Starting phenix.real_space_refine on Sun Jun 8 19:24:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wcs_37448/06_2025/8wcs_37448.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wcs_37448/06_2025/8wcs_37448.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wcs_37448/06_2025/8wcs_37448.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wcs_37448/06_2025/8wcs_37448.map" model { file = "/net/cci-nas-00/data/ceres_data/8wcs_37448/06_2025/8wcs_37448.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wcs_37448/06_2025/8wcs_37448.cif" } resolution = 3.1 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= 0.001 sd= 0.077 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: 6 Type Number sf(0) Gaussians P 66 5.49 5 Mg 1 5.21 5 S 31 5.16 5 C 6245 2.51 5 N 1692 2.21 5 O 2061 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 10096 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1044, 8685 Classifications: {'peptide': 1044} Link IDs: {'PTRANS': 26, 'TRANS': 1017} Chain breaks: 2 Chain: "G" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1410 Classifications: {'RNA': 66} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 10, 'rna3p_pur': 26, 'rna3p_pyr': 19} Link IDs: {'rna2p': 20, 'rna3p': 45} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.87, per 1000 atoms: 0.68 Number of scatterers: 10096 At special positions: 0 Unit cell: (93.5, 86.7, 119.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 31 16.00 P 66 15.00 Mg 1 11.99 O 2061 8.00 N 1692 7.00 C 6245 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.35 Conformation dependent library (CDL) restraints added in 1.1 seconds 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1994 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 3 sheets defined 56.7% alpha, 1.5% beta 8 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 2.95 Creating SS restraints... Processing helix chain 'A' and resid 9 through 30 Processing helix chain 'A' and resid 41 through 50 removed outlier: 3.502A pdb=" N LYS A 44 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU A 45 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLY A 46 " --> pdb=" O ASP A 43 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ASN A 47 " --> pdb=" O LYS A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.873A pdb=" N LYS A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 132 removed outlier: 3.852A pdb=" N LEU A 105 " --> pdb=" O HIS A 101 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU A 132 " --> pdb=" O ALA A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 163 removed outlier: 3.513A pdb=" N LEU A 156 " --> pdb=" O GLY A 152 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N PHE A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 177 Processing helix chain 'A' and resid 180 through 204 removed outlier: 4.465A pdb=" N GLU A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 261 removed outlier: 3.666A pdb=" N GLU A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 280 Processing helix chain 'A' and resid 290 through 303 removed outlier: 4.313A pdb=" N ALA A 294 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 316 Processing helix chain 'A' and resid 322 through 324 No H-bonds generated for 'chain 'A' and resid 322 through 324' Processing helix chain 'A' and resid 325 through 334 removed outlier: 4.678A pdb=" N PHE A 332 " --> pdb=" O THR A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 361 Processing helix chain 'A' and resid 371 through 390 removed outlier: 3.826A pdb=" N GLU A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS A 388 " --> pdb=" O SER A 384 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU A 390 " --> pdb=" O SER A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 403 removed outlier: 3.733A pdb=" N GLU A 399 " --> pdb=" O LYS A 395 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS A 400 " --> pdb=" O GLU A 396 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE A 401 " --> pdb=" O GLU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 425 Processing helix chain 'A' and resid 438 through 449 removed outlier: 3.559A pdb=" N ASN A 449 " --> pdb=" O TYR A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 504 removed outlier: 3.506A pdb=" N ARG