Starting phenix.real_space_refine on Wed Feb 14 07:59:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dp0_27627/02_2024/8dp0_27627.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dp0_27627/02_2024/8dp0_27627.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dp0_27627/02_2024/8dp0_27627.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dp0_27627/02_2024/8dp0_27627.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dp0_27627/02_2024/8dp0_27627.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dp0_27627/02_2024/8dp0_27627.pdb" } resolution = 2.96 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= -0.017 sd= 0.061 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 43 5.16 5 C 5699 2.51 5 N 1529 2.21 5 O 1623 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 146": "OE1" <-> "OE2" Residue "A PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 239": "OD1" <-> "OD2" Residue "A GLU 301": "OE1" <-> "OE2" Residue "A ASP 358": "OD1" <-> "OD2" Residue "A ASP 369": "OD1" <-> "OD2" Residue "A GLU 384": "OE1" <-> "OE2" Residue "A PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 556": "OE1" <-> "OE2" Residue "A ASP 571": "OD1" <-> "OD2" Residue "A ASP 632": "OD1" <-> "OD2" Residue "A GLU 638": "OE1" <-> "OE2" Residue "A GLU 649": "OE1" <-> "OE2" Residue "A ASP 654": "OD1" <-> "OD2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A GLU 880": "OE1" <-> "OE2" Residue "A ASP 884": "OD1" <-> "OD2" Residue "A ASP 950": "OD1" <-> "OD2" Residue "A GLU 1049": "OE1" <-> "OE2" Residue "B ASP 61": "OD1" <-> "OD2" Residue "B ASP 72": "OD1" <-> "OD2" Residue "B GLU 88": "OE1" <-> "OE2" Residue "B PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8894 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 979, 7964 Classifications: {'peptide': 979} Link IDs: {'PTRANS': 46, 'TRANS': 932} Chain breaks: 6 Chain: "B" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 930 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Time building chain proxies: 5.32, per 1000 atoms: 0.60 Number of scatterers: 8894 At special positions: 0 Unit cell: (87.98, 92.96, 107.9, 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 43 16.00 O 1623 8.00 N 1529 7.00 C 5699 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: 3.44 Conformation dependent library (CDL) restraints added in 1.7 seconds 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2082 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 10 sheets defined 46.7% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 69 through 82 Processing helix chain 'A' and resid 82 through 90 removed outlier: 4.119A pdb=" N ARG A 90 " --> pdb=" O ASP A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 117 removed outlier: 3.540A pdb=" N GLN A 117 " --> pdb=" O GLN A 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 114 through 117' Processing helix chain 'A' and resid 118 through 128 Processing helix chain 'A' and resid 144 through 159 Processing helix chain 'A' and resid 171 through 180 Processing helix chain 'A' and resid 180 through 190 Processing helix chain 'A' and resid 192 through 199 Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 240 through 251 Processing helix chain 'A' and resid 286 through 289 Processing helix chain 'A' and resid 290 through 300 Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 328 through 332 removed outlier: 4.097A pdb=" N GLY A 331 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL A 332 " --> pdb=" O CYS A 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 328 through 332' Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 548 through 561 Processing helix chain 'A' and resid 568 through 578 Processing helix chain 'A' and resid 578 through 583 Processing helix chain 'A' and resid 584 through 587 removed outlier: 6.568A pdb=" N LYS A 587 " --> pdb=" O LYS A 584 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 584 through 587' Processing helix chain 'A' and resid 588 through 595 Processing helix chain 'A' and resid 600 through 613 removed outlier: 3.721A pdb=" N ARG A 613 " --> pdb=" O GLN A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 631 Processing helix chain 'A' and resid 637 through 649 Processing helix chain 'A' and resid 652 through 659 Processing helix chain 'A' and resid 659 through 667 Processing helix chain 'A' and resid 668 through 670 No H-bonds generated for 'chain 'A' and resid 668 through 670' Processing helix chain 'A' and resid 675 through 688 Processing helix chain 'A' and resid 688 through 706 Processing helix chain 'A' and resid 709 through 724 removed outlier: 3.503A pdb=" N PHE A 713 " --> pdb=" O TYR A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 752 removed outlier: 3.641A pdb=" N LEU A 752 " --> pdb=" O ASP A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 776 Processing helix chain 'A' and resid 798 through 801 Processing helix chain 'A' and resid 838 through 857 Processing helix chain 'A' and resid 888 through 896 removed outlier: 3.987A