Starting phenix.real_space_refine on Mon Mar 11 08:25:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xow_22282/03_2024/6xow_22282.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xow_22282/03_2024/6xow_22282.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xow_22282/03_2024/6xow_22282.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xow_22282/03_2024/6xow_22282.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xow_22282/03_2024/6xow_22282.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xow_22282/03_2024/6xow_22282.pdb" } resolution = 4.6 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= 0.006 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 39 5.16 5 C 4904 2.51 5 N 1307 2.21 5 O 1461 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 35": "OE1" <-> "OE2" Residue "A PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 71": "OD1" <-> "OD2" Residue "A TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "A ASP 304": "OD1" <-> "OD2" Residue "A PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 367": "OE1" <-> "OE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 518": "OE1" <-> "OE2" Residue "A GLU 543": "OE1" <-> "OE2" Residue "A GLU 634": "OE1" <-> "OE2" Residue "A GLU 697": "OE1" <-> "OE2" Residue "A TYR 721": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 793": "OE1" <-> "OE2" Residue "A PHE 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 935": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 960": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7711 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7711 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 966, 7697 Classifications: {'peptide': 966} Modifications used: {'COO': 1} Link IDs: {'CIS': 4, 'PTRANS': 60, 'TRANS': 901} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 966, 7697 Classifications: {'peptide': 966} Modifications used: {'COO': 1} Link IDs: {'CIS': 4, 'PTRANS': 60, 'TRANS': 901} Chain breaks: 1 bond proxies already assigned to first conformer: 7872 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ASER A 723 " occ=0.42 ... (10 atoms not shown) pdb=" OG BSER A 723 " occ=0.58 residue: pdb=" N AASN A 915 " occ=0.59 ... (14 atoms not shown) pdb=" ND2BASN A 915 " occ=0.41 Time building chain proxies: 8.24, per 1000 atoms: 1.07 Number of scatterers: 7711 At special positions: 0 Unit cell: (87.21, 87.21, 97.47, 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 39 16.00 O 1461 8.00 N 1307 7.00 C 4904 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.41 Conformation dependent library (CDL) restraints added in 2.8 seconds 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1828 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 7 sheets defined 54.7% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 32 through 38 Processing helix chain 'A' and resid 58 through 60 No H-bonds generated for 'chain 'A' and resid 58 through 60' Processing helix chain 'A' and resid 101 through 111 Processing helix chain 'A' and resid 121 through 127 removed outlier: 3.775A pdb=" N LYS A 125 " --> pdb=" O ASP A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 169 Processing helix chain 'A' and resid 173 through 181 Processing helix chain 'A' and resid 200 through 210 Processing helix chain 'A' and resid 212 through 226 Processing helix chain 'A' and resid 229 through 233 Processing helix chain 'A' and resid 241 through 245 Processing helix chain 'A' and resid 246 through 258 Processing helix chain 'A' and resid 259 through 261 No H-bonds generated for 'chain 'A' and resid 259 through 261' Processing helix chain 'A' and resid 272 through 284 removed outlier: 3.909A pdb=" N HIS A 276 " --> pdb=" O PRO A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 288 Processing helix chain 'A' and resid 339 through 355 Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'A' and resid 400 through 419 Processing helix chain 'A' and resid 421 through 438 removed outlier: 3.573A pdb=" N ILE A 425 " --> pdb=" O GLU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 457 removed outlier: 4.852A pdb=" N SER A 453 " --> pdb=" O SER A 449 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N CYS A 454 " --> pdb=" O TYR A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 465 Processing helix chain 'A' and resid 466 through 481 Processing helix chain 'A' and resid 483 through 494 Processing helix chain 'A' and resid 509 through 528 Processing helix chain 'A' and resid 530 through 550 Processing helix chain 'A' and resid 561 through 565 Processing helix chain 'A' and resid 608 through 613 Proline residue: A 613 - end of helix Processing