A 504 " --> pdb=" O LYS A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 536 removed outlier: 3.639A pdb=" N GLY A 535 " --> pdb=" O GLU A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 559 removed outlier: 3.843A pdb=" N LEU A 549 " --> pdb=" O SER A 545 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N MET A 550 " --> pdb=" O PRO A 546 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS A 551 " --> pdb=" O ASP A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 591 removed outlier: 3.615A pdb=" N ILE A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 647 removed outlier: 3.786A pdb=" N ILE A 627 " --> pdb=" O ASP A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 654 removed outlier: 3.556A pdb=" N ARG A 653 " --> pdb=" O ALA A 650 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE A 654 " --> pdb=" O PRO A 651 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 650 through 654' Processing helix chain 'A' and resid 658 through 677 removed outlier: 3.594A pdb=" N ILE A 663 " --> pdb=" O LYS A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 688 removed outlier: 3.846A pdb=" N ARG A 686 " --> pdb=" O VAL A 682 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU A 688 " --> pdb=" O ALA A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 704 Processing helix chain 'A' and resid 711 through 718 removed outlier: 3.864A pdb=" N LYS A 715 " --> pdb=" O THR A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 759 removed outlier: 3.706A pdb=" N ASN A 744 " --> pdb=" O GLU A 740 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N PHE A 745 " --> pdb=" O GLY A 741 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA A 746 " --> pdb=" O VAL A 742 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER A 759 " --> pdb=" O LYS A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 789 removed outlier: 3.588A pdb=" N GLU A 789 " --> pdb=" O GLY A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 817 Processing helix chain 'A' and resid 824 through 836 removed outlier: 3.898A pdb=" N PHE A 828 " --> pdb=" O SER A 824 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG A 836 " --> pdb=" O VAL A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 853 Processing helix chain 'A' and resid 865 through 893 removed outlier: 4.458A pdb=" N VAL A 871 " --> pdb=" O THR A 867 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA A 872 " --> pdb=" O GLN A 868 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASN A 879 " --> pdb=" O ARG A 875 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLU A 885 " --> pdb=" O LEU A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 922 Processing helix chain 'A' and resid 922 through 928 Processing helix chain 'A' and resid 962 through 979 removed outlier: 3.837A pdb=" N GLN A 970 " --> pdb=" O GLN A 966 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL A 974 " --> pdb=" O GLN A 970 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ASP A 975 " --> pdb=" O GLU A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1005 removed outlier: 4.221A pdb=" N ARG A1005 " --> pdb=" O ASP A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1023 removed outlier: 3.944A pdb=" N LYS A1023 " --> pdb=" O HIS A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1030 Processing helix chain 'A' and resid 1053 through 1059 Processing helix chain 'A' and resid 1068 through 1082 Processing helix chain 'A' and resid 1087 through 1105 removed outlier: 3.509A pdb=" N TYR A1091 " --> pdb=" O LYS A1087 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN A1105 " --> pdb=" O TYR A1101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 433 through 436 removed outlier: 3.532A pdb=" N LYS A 509 " --> pdb=" O ILE A 433 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 525 through 529 removed outlier: 3.656A pdb=" N PHE A 527 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 954 through 955 382 hydrogen bonds defined for protein. 