pdb=" N THR A 895 " --> pdb=" O ILE A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 915 removed outlier: 4.542A pdb=" N ASN A 908 " --> pdb=" O ASP A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 943 Processing helix chain 'A' and resid 948 through 950 No H-bonds generated for 'chain 'A' and resid 948 through 950' Processing helix chain 'A' and resid 964 through 976 removed outlier: 3.820A pdb=" N ILE A 968 " --> pdb=" O ASP A 964 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY A 970 " --> pdb=" O GLY A 966 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN A 971 " --> pdb=" O HIS A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 996 Processing helix chain 'A' and resid 1003 through 1023 removed outlier: 3.699A pdb=" N HIS A1023 " --> pdb=" O ALA A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1039 removed outlier: 3.609A pdb=" N MET A1039 " --> pdb=" O LEU A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1055 removed outlier: 4.315A pdb=" N ARG A1052 " --> pdb=" O ILE A1048 " (cutoff:3.500A) Processing helix chain 'A' and resid 1060 through 1078 Processing helix chain 'A' and resid 1080 through 1091 Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'B' and resid 103 through 109 removed outlier: 3.949A pdb=" N TRP B 107 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLY B 109 " --> pdb=" O SER B 105 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 58 removed outlier: 3.835A pdb=" N GLU A 55 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N GLN A 134 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N GLN A 101 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 229 through 235 removed outlier: 7.145A pdb=" N PHE A 221 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N VAL A 305 " --> pdb=" O PHE A 221 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL A 223 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LEU A 307 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N HIS A 225 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU A 272 " --> pdb=" O LEU A 281 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 352 through 353 removed outlier: 6.058A pdb=" N VAL A 352 " --> pdb=" O ALA A 528 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 407 through 419 removed outlier: 7.421A pdb=" N VAL A 408 " --> pdb=" O ASP A 369 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ASP A 369 " --> pdb=" O VAL A 408 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TRP A 410 " --> pdb=" O GLY A 367 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N GLY A 367 " --> pdb=" O TRP A 410 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A 412 " --> pdb=" O ILE A 365 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N PHE A 361 " --> pdb=" O PHE A 416 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ILE A 365 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU A 519 " --> pdb=" O ILE A 365 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY A 478 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 393 through 398 removed outlier: 6.734A pdb=" N ILE A 387 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLN A 396 " --> pdb=" O ALA A 385 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ALA A 385 " --> pdb=" O GLN A 396 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ARG A 398 " --> pdb=" O VAL A 383 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL A 383 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU A 429 " --> pdb=" O ASN A 465 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ASN A 465 " --> pdb=" O LEU A 429 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU A 431 " --> pdb=" O TYR A 463 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N TYR A 463 " --> pdb=" O LEU A 431 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE A 433 " --> pdb=" O LEU A 461 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 783 through 785 removed outlier: 5.910A pdb=" N LEU A 791 " --> pdb=" O VAL A 785 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N LYS A 816 " --> pdb=" O GLY A 794 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N LEU A 796 " --> pdb=" O GLU A 814 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N GLU A 814 " --> pdb=" O LEU A 796 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 783 through 785 removed outlier: 5.910A pdb=" N LEU A 791 " --> pdb=" O VAL A 785 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N LYS A 816 " --> pdb=" O GLY A 794 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N LEU A 796 " --> pdb=" O GLU A 814 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N GLU A 814 " --> pdb=" O LEU A 796 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE A 876 " --> pdb=" O THR A 872 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 885 through 887 Processing sheet with id=AA9, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.560A pdb=" N ALA B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ARG B 38 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N LEU B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) 428 hydrogen bonds defined for protein. 