helix chain 'A' and resid 614 through 622 Processing helix chain 'A' and resid 623 through 625 No H-bonds generated for 'chain 'A' and resid 623 through 625' Processing helix chain 'A' and resid 631 through 643 Processing helix chain 'A' and resid 676 through 690 Processing helix chain 'A' and resid 695 through 713 Processing helix chain 'A' and resid 714 through 716 No H-bonds generated for 'chain 'A' and resid 714 through 716' Processing helix chain 'A' and resid 717 through 727 Processing helix chain 'A' and resid 731 through 742 Processing helix chain 'A' and resid 742 through 755 Processing helix chain 'A' and resid 758 through 763 Processing helix chain 'A' and resid 764 through 773 removed outlier: 3.865A pdb=" N HIS A 771 " --> pdb=" O ARG A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 787 No H-bonds generated for 'chain 'A' and resid 785 through 787' Processing helix chain 'A' and resid 788 through 802 Processing helix chain 'A' and resid 878 through 894 removed outlier: 4.200A pdb=" N SER A 882 " --> pdb=" O PRO A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 902 Processing helix chain 'A' and resid 928 through 945 removed outlier: 3.512A pdb=" N LEU A 932 " --> pdb=" O THR A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 964 Processing helix chain 'A' and resid 973 through 980 removed outlier: 3.808A pdb=" N PHE A 977 " --> pdb=" O GLY A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 995 removed outlier: 3.693A pdb=" N LYS A 986 " --> pdb=" O SER A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1009 Processing helix chain 'A' and resid 1025 through 1030 Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 46 removed outlier: 6.227A pdb=" N VAL A 51 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N THR A 68 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A 63 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG A 75 " --> pdb=" O ALA A 263 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N MET A 135 " --> pdb=" O PRO A 147 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N SER A 149 " --> pdb=" O THR A 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46 removed outlier: 6.227A pdb=" N VAL A 51 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N THR A 68 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A 63 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG A 75 " --> pdb=" O ALA A 263 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 183 through 185 Processing sheet with id=AA4, first strand: chain 'A' and resid 307 through 313 removed outlier: 6.298A pdb=" N ARG A 307 " --> pdb=" O THR A 501 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N SER A 503 " --> pdb=" O ARG A 307 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N PHE A 309 " --> pdb=" O SER A 503 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ARG A 505 " --> pdb=" O PHE A 309 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ILE A 311 " --> pdb=" O ARG A 505 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL A 328 " --> pdb=" O GLN A 394 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N GLN A 394 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL A 330 " --> pdb=" O GLY A 392 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N GLY A 392 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N PHE A 332 " --> pdb=" O SER A 390 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N SER A 390 " --> pdb=" O PHE A 332 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU A 334 " --> pdb=" O TYR A 388 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N TYR A 388 " --> pdb=" O LEU A 334 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ASP A 336 " --> pdb=" O GLU A 386 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N GLU A 386 " --> pdb=" O ASP A 336 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR A 388 " --> pdb=" O ASN A 381 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN A 381 " --> pdb=" O TYR A 388 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER A 390 " --> pdb=" O GLY A 379 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 576 through 579 removed outlier: 7.402A pdb=" N VAL A 782 " --> pdb=" O PRO A 584 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N GLN A 586 " --> pdb=" O VAL A 782 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA A 784 " --> pdb=" O GLN A 586 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N CYS A 588 " --> pdb=" O ALA A 784 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU A 667 " --> pdb=" O SER A 649 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 576 through 579 removed outlier: 7.402A pdb=" N VAL