640 13.975 16320 Z= 0.320 Chirality : 0.041 0.149 1796 Planarity : 0.005 0.075 2044 Dihedral : 4.801 23.850 1584 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.95 % Allowed : 22.97 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.22), residues: 1416 helix: 1.05 (0.18), residues: 836 sheet: -1.42 (0.98), residues: 32 loop : -2.84 (0.24), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 427 HIS 0.007 0.001 HIS B 402 PHE 0.017 0.001 PHE A 617 TYR 0.027 0.001 TYR B 251 ARG 0.011 0.000 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 166 time to evaluate : 1.398 Fit side-chains REVERT: A 418 LEU cc_start: 0.8004 (tt) cc_final: 0.7695 (mp) REVERT: A 491 PHE cc_start: 0.5078 (t80) cc_final: 0.4843 (t80) REVERT: A 515 ARG cc_start: 0.6512 (tpm170) cc_final: 0.5979 (ttt180) REVERT: A 524 MET cc_start: 0.2300 (ptt) cc_final: 0.1624 (ttt) REVERT: A 560 ILE cc_start: 0.8593 (tp) cc_final: 0.8241 (tt) REVERT: A 909 MET cc_start: 0.5517 (ttt) cc_final: 0.5290 (ttt) REVERT: B 418 LEU cc_start: 0.7984 (tt) cc_final: 0.7685 (mp) REVERT: B 515 ARG cc_start: 0.6567 (tpm170) cc_final: 0.6016 (ttt180) REVERT: B 524 MET cc_start: 0.2339 (ptt) cc_final: 0.1516 (ttt) REVERT: B 560 ILE cc_start: 0.8632 (tp) cc_final: 0.8245 (tt) outliers start: 25 outliers final: 22 residues processed: 187 average time/residue: 0.2439 time to fit residues: 64.7035 Evaluate side-chains 177 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 155 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 849 HIS Chi-restraints excluded: chain A residue 883 ASP Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 849 HIS Chi-restraints excluded: chain B residue 883 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 120 optimal weight: 0.8980 chunk 83 optimal weight: 9.9990 chunk 134 optimal weight: 0.1980 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 GLN A 775 ASN B 431 GLN B 637 GLN ** B 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 775 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12064 Z= 0.316 Angle : 0.705 14.826 16320 Z= 0.359 Chirality : 0.044 0.158 1796 Planarity : 0.005 0.072 2044 Dihedral : 4.995 23.816 1584 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 2.66 % Allowed : 23.12 % Favored : 74.22 % 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: -0.84 (0.22), residues: 1416 helix: 0.88 (0.18), residues: 844 sheet: -1.49 (0.97), residues: 32 loop : -2.95 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 427 HIS 0.008 0.001 HIS A 402 PHE 0.017 0.002 PHE A 585 TYR 0.028 0.002 TYR A 277 ARG 0.009 0.001 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 163 time to evaluate : 1.294 Fit side-chains revert: symmetry clash REVERT: A 515 ARG cc_start: 0.6670 (tpm170) cc_final: 0.6099 (ttt180) REVERT: A 524 MET cc_start: 0.2483 (ptt) cc_final: 0.1657 (ttt) REVERT: A 560 ILE cc_start: 0.8611 (tp) cc_final: 0.8253 (tt) REVERT: B 515 ARG cc_start: 0.6700 (tpm170) cc_final: 0.6178 (ttt180) REVERT: B 524 MET cc_start: 0.2631 (ptt) cc_final: 0.1545 (ttt) REVERT: B 560 ILE cc_start: 0.8645 (tp) cc_final: 0.8269 (tt) outliers start: 34 outliers final: 23 residues processed: 188 average time/residue: 0.2542 time to fit residues: 66.9795 Evaluate side-chains 179 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 156 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 849 HIS Chi-restraints excluded: chain A residue 883 ASP Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 431 GLN Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 849 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 10.0000 chunk 63 optimal weight: 0.0270 chunk 93 optimal weight: 0.9980 chunk 141 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 87 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 120 optimal weight: 0.0060 overall best weight: 0.5654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 GLN A 775 ASN ** B 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 775 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12064 Z= 0.177 Angle : 0.644 13.648 16320 Z= 0.324 Chirality : 0.041 0.146 1796 Planarity : 0.005 0.075 2044 Dihedral : 4.826 22.228 1584 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.72 % Allowed : 23.91 % Favored : 74.38 % 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: -0.60 (0.22), residues: 1416 helix: 1.03 (0.18), residues: 838 sheet: -1.41 (0.98), residues: 32 loop : -2.74 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 427 HIS 0.007 0.001 HIS B 402 PHE 0.017 0.001 PHE A 617 TYR 0.025 0.001 TYR B 251 ARG 0.004 0.000 ARG A 125 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 156 time to evaluate : 1.589 Fit side-chains revert: symmetry clash REVERT: A 277 TYR cc_start: 0.5387 (m-80) cc_final: 0.5020 (m-80) REVERT: A 346 SER cc_start: 0.8032 (t) cc_final: 0.7097 (p) REVERT: A 491 PHE cc_start: 0.5007 (t80) cc_final: 0.4774 (t80) REVERT: A 515 ARG cc_start: 0.6552 (tpm170) cc_final: 0.6062 (ttt180) REVERT: A 524 MET cc_start: 0.2317 (ptt) cc_final: 0.1584 (ttt) REVERT: A 560 ILE cc_start: 0.8567 (tp) cc_final: 0.8229 (tt) REVERT: A 745 GLU cc_start: 0.7710 (tm-30) cc_final: 0.7495 (tp30) REVERT: A 755 LYS cc_start: 0.6829 (mptt) cc_final: 0.6533 (mmtm) REVERT: B 515 ARG cc_start: 0.6524 (tpm170) cc_final: 0.6044 (ttt180) REVERT: B 524 MET cc_start: 0.2564 (ptt) cc_final: 0.1645 (ttt) REVERT: B 560 ILE cc_start: 0.8637 (tp) cc_final: 0.8237 (tt) REVERT: B 851 TYR cc_start: 0.7707 (m-80) cc_final: 0.7477 (m-10) outliers start: 22 outliers final: 19 residues processed: 175 average time/residue: 0.2675 time to fit residues: 65.4939 Evaluate side-chains 172 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 153 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 849 HIS Chi-restraints excluded: chain A residue 883 ASP Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 773 ILE Chi-restraints excluded: chain B residue 849 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 9.9990 chunk 103 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 112 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 20 optimal weight: 0.0980 chunk 99 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 431 GLN B 637 GLN ** B 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.145664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.118340 restraints weight = 18161.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.118096 restraints weight = 15061.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.118522 restraints weight = 12901.450| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12064 Z= 0.186 Angle : 0.641 13.183 16320 Z= 0.322 Chirality : 0.041 0.150 1796 Planarity : 0.005 0.075 2044 Dihedral : 4.718 21.056 1584 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.03 % Allowed : 23.83 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.23), residues: 1416 helix: 1.17 (0.18), residues: 838 sheet: -1.38 (0.97), residues: 32 loop : -2.66 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 427 HIS 0.006 0.001 HIS B 402 PHE 0.032 0.001 PHE A 617 TYR 0.030 0.002 TYR A 251 ARG 0.005 0.000 ARG A 125 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2324.68 seconds wall clock time: 43 minutes 52.00 seconds (2632.00 seconds total)