1200 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: 3.02 Time building geometry restraints manager: 3.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2890 1.34 - 1.46: 1560 1.46 - 1.57: 4590 1.57 - 1.69: 0 1.69 - 1.81: 65 Bond restraints: 9105 Sorted by residual: bond pdb=" C ARG A 614 " pdb=" N GLU A 615 " ideal model delta sigma weight residual 1.332 1.315 0.017 1.29e-02 6.01e+03 1.75e+00 bond pdb=" C ALA B 98 " pdb=" O ALA B 98 " ideal model delta sigma weight residual 1.243 1.234 0.010 9.50e-03 1.11e+04 1.07e+00 bond pdb=" N PRO A 54 " pdb=" CA PRO A 54 " ideal model delta sigma weight residual 1.469 1.481 -0.013 1.28e-02 6.10e+03 9.90e-01 bond pdb=" CB ILE A 643 " pdb=" CG2 ILE A 643 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.20e-01 bond pdb=" N GLY A 996 " pdb=" CA GLY A 996 " ideal model delta sigma weight residual 1.449 1.437 0.012 1.45e-02 4.76e+03 6.78e-01 ... (remaining 9100 not shown) Histogram of bond angle deviations from ideal: 98.76 - 105.81: 199 105.81 - 112.86: 4955 112.86 - 119.91: 2969 119.91 - 126.96: 4076 126.96 - 134.01: 142 Bond angle restraints: 12341 Sorted by residual: angle pdb=" C ALA B 98 " pdb=" CA ALA B 98 " pdb=" CB ALA B 98 " ideal model delta sigma weight residual 117.23 109.41 7.82 1.36e+00 5.41e-01 3.30e+01 angle pdb=" CA ALA B 98 " pdb=" C ALA B 98 " pdb=" N GLY B 99 " ideal model delta sigma weight residual 119.98 116.67 3.31 8.50e-01 1.38e+00 1.52e+01 angle pdb=" N VAL A 67 " pdb=" CA VAL A 67 " pdb=" C VAL A 67 " ideal model delta sigma weight residual 111.77 108.49 3.28 1.04e+00 9.25e-01 9.96e+00 angle pdb=" N ALA B 98 " pdb=" CA ALA B 98 " pdb=" C ALA B 98 " ideal model delta sigma weight residual 108.67 113.69 -5.02 1.67e+00 3.59e-01 9.05e+00 angle pdb=" N VAL A 326 " pdb=" CA VAL A 326 " pdb=" CB VAL A 326 " ideal model delta sigma weight residual 112.21 109.01 3.20 1.10e+00 8.26e-01 8.49e+00 ... (remaining 12336 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.95: 4870 15.95 - 31.90: 456 31.90 - 47.85: 91 47.85 - 63.80: 22 63.80 - 79.75: 9 Dihedral angle restraints: 5448 sinusoidal: 2234 harmonic: 3214 Sorted by residual: dihedral pdb=" CA ASP B 61 " pdb=" CB ASP B 61 " pdb=" CG ASP B 61 " pdb=" OD1 ASP B 61 " ideal model delta sinusoidal sigma weight residual -30.00 -89.15 59.15 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ASN B 96 " pdb=" C ASN B 96 " pdb=" N GLU B 97 " pdb=" CA GLU B 97 " ideal model delta harmonic sigma weight residual -180.00 -162.92 -17.08 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA GLU A 68 " pdb=" C GLU A 68 " pdb=" N GLN A 69 " pdb=" CA GLN A 69 " ideal model delta harmonic sigma weight residual 180.00 163.21 16.79 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 5445 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 921 0.033 - 0.065: 302 0.065 - 0.098: 92 0.098 - 0.131: 48 0.131 - 0.164: 3 Chirality restraints: 1366 Sorted by residual: chirality pdb=" CA THR A 182 " pdb=" N THR A 182 " pdb=" C THR A 182 " pdb=" CB THR A 182 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.16 2.00e-01 2.50e+01 6.69e-01 chirality pdb=" CB ILE A 643 " pdb=" CA ILE A 643 " pdb=" CG1 ILE A 643 " pdb=" CG2 ILE A 643 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA ILE A 368 " pdb=" N ILE A 368 " pdb=" C ILE A 368 " pdb=" CB ILE A 368 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 1363 not shown) Planarity restraints: 1577 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 547 " 0.046 5.00e-02 4.00e+02 7.03e-02 7.91e+00 pdb=" N PRO A 548 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 548 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 548 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 988 " -0.036 5.00e-02 4.00e+02 5.52e-02 4.87e+00 pdb=" N PRO A 989 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 989 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 989 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 370 " -0.027 5.00e-02 4.00e+02 4.05e-02 2.63e+00 pdb=" N PRO A 371 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 371 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 371 " -0.023 5.00e-02 4.00e+02 ... (remaining 1574 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 979 2.75 - 3.29: 8630 3.29 - 3.83: 14731 3.83 - 4.36: 17801 4.36 - 4.90: 30811 Nonbonded interactions: 72952 Sorted by model distance: nonbonded pdb=" OH TYR A1017 " pdb=" O ALA A1054 " model vdw 2.213 2.440 nonbonded pdb=" O TRP A 617 " pdb=" OG SER A 620 " model vdw 2.221 2.440 nonbonded pdb=" OE1 GLN A 705 " pdb=" OG SER A 871 " model vdw 2.268 2.440 nonbonded pdb=" O MET A1033 " pdb=" OG1 THR A1037 " model vdw 2.270 2.440 nonbonded pdb=" OE2 GLU A 384 " pdb=" NE2 GLN A 396 " model vdw 2.280 2.520 ... (remaining 72947 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.910 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: 0.000 Extract box with map and model: 11.610 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 27.840 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:12.