A 782 " --> pdb=" O PRO A 584 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N GLN A 586 " --> pdb=" O VAL A 782 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA A 784 " --> pdb=" O GLN A 586 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N CYS A 588 " --> pdb=" O ALA A 784 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 907 through 912 removed outlier: 3.889A pdb=" N VAL A 866 " --> pdb=" O SER A 922 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N LYS A 854 " --> pdb=" O ILE A1035 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ARG A1037 " --> pdb=" O LYS A 854 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N HIS A 856 " --> pdb=" O ARG A1037 " (cutoff:3.500A) 472 hydrogen bonds defined for protein. 1336 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: 3.05 Time building geometry restraints manager: 3.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2455 1.33 - 1.45: 1286 1.45 - 1.57: 4101 1.57 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 7904 Sorted by residual: bond pdb=" CG ARG A 545 " pdb=" CD ARG A 545 " ideal model delta sigma weight residual 1.520 1.469 0.051 3.00e-02 1.11e+03 2.86e+00 bond pdb=" CB GLN A 91 " pdb=" CG GLN A 91 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.45e+00 bond pdb=" N ILE A 724 " pdb=" CA ILE A 724 " ideal model delta sigma weight residual 1.460 1.443 0.017 1.21e-02 6.83e+03 1.87e+00 bond pdb=" CA GLY A 644 " pdb=" C GLY A 644 " ideal model delta sigma weight residual 1.514 1.496 0.019 1.41e-02 5.03e+03 1.74e+00 bond pdb=" CA THR A 144 " pdb=" CB THR A 144 " ideal model delta sigma weight residual 1.532 1.508 0.024 1.82e-02 3.02e+03 1.69e+00 ... (remaining 7899 not shown) Histogram of bond angle deviations from ideal: 96.20 - 103.80: 154 103.80 - 111.40: 3331 111.40 - 119.00: 3068 119.00 - 126.59: 4056 126.59 - 134.19: 111 Bond angle restraints: 10720 Sorted by residual: angle pdb=" C TYR A 614 " pdb=" N VAL A 615 " pdb=" CA VAL A 615 " ideal model delta sigma weight residual 120.24 123.48 -3.24 6.30e-01 2.52e+00 2.64e+01 angle pdb=" C ILE A 899 " pdb=" N ARG A 900 " pdb=" CA ARG A 900 " ideal model delta sigma weight residual 120.88 114.63 6.25 1.62e+00 3.81e-01 1.49e+01 angle pdb=" CB MET A 749 " pdb=" CG MET A 749 " pdb=" SD MET A 749 " ideal model delta sigma weight residual 112.70 101.17 11.53 3.00e+00 1.11e-01 1.48e+01 angle pdb=" CA TYR A 492 " pdb=" CB TYR A 492 " pdb=" CG TYR A 492 " ideal model delta sigma weight residual 113.90 107.22 6.68 1.80e+00 3.09e-01 1.38e+01 angle pdb=" N GLU A 709 " pdb=" CA GLU A 709 " pdb=" CB GLU A 709 " ideal model delta sigma weight residual 110.16 115.32 -5.16 1.48e+00 4.57e-01 1.21e+01 ... (remaining 10715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 4413 17.91 - 35.83: 294 35.83 - 53.74: 46 53.74 - 71.65: 18 71.65 - 89.56: 10 Dihedral angle restraints: 4781 sinusoidal: 1955 harmonic: 2826 Sorted by residual: dihedral pdb=" CA ALA A 319 " pdb=" C ALA A 319 " pdb=" N THR A 320 " pdb=" CA THR A 320 " ideal model delta harmonic sigma weight residual -180.00 -158.15 -21.85 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA GLN A 394 " pdb=" C GLN A 394 " pdb=" N GLY A 395 " pdb=" CA GLY A 395 " ideal model delta harmonic sigma weight residual 180.00 158.36 21.64 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA ARG A 129 " pdb=" C ARG A 129 " pdb=" N SER A 130 " pdb=" CA SER A 130 " ideal model delta harmonic sigma weight residual 180.00 -159.50 -20.50 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 4778 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 733 0.044 - 0.089: 324 0.089 - 0.133: 100 0.133 - 0.177: 15 0.177 - 0.222: 2 Chirality restraints: 1174 Sorted by residual: chirality pdb=" CA TYR A 163 " pdb=" N TYR A 163 " pdb=" C TYR A 163 " pdb=" CB TYR A 163 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CB ILE A1020 " pdb=" CA ILE A1020 " pdb=" CG1 ILE A1020 " pdb=" CG2 ILE A1020 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.17e-01 chirality pdb=" CA LYS A 437 " pdb=" N LYS A 437 " pdb=" C LYS A 437 " pdb=" CB LYS A 437 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.10e-01 ... (remaining 1171 not shown) Planarity restraints: 1401 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 303 " -0.033 2.00e-02 2.50e+03 2.63e-02 1.73e+01 pdb=" CG TRP A 303 " 0.069 2.00e-02 2.50e+03 pdb=" CD1 TRP A 303 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP A 303 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP A 303 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 303 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 303 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 