1119 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 20 hydrogen bonds 36 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 3.24 Time building geometry restraints manager: 2.83 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: 2406 1.33 - 1.45: 2487 1.45 - 1.57: 5374 1.57 - 1.69: 131 1.69 - 1.81: 56 Bond restraints: 10454 Sorted by residual: bond pdb=" CA ASP A1008 " pdb=" C ASP A1008 " ideal model delta sigma weight residual 1.524 1.487 0.037 1.29e-02 6.01e+03 8.22e+00 bond pdb=" CA LEU A 187 " pdb=" C LEU A 187 " ideal model delta sigma weight residual 1.524 1.498 0.026 1.27e-02 6.20e+03 4.12e+00 bond pdb=" N ASP A 721 " pdb=" CA ASP A 721 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.29e-02 6.01e+03 4.09e+00 bond pdb=" C ASP A1008 " pdb=" N ASP A1009 " ideal model delta sigma weight residual 1.335 1.312 0.023 1.31e-02 5.83e+03 3.14e+00 bond pdb=" O3' C G 12 " pdb=" P C G 13 " ideal model delta sigma weight residual 1.607 1.582 0.025 1.50e-02 4.44e+03 2.84e+00 ... (remaining 10449 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 13948 1.98 - 3.96: 332 3.96 - 5.94: 63 5.94 - 7.92: 14 7.92 - 9.91: 5 Bond angle restraints: 14362 Sorted by residual: angle pdb=" N ASP A1008 " pdb=" CA ASP A1008 " pdb=" C ASP A1008 " ideal model delta sigma weight residual 111.36 105.86 5.50 1.09e+00 8.42e-01 2.54e+01 angle pdb=" C ILE A 568 " pdb=" N THR A 569 " pdb=" CA THR A 569 " ideal model delta sigma weight residual 121.54 129.60 -8.06 1.91e+00 2.74e-01 1.78e+01 angle pdb=" C LYS A 574 " pdb=" N ILE A 575 " pdb=" CA ILE A 575 " ideal model delta sigma weight residual 121.97 129.13 -7.16 1.80e+00 3.09e-01 1.58e+01 angle pdb=" C GLU A 178 " pdb=" N THR A 179 " pdb=" CA THR A 179 " ideal model delta sigma weight residual 122.46 127.94 -5.48 1.41e+00 5.03e-01 1.51e+01 angle pdb=" CB GLU A 859 " pdb=" CG GLU A 859 " pdb=" CD GLU A 859 " ideal model delta sigma weight residual 112.60 119.10 -6.50 1.70e+00 3.46e-01 1.46e+01 ... (remaining 14357 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.32: 5900 34.32 - 68.65: 466 68.65 - 102.97: 33 102.97 - 137.29: 0 137.29 - 171.61: 5 Dihedral angle restraints: 6404 sinusoidal: 3308 harmonic: 3096 Sorted by residual: dihedral pdb=" O4' C G -24 " pdb=" C1' C G -24 " pdb=" N1 C G -24 " pdb=" C2 C G -24 " ideal model delta sinusoidal sigma weight residual 200.00 51.20 148.80 1 1.50e+01 4.44e-03 7.92e+01 dihedral pdb=" O4' U G 18 " pdb=" C1' U G 18 " pdb=" N1 U G 18 " pdb=" C2 U G 18 " ideal model delta sinusoidal sigma weight residual 200.00 56.08 143.92 1 1.50e+01 4.44e-03 7.72e+01 dihedral pdb=" O4' C G -8 " pdb=" C1' C G -8 " pdb=" N1 C G -8 " pdb=" C2 C G -8 " ideal model delta sinusoidal sigma weight residual 232.00 62.06 169.94 1 1.70e+01 3.46e-03 6.59e+01 ... (remaining 6401 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1327 0.064 - 0.128: 221 0.128 - 0.193: 34 0.193 - 0.257: 4 0.257 - 0.321: 3 Chirality restraints: 1589 Sorted by residual: chirality pdb=" CB ILE A1044 " pdb=" CA ILE A1044 " pdb=" CG1 ILE A1044 " pdb=" CG2 ILE A1044 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CG LEU A 16 " pdb=" CB LEU A 16 " pdb=" CD1 LEU A 16 " pdb=" CD2 LEU A 16 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CB VAL A1021 " pdb=" CA VAL A1021 " pdb=" CG1 VAL A1021 " pdb=" CG2 VAL A1021 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 1586 not shown) Planarity restraints: 1558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 211 " -0.037 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO A 212 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 212 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 212 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 25 " 0.010 2.00e-02 2.50e+03 2.11e-02 4.46e+00 pdb=" CD GLU A 25 " -0.037 2.00e-02 2.50e+03 pdb=" OE1 GLU A 25 " 0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU A 25 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1007 " -0.010 2.00e-02 2.50e+03 2.04e-02 4.16e+00 pdb=" C LEU A1007 " 0.035 2.00e-02 2.50e+03 pdb=" O LEU A1007 " -0.013 2.00e-02 2.50e+03 pdb=" N ASP A1008 " -0.012 2.00e-02 2.50e+03 ... (remaining 1555 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 364 2.70 - 3.25: 9184 3.25 - 3.80: 16329 3.80 - 4.35: 20398 4.35 - 4.90: 33314 Nonbonded interactions: 79589 Sorted by model distance: nonbonded pdb=" OP1 A G 22 " pdb="MG MG G 101 " model vdw 2.148 2.170 nonbonded pdb=" OH TYR A1006 " pdb=" O ILE A1083 " model vdw 2.211 3.040 nonbonded pdb=" O PHE A 325 " pdb=" OG1 THR A 328 " model vdw 2.231 