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 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 : 0.002 0.030 9105 Z= 0.162 Angle : 0.500 7.818 12341 Z= 0.278 Chirality : 0.040 0.164 1366 Planarity : 0.004 0.070 1577 Dihedral : 13.313 79.755 3366 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.26), residues: 1088 helix: 1.71 (0.25), residues: 452 sheet: 0.23 (0.36), residues: 186 loop : 0.03 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 125 HIS 0.006 0.001 HIS A1023 PHE 0.011 0.001 PHE A 473 TYR 0.016 0.001 TYR A 110 ARG 0.007 0.000 ARG A 552 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 1.043 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 1.0379 time to fit residues: 251.1525 Evaluate side-chains 112 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 GLN ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 GLN A 512 ASN A 951 ASN A 959 ASN A1083 GLN B 118 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 9105 Z= 0.284 Angle : 0.645 8.931 12341 Z= 0.334 Chirality : 0.045 0.165 1366 Planarity : 0.005 0.061 1577 Dihedral : 4.142 16.564 1185 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.09 % Allowed : 11.67 % Favored : 84.24 % 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: 0.80 (0.25), residues: 1088 helix: 1.49 (0.24), residues: 457 sheet: -0.01 (0.36), residues: 175 loop : -0.14 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 812 HIS 0.008 0.001 HIS A 95 PHE 0.015 0.002 PHE B 113 TYR 0.020 0.002 TYR A1067 ARG 0.006 0.001 ARG A 552 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 111 time to evaluate : 1.134 Fit side-chains revert: symmetry clash REVERT: A 501 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8336 (mtmt) REVERT: A 679 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8076 (mtt-85) outliers start: 40 outliers final: 12 residues processed: 137 average time/residue: 1.0264 time to fit residues: 152.4964 Evaluate side-chains 94 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 80 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 501 LYS Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 679 ARG Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain A residue 904 ASP Chi-restraints excluded: chain A residue 961 PHE Chi-restraints excluded: chain B residue 63 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 1.9990 chunk 30 optimal weight: 0.0170 chunk 82 optimal weight: 1.9990 chunk 67 optimal weight: 0.2980 chunk 27 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 107 optimal weight: 0.3980 chunk 88 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 ASN B 96 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.5856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9105 Z= 0.216 Angle : 0.544 9.364 12341 Z= 0.275 Chirality : 0.042 0.160 1366 Planarity : 0.004 0.058 1577 Dihedral : 3.677 16.896 1185 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.68 % Allowed : 15.15 % Favored : 81.17 % 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: 1.03 (0.26), residues: 1088 helix: 1.72 (0.24), residues: 461 sheet: 0.07 (0.36), residues: 183 loop : -0.05 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 812 HIS 0.007 0.001 HIS B 50 PHE 0.017 0.001 PHE A 578 TYR 0.016 0.001 TYR B 94 ARG 0.004 0.001 ARG A 613 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 88 time to evaluate : 1.076 Fit side-chains REVERT: B 28 ILE cc_start: 0.7019 (tp) cc_final: 0.6812 (tp) outliers start: 36 outliers final: 12 residues processed: 117 average time/residue: 0.9000 time to fit residues: 115.6039 Evaluate side-chains 83 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain A residue 904 ASP Chi-restraints excluded: chain A residue 961 PHE Chi-restraints excluded: chain B residue 12 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 99 optimal weight: 0.0870 chunk 105 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 28 optimal weight: 10.0000 chunk 87 optimal weight: 0.9990 overall best weight: 1.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.6897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 9105 Z= 0.285 Angle : 0.571 9.324 12341 Z= 0.287 Chirality : 0.043 0.146 1366 Planarity : 0.004 0.060 1577 Dihedral : 3.907 16.441 1185 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.48 % Allowed : 16.07 % Favored : 80.45 % 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: 0.94 (0.25), residues: 1088 helix: 1.68 (0.24), residues: 460 sheet: -0.05 (0.37), residues: 171 loop : -0.11 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 125 HIS 0.006 0.001 HIS B 50 PHE 0.011 0.001 PHE A 382 TYR 0.014 0.002 TYR A1067 ARG 0.005 0.001 ARG A 849 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 71 time to evaluate : 1.099 Fit side-chains outliers start: 34 outliers final: 13 residues processed: 93 