303 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 303 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 303 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 314 " -0.065 5.00e-02 4.00e+02 9.81e-02 1.54e+01 pdb=" N PRO A 315 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO A 315 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 315 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 242 " 0.050 5.00e-02 4.00e+02 7.58e-02 9.20e+00 pdb=" N PRO A 243 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 243 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 243 " 0.042 5.00e-02 4.00e+02 ... (remaining 1398 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 117 2.57 - 3.15: 7115 3.15 - 3.74: 12800 3.74 - 4.32: 17159 4.32 - 4.90: 26933 Nonbonded interactions: 64124 Sorted by model distance: nonbonded pdb=" OG1 THR A 872 " pdb=" O GLY A 916 " model vdw 1.991 2.440 nonbonded pdb=" O ASP A 377 " pdb=" OG SER A 390 " model vdw 2.033 2.440 nonbonded pdb=" OD2 ASP A 336 " pdb=" OG1 THR A 338 " model vdw 2.060 2.440 nonbonded pdb=" ND1 HIS A 186 " pdb=" O THR A 194 " model vdw 2.070 2.520 nonbonded pdb=" O ILE A 803 " pdb=" NH1 ARG A 805 " model vdw 2.089 2.520 ... (remaining 64119 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.41 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.070 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: 0.710 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 31.230 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 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: 35.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 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 : 0.006 0.051 7904 Z= 0.409 Angle : 0.998 11.533 10720 Z= 0.543 Chirality : 0.053 0.222 1174 Planarity : 0.007 0.098 1401 Dihedral : 13.389 89.563 2953 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 24.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.23 % Allowed : 0.23 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.44 % 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: -0.98 (0.26), residues: 968 helix: -0.40 (0.22), residues: 458 sheet: 0.30 (0.38), residues: 176 loop : -1.35 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.006 TRP A 303 HIS 0.012 0.002 HIS A 498 PHE 0.024 0.003 PHE A 138 TYR 0.032 0.003 TYR A 597 ARG 0.016 0.002 ARG A 410 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 PHE cc_start: 0.7623 (t80) cc_final: 0.7296 (t80) REVERT: A 266 PHE cc_start: 0.7046 (t80) cc_final: 0.6057 (t80) REVERT: A 436 MET cc_start: 0.9288 (mtp) cc_final: 0.8949 (mtt) REVERT: A 454 CYS cc_start: 0.8124 (t) cc_final: 0.7782 (p) REVERT: A 667 LEU cc_start: 0.9016 (tp) cc_final: 0.8585 (tp) REVERT: A 702 LEU cc_start: 0.9307 (mt) cc_final: 0.9061 (pp) REVERT: A 917 ILE cc_start: 0.7541 (mm) cc_final: 0.7304 (mm) REVERT: A 985 MET cc_start: 0.7967 (mpp) cc_final: 0.6747 (mpp) REVERT: A 1037 ARG cc_start: 0.7777 (mmt90) cc_final: 0.7224 (mmm160) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2030 time to fit residues: 36.4390 Evaluate side-chains 77 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 40 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 29 optimal weight: 20.0000 chunk 45 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 87 optimal weight: 0.1980 overall best weight: 4.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 ASN ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 880 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 976 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7904 Z= 0.246 Angle : 0.772 8.243 10720 Z= 0.403 Chirality : 0.047 0.250 1174 Planarity : 0.006 0.080 1401 Dihedral : 5.515 19.441 1039 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 22.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.23 % Allowed : 2.79 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.44 % 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: -0.26 (0.27), residues: 968 helix: 0.43 (0.23), residues: 464 sheet: 0.33 (0.38), residues: 176 loop : -1.21 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP A 303 HIS 0.009 0.002 HIS A 276 PHE 0.022 0.002 PHE A 935 TYR 0.033 0.002 TYR A 597 ARG 0.007 0.001 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 PHE cc_start: 0.7588 (t80) cc_final: 0.7326 (t80) REVERT: A 245 LEU cc_start: 0.9227 (tp) cc_final: 0.9011 (tp) REVERT: A 667 LEU cc_start: 0.9083 (tp) cc_final: 0.8681 (tp) REVERT: A 702 LEU cc_start: 0.9492 (mt) cc_final: 0.8996 (pp) REVERT: A 920 LEU cc_start: 0.8601 (mp) cc_final: 0.8242 (mm) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1726 time to fit residues: 26.1928 Evaluate side-chains 76 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 72 optimal weight: 9.9990 chunk 59 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 94 optimal weight: 40.0000 chunk 77 optimal weight: 20.0000 chunk 86 optimal weight: 10.0000 chunk 29 optimal weight: 40.0000 chunk 70 optimal weight: 8.