3.040 nonbonded pdb=" OD2 ASP A 673 " pdb=" OH TYR A 753 " model vdw 2.287 3.040 nonbonded pdb=" OD2 ASP A 424 " pdb=" OH TYR A 890 " model vdw 2.304 3.040 ... (remaining 79584 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.870 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.150 Process input model: 27.610 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 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 : 0.004 0.049 10454 Z= 0.198 Angle : 0.771 9.905 14362 Z= 0.425 Chirality : 0.051 0.321 1589 Planarity : 0.005 0.056 1558 Dihedral : 21.585 171.613 4410 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 0.74 % Allowed : 31.72 % Favored : 67.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.22), residues: 1038 helix: -0.94 (0.19), residues: 557 sheet: -2.54 (0.76), residues: 30 loop : -2.59 (0.25), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 884 HIS 0.004 0.001 HIS A 787 PHE 0.026 0.002 PHE A 331 TYR 0.023 0.002 TYR A 695 ARG 0.010 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.14026 ( 402) hydrogen bonds : angle 5.60782 ( 1155) covalent geometry : bond 0.00371 (10454) covalent geometry : angle 0.77110 (14362) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 1.141 Fit side-chains REVERT: A 1006 TYR cc_start: 0.5842 (OUTLIER) cc_final: 0.5537 (t80) outliers start: 7 outliers final: 0 residues processed: 105 average time/residue: 0.2230 time to fit residues: 34.1771 Evaluate side-chains 92 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1006 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 46 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 0.3980 chunk 86 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 GLN A 996 ASN A1081 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.157841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.132088 restraints weight = 15198.198| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 2.66 r_work: 0.3708 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10454 Z= 0.116 Angle : 0.531 6.813 14362 Z= 0.285 Chirality : 0.039 0.211 1589 Planarity : 0.003 0.045 1558 Dihedral : 18.995 170.378 2143 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 3.16 % Allowed : 29.40 % Favored : 67.44 % 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: -1.19 (0.25), residues: 1038 helix: 0.39 (0.22), residues: 560 sheet: -1.39 (0.78), residues: 36 loop : -2.36 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 884 HIS 0.003 0.001 HIS A 114 PHE 0.014 0.001 PHE A 110 TYR 0.019 0.001 TYR A 155 ARG 0.004 0.000 ARG A 304 Details of bonding type rmsd hydrogen bonds : bond 0.04612 ( 402) hydrogen bonds : angle 3.86095 ( 1155) covalent geometry : bond 0.00230 (10454) covalent geometry : angle 0.53055 (14362) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 106 time to evaluate : 0.993 Fit side-chains revert: symmetry clash REVERT: A 97 MET cc_start: 0.8025 (ptm) cc_final: 0.7714 (ptm) REVERT: A 313 LYS cc_start: 0.8539 (pttp) cc_final: 0.8143 (pttp) REVERT: A 329 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8094 (mp-120) REVERT: A 330 SER cc_start: 0.8536 (m) cc_final: 0.7987 (t) REVERT: A 591 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8369 (tt) REVERT: A 884 TRP cc_start: 0.8496 (t60) cc_final: 0.7969 (t-100) outliers start: 30 outliers final: 14 residues processed: 128 average time/residue: 0.2072 time to fit residues: 38.4455 Evaluate side-chains 106 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1102 CYS Chi-restraints excluded: chain A residue 1108 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 104 optimal weight: 20.0000 chunk 45 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 107 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 chunk 19 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 overall best weight: 2.