average time/residue: 0.9054 time to fit residues: 92.5169 Evaluate side-chains 78 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 65 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain A residue 904 ASP Chi-restraints excluded: chain A residue 961 PHE Chi-restraints excluded: chain B residue 123 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 43 optimal weight: 20.0000 chunk 89 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1041 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.7935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.124 9105 Z= 0.444 Angle : 0.642 9.408 12341 Z= 0.326 Chirality : 0.046 0.234 1366 Planarity : 0.005 0.061 1577 Dihedral : 4.353 17.378 1185 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.48 % Allowed : 16.79 % Favored : 79.73 % 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 (0.25), residues: 1088 helix: 1.35 (0.24), residues: 460 sheet: -0.15 (0.37), residues: 171 loop : -0.26 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 125 HIS 0.006 0.001 HIS B 50 PHE 0.016 0.002 PHE A 382 TYR 0.015 0.002 TYR A1067 ARG 0.005 0.001 ARG A 614 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 66 time to evaluate : 1.094 Fit side-chains outliers start: 34 outliers final: 14 residues processed: 91 average time/residue: 1.0061 time to fit residues: 100.0213 Evaluate side-chains 69 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 55 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 904 ASP Chi-restraints excluded: chain A residue 961 PHE Chi-restraints excluded: chain B residue 12 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 105 optimal weight: 0.5980 chunk 87 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 101 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 735 GLN A1089 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.7991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9105 Z= 0.199 Angle : 0.540 10.504 12341 Z= 0.269 Chirality : 0.042 0.186 1366 Planarity : 0.004 0.062 1577 Dihedral : 3.952 16.920 1185 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.07 % Allowed : 18.42 % Favored : 78.51 % 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: 0.89 (0.25), residues: 1088 helix: 1.65 (0.24), residues: 464 sheet: -0.16 (0.38), residues: 172 loop : -0.13 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 125 HIS 0.006 0.001 HIS B 50 PHE 0.012 0.001 PHE B 29 TYR 0.012 0.001 TYR A1067 ARG 0.006 0.000 ARG A 614 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 64 time to evaluate : 0.996 Fit side-chains REVERT: A 911 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8512 (tt) REVERT: A 1039 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.8198 (mmp) REVERT: A 1049 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7324 (mp0) outliers start: 30 outliers final: 12 residues processed: 87 average time/residue: 0.8206 time to fit residues: 79.3540 Evaluate side-chains 74 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 59 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 904 ASP Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 917 THR Chi-restraints excluded: chain A residue 961 PHE Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1049 GLU Chi-restraints excluded: chain B residue 12 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.0770 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 88 optimal weight: 0.1980 chunk 58 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.8078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9105 Z= 0.173 Angle : 0.517 11.190 12341 Z= 0.256 Chirality : 0.041 0.194 1366 Planarity : 0.004 0.063 1577 Dihedral : 3.696 15.979 1185 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.28 % Allowed : 18.53 % Favored : 78.20 % 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: 1.09 (0.26), residues: 1088 helix: 1.83 (0.24), residues: 466 sheet: -0.09 (0.38), residues: 172 loop : -0.04 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 125 HIS 0.005 0.001 HIS B 50 PHE 0.015 0.001 PHE A 42 TYR 0.014 0.001 TYR A 462 ARG 0.006 0.000 ARG A 614 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 71 time to evaluate : 1.002 Fit side-chains outliers start: 32 outliers final: 16 residues processed: 94 average time/residue: 0.9461 time to fit residues: 97.8500 Evaluate side-chains 77 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 61 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 904 ASP Chi-restraints excluded: chain A residue 961 PHE Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 12 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.0970 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 0.0970 chunk 82 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.8143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9105 Z= 0.183 Angle : 0.534 11.336 12341 Z= 0.262 Chirality : 0.041 0.209 1366 Planarity : 0.004 0.069 1577 Dihedral : 3.665 15.936 1185 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.07 % Allowed : 19.04 % Favored : 77.89 % 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: 1.15 (0.26), residues: 1088 helix: 2.00 (0.24), residues: 460 sheet: -0.13 (0.37), residues: 172 loop : -0.08 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 125 HIS 0.005 0.001 HIS B 50 PHE 0.011 0.001 PHE B 29 TYR 0.013 0.001 TYR A 462 ARG 0.019 0.001 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 62 time to evaluate : 1.059 Fit side-chains outliers start: 30 outliers final: 21 residues processed: 86 average time/residue: 0.9197 time to fit residues: 87.1993 Evaluate side-chains 81 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 60 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 898 ASN Chi-restraints excluded: chain A residue 904 ASP Chi-restraints excluded: chain A residue 961 PHE Chi-restraints excluded: chain A residue 1049 GLU Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 12 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 88 optimal weight: 0.5980 chunk 92 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.8235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 9105 Z= 0.222 Angle : 0.540 10.551 12341 Z= 0.266 Chirality : 0.042 0.211 1366 Planarity : 0.004 0.073 1577 Dihedral : 3.712 16.188 1185 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.56 % Allowed : 19.86 % Favored : 77.58 % 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: 1.10 (0.26), residues: 1088 helix: 1.85 (0.24), residues: 466 sheet: -0.12 (0.37), residues: 172 loop : -0.03 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 125 HIS 0.005 0.001 HIS B 50 PHE 0.011 0.001 PHE B 29 TYR 0.013 0.001 TYR A 462 ARG 0.017 0.001 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 62 time to evaluate : 1.088 Fit side-chains outliers start: 25 outliers final: 18 residues processed: 82 average time/residue: 0.9266 time to fit residues: 83.7382 Evaluate side-chains 78 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 60 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 898 ASN Chi-restraints excluded: chain A residue 904 ASP Chi-restraints excluded: chain A residue 917 THR Chi-restraints excluded: chain A residue 961 PHE Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 12 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.5980 chunk 71 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 8 optimal weight: 0.0060 chunk 66 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 26 optimal weight: 0.1980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.8263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9105 Z= 0.174 Angle : 0.536 11.641 12341 Z= 0.264 Chirality : 0.041 0.192 1366 Planarity : 0.004 0.067 1577 Dihedral : 3.609 14.914 1185 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.15 % Allowed : 20.16 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.26), residues: 1088 helix: 2.00 (0.24), residues: 460 sheet: -0.03 (0.36), residues: 182 loop : -0.14 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 125 HIS 0.005 0.001 HIS B 50 PHE 0.011 0.001 PHE B 29 TYR 0.012 0.001 TYR A 462 ARG 0.016 0.001 ARG A 130 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 64 time to evaluate : 1.065 Fit side-chains outliers start: 21 outliers final: 16 residues processed: 81 average time/residue: 0.9548 time to fit residues: 85.2802 Evaluate side-chains 77 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 61 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 898 ASN Chi-restraints excluded: chain A residue 904 ASP Chi-restraints excluded: chain A residue 917 THR Chi-restraints excluded: chain A residue 959 ASN Chi-restraints excluded: chain A residue 961 PHE Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 12 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 86 optimal weight: 0.4980 chunk 36 optimal weight: 0.2980 chunk 88 optimal weight: 0.3980 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 3 GLN ** 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 = 0.3546 r_free = 0.3546 target = 0.102620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.074993 restraints weight = 17728.710| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 3.02 r_work: 0.2893 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.8294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9105 Z= 0.167 Angle : 0.524 10.939 12341 Z= 0.258 Chirality : 0.041 0.188 1366 Planarity : 0.004 0.062 1577 Dihedral : 3.566 14.657 1185 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.84 % Allowed : 20.68 % Favored : 77.48 % 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: 1.20 (0.26), residues: 1088 helix: 2.12 (0.24), residues: 454 sheet: -0.04 (0.36), residues: 182 loop : -0.15 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP A 125 HIS 0.004 0.001 HIS B 50 PHE 0.012 0.001 PHE A 42 TYR 0.013 0.001 TYR A 462 ARG 0.008 0.000 ARG A 130 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2965.20 seconds wall clock time: 53 minutes 40.61 seconds (3220.61 seconds total)