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 53 GLN ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 ASN A 737 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7904 Z= 0.242 Angle : 0.718 8.329 10720 Z= 0.373 Chirality : 0.045 0.224 1174 Planarity : 0.006 0.067 1401 Dihedral : 5.278 17.108 1039 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 24.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.23 % Allowed : 2.56 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.44 % 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: -0.11 (0.27), residues: 968 helix: 0.50 (0.23), residues: 473 sheet: 0.31 (0.39), residues: 174 loop : -1.02 (0.37), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 303 HIS 0.011 0.002 HIS A 498 PHE 0.025 0.002 PHE A 217 TYR 0.024 0.002 TYR A 597 ARG 0.006 0.001 ARG A 505 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 PHE cc_start: 0.6897 (t80) cc_final: 0.6665 (t80) REVERT: A 361 PHE cc_start: 0.8232 (m-80) cc_final: 0.7568 (m-80) REVERT: A 667 LEU cc_start: 0.8899 (tp) cc_final: 0.8615 (tp) REVERT: A 702 LEU cc_start: 0.9405 (mt) cc_final: 0.9184 (pp) REVERT: A 749 MET cc_start: 0.8585 (tmm) cc_final: 0.8044 (tmm) REVERT: A 918 PHE cc_start: 0.7384 (t80) cc_final: 0.7144 (t80) REVERT: A 1037 ARG cc_start: 0.7762 (mmt90) cc_final: 0.7357 (mmt90) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1763 time to fit residues: 23.5057 Evaluate side-chains 71 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 41 optimal weight: 9.9990 chunk 58 optimal weight: 20.0000 chunk 87 optimal weight: 9.9990 chunk 92 optimal weight: 20.0000 chunk 83 optimal weight: 50.0000 chunk 25 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 overall best weight: 6.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7904 Z= 0.264 Angle : 0.751 9.308 10720 Z= 0.393 Chirality : 0.046 0.292 1174 Planarity : 0.006 0.062 1401 Dihedral : 5.247 19.608 1039 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 28.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.23 % Allowed : 1.86 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.44 % 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: -0.17 (0.27), residues: 968 helix: 0.45 (0.23), residues: 466 sheet: 0.11 (0.38), residues: 178 loop : -0.91 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 684 HIS 0.008 0.002 HIS A 498 PHE 0.014 0.002 PHE A 217 TYR 0.025 0.002 TYR A 492 ARG 0.007 0.001 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 667 LEU cc_start: 0.8766 (tp) cc_final: 0.8378 (tp) REVERT: A 918 PHE cc_start: 0.7954 (t80) cc_final: 0.7622 (t80) REVERT: A 920 LEU cc_start: 0.9170 (mt) cc_final: 0.8913 (mm) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1607 time to fit residues: 21.4978 Evaluate side-chains 60 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 8.9990 chunk 1 optimal weight: 8.9990 chunk 69 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 79 optimal weight: 20.0000 chunk 64 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 47 optimal weight: 20.0000 chunk 83 optimal weight: 50.0000 chunk 23 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 GLN ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 HIS ** A 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 ASN A 708 GLN A 745 GLN ** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 927 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7904 Z= 0.272 Angle : 0.730 8.756 10720 Z= 0.380 Chirality : 0.045 0.157 1174 Planarity : 0.005 0.047 1401 Dihedral : 5.257 23.580 1039 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 29.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.23 % Allowed : 1.51 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.44 % 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: -0.19 (0.27), residues: 968 helix: 0.39 (0.23), residues: 470 sheet: -0.04 (0.38), residues: 175 loop : -0.73 (0.37), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 303 HIS 0.006 0.002 HIS A 229 PHE 0.027 0.002 PHE A 935 TYR 0.026 0.002 TYR A 492 ARG 0.007 0.001 ARG A 545 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 667 LEU cc_start: 0.8806 (tp) cc_final: 0.8436 (tp) REVERT: A 920 LEU cc_start: 0.9159 (mt) cc_final: 0.8919 (mt) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1565 time to fit residues: 19.9303 Evaluate side-chains 57 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 54 optimal weight: 30.0000 chunk 22 optimal weight: 20.0000 chunk 92 optimal weight: 20.0000 chunk 77 optimal weight: 20.0000 chunk 43 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 48 optimal weight: 20.0000 chunk 89 optimal weight: 20.0000 overall best weight: 8.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1016 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.4777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 7904 Z= 0.314 Angle : 0.775 9.240 10720 Z= 0.408 Chirality : 0.046 0.213 1174 Planarity : 0.006 0.050 1401 Dihedral : 5.469 27.593 1039 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 33.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.23 % Allowed : 1.75 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.44 % 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: -0.46 (0.27), residues: 968 helix: 0.04 (0.23), residues: 472 sheet: -0.17 (0.38), residues: 173 loop : -0.64 (0.38), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 303 HIS 0.008 0.002 HIS A 78 PHE 0.031 0.003 PHE A 935 TYR 0.030 0.002 TYR A 492 ARG 0.007 0.001 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 LEU cc_start: 0.9210 (tp) cc_final: 0.8962 (tp) REVERT: A 436 MET cc_start: 0.8782 (ptp) cc_final: 0.8566 (ptp) REVERT: A 667 LEU cc_start: 0.8804 (tp) cc_final: 0.8434 (tp) REVERT: A 702 LEU cc_start: 0.9556 (mt) cc_final: 0.9330 (mt) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1621 time to fit residues: 19.2067 Evaluate side-chains 56 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 50.0000 chunk 52 optimal weight: 0.0030 chunk 67 optimal weight: 20.0000 chunk 78 optimal weight: 8.9990 chunk 51 optimal weight: 9.9990 chunk 92 optimal weight: 20.0000 chunk 57 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 42 optimal weight: 20.0000 chunk 36 optimal weight: 7.9990 chunk 55 optimal weight: 40.0000 overall best weight: 6.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.4959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7904 Z= 0.245 Angle : 0.712 8.749 10720 Z= 0.371 Chirality : 0.045 0.175 1174 Planarity : 0.005 0.041 1401 Dihedral : 5.346 30.341 1039 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 28.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.23 % Allowed : 0.81 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.44 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.27), residues: 968 helix: 0.27 (0.23), residues: 465 sheet: -0.14 (0.39), residues: 173 loop : -0.59 (0.38), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 303 HIS 0.007 0.001 HIS A 78 PHE 0.027 0.002 PHE A 935 TYR 0.021 0.002 TYR A 492 ARG 0.007 0.001 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 PHE cc_start: 0.7551 (t80) cc_final: 0.7244 (t80) REVERT: A 667 LEU cc_start: 0.8712 (tp) cc_final: 0.8420 (tp) REVERT: A 702 LEU cc_start: 0.9457 (mt) cc_final: 0.9097 (mt) REVERT: A 918 PHE cc_start: 0.8078 (t80) cc_final: 0.7810 (t80) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1638 time to fit residues: 19.1524 Evaluate side-chains 56 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 17 optimal weight: 8.9990 chunk 58 optimal weight: 9.9990 chunk 63 optimal weight: 40.0000 chunk 45 optimal weight: 0.9990 chunk 8 optimal weight: 0.0970 chunk 72 optimal weight: 20.0000 chunk 84 optimal weight: 6.9990 chunk 88 optimal weight: 30.0000 chunk 80 optimal weight: 10.0000 overall best weight: 4.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.5127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7904 Z= 0.211 Angle : 0.680 8.313 10720 Z= 0.350 Chirality : 0.045 0.159 1174 Planarity : 0.005 0.040 1401 Dihedral : 5.131 30.854 1039 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 25.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.23 % Allowed : 0.58 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.44 % 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: 0.02 (0.28), residues: 968 helix: 0.49 (0.24), residues: 469 sheet: -0.05 (0.40), residues: 173 loop : -0.45 (0.38), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 303 HIS 0.007 0.001 HIS A 78 PHE 0.015 0.002 PHE A 124 TYR 0.017 0.002 TYR A 492 ARG 0.010 0.001 ARG A 505 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 LEU cc_start: 0.9101 (tp) cc_final: 0.8780 (tt) REVERT: A 361 PHE cc_start: 0.8154 (m-80) cc_final: 0.7413 (m-80) REVERT: A 667 LEU cc_start: 0.8873 (tp) cc_final: 0.8579 (tp) REVERT: A 702 LEU cc_start: 0.9460 (mt) cc_final: 0.9093 (mt) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1589 time to fit residues: 19.4874 Evaluate side-chains 54 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 7.9990 chunk 88 optimal weight: 40.0000 chunk 51 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 67 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.5300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7904 Z= 0.208 Angle : 0.689 9.034 10720 Z= 0.353 Chirality : 0.044 0.155 1174 Planarity : 0.005 0.038 1401 Dihedral : 5.077 30.008 1039 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 25.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.23 % Allowed : 0.47 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.44 % 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: 0.07 (0.28), residues: 968 helix: 0.52 (0.24), residues: 469 sheet: -0.03 (0.40), residues: 173 loop : -0.38 (0.38), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 303 HIS 0.007 0.001 HIS A 78 PHE 0.014 0.002 PHE A 318 TYR 0.018 0.002 TYR A 492 ARG 0.006 0.001 ARG A 505 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 LEU cc_start: 0.9075 (tp) cc_final: 0.8772 (tt) REVERT: A 361 PHE cc_start: 0.8144 (m-80) cc_final: 0.7508 (m-80) REVERT: A 667 LEU cc_start: 0.8859 (tp) cc_final: 0.8562 (tp) REVERT: A 702 LEU cc_start: 0.9526 (mt) cc_final: 0.9213 (mt) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1544 time to fit residues: 17.8422 Evaluate side-chains 53 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 30.0000 chunk 43 optimal weight: 2.9990 chunk 63 optimal weight: 40.0000 chunk 95 optimal weight: 6.9990 chunk 88 optimal weight: 30.0000 chunk 76 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 chunk 81 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 GLN ** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.5534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7904 Z= 0.225 Angle : 0.695 8.339 10720 Z= 0.358 Chirality : 0.044 0.154 1174 Planarity : 0.005 0.052 1401 Dihedral : 5.112 30.602 1039 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 27.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.23 % Allowed : 0.00 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.44 % 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: 0.02 (0.28), residues: 968 helix: 0.48 (0.24), residues: 469 sheet: -0.13 (0.39), residues: 175 loop : -0.36 (0.38), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 303 HIS 0.006 0.001 HIS A 78 PHE 0.018 0.002 PHE A 124 TYR 0.024 0.002 TYR A 492 ARG 0.006 0.001 ARG A 505 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 LEU cc_start: 0.9176 (tp) cc_final: 0.8864 (tt) REVERT: A 361 PHE cc_start: 0.8305 (m-80) cc_final: 0.7580 (m-80) REVERT: A 667 LEU cc_start: 0.8860 (tp) cc_final: 0.8573 (tp) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1704 time to fit residues: 19.6721 Evaluate side-chains 54 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 5.9990 chunk 70 optimal weight: 40.0000 chunk 11 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 76 optimal weight: 0.7980 chunk 31 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 9 optimal weight: 20.0000 chunk 14 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.040829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.029057 restraints weight = 221999.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.030525 restraints weight = 120616.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.031687 restraints weight = 83085.820| |-----------------------------------------------------------------------------| r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2610 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2610 r_free = 0.2610 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2611 r_free = 0.2611 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2611 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.5764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7904 Z= 0.221 Angle : 0.687 8.269 10720 Z= 0.353 Chirality : 0.044 0.160 1174 Planarity : 0.005 0.043 1401 Dihedral : 5.089 31.352 1039 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 27.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.23 % Allowed : 0.12 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.44 % 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: 0.07 (0.28), residues: 968 helix: 0.55 (0.24), residues: 468 sheet: -0.22 (0.39), residues: 176 loop : -0.30 (0.38), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 303 HIS 0.006 0.001 HIS A 78 PHE 0.015 0.002 PHE A 318 TYR 0.016 0.002 TYR A 492 ARG 0.005 0.001 ARG A 173 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1434.36 seconds wall clock time: 27 minutes 28.05 seconds (1648.05 seconds total)