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A1081 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.150016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.124710 restraints weight = 15252.443| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.55 r_work: 0.3624 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10454 Z= 0.193 Angle : 0.615 6.576 14362 Z= 0.328 Chirality : 0.042 0.228 1589 Planarity : 0.004 0.049 1558 Dihedral : 19.038 164.112 2141 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 3.58 % Allowed : 29.93 % Favored : 66.49 % 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: -1.00 (0.25), residues: 1038 helix: 0.66 (0.22), residues: 565 sheet: -2.37 (0.72), residues: 41 loop : -2.34 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 884 HIS 0.004 0.001 HIS A 114 PHE 0.013 0.002 PHE A 506 TYR 0.021 0.002 TYR A 155 ARG 0.004 0.000 ARG A 432 Details of bonding type rmsd hydrogen bonds : bond 0.05439 ( 402) hydrogen bonds : angle 3.84394 ( 1155) covalent geometry : bond 0.00431 (10454) covalent geometry : angle 0.61485 (14362) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 96 time to evaluate : 1.123 Fit side-chains REVERT: A 88 TRP cc_start: 0.2637 (OUTLIER) cc_final: 0.2327 (t60) REVERT: A 150 LEU cc_start: 0.6862 (mt) cc_final: 0.6614 (mt) REVERT: A 329 GLN cc_start: 0.9054 (OUTLIER) cc_final: 0.8821 (mm-40) REVERT: A 400 LYS cc_start: 0.7553 (OUTLIER) cc_final: 0.7009 (mmtm) REVERT: A 591 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8457 (tt) REVERT: A 1006 TYR cc_start: 0.6544 (m-80) cc_final: 0.6229 (m-80) outliers start: 34 outliers final: 22 residues processed: 124 average time/residue: 0.2432 time to fit residues: 42.6260 Evaluate side-chains 112 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 687 HIS Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 791 PHE Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 1044 ILE Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1070 ASP Chi-restraints excluded: chain A residue 1108 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 66 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 74 optimal weight: 0.4980 chunk 90 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 GLN A 970 GLN A1081 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.153970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.128182 restraints weight = 15193.593| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.63 r_work: 0.3660 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10454 Z= 0.124 Angle : 0.539 7.107 14362 Z= 0.288 Chirality : 0.040 0.189 1589 Planarity : 0.003 0.051 1558 Dihedral : 18.856 168.598 2141 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 4.00 % Allowed : 29.61 % Favored : 66.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.26), residues: 1038 helix: 1.10 (0.22), residues: 562 sheet: -2.06 (0.73), residues: 42 loop : -2.28 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 884 HIS 0.003 0.001 HIS A 114 PHE 0.007 0.001 PHE A 506 TYR 0.018 0.001 TYR A 155 ARG 0.002 0.000 ARG A 432 Details of bonding type rmsd hydrogen bonds : bond 0.04568 ( 402) hydrogen bonds : angle 3.61669 ( 1155) covalent geometry : bond 0.00266 (10454) covalent geometry : angle 0.53920 (14362) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 95 time to evaluate : 1.426 Fit side-chains revert: symmetry clash REVERT: A 131 TYR cc_start: 0.6816 (t80) cc_final: 0.6511 (t80) REVERT: A 150 LEU cc_start: 0.6823 (mt) cc_final: 0.6598 (mt) REVERT: A 591 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8436 (tt) REVERT: A 882 MET cc_start: 0.8109 (mmm) cc_final: 0.7648 (mmt) REVERT: A 1006 TYR cc_start: 0.6531 (m-80) cc_final: 0.6122 (m-80) outliers start: 38 outliers final: 27 residues processed: 123 average time/residue: 0.2435 time to fit residues: 43.8295 Evaluate side-chains 121 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 93 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 945 VAL Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1108 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 25 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 970 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.150932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.124953 restraints weight = 15304.653| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.61 r_work: 0.3626 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10454 Z= 0.164 Angle : 0.574 7.468 14362 Z= 0.304 Chirality : 0.041 0.198 1589 Planarity : 0.003 0.051 1558 Dihedral : 18.876 164.879 2141 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer: Outliers : 4.74 % Allowed : 29.08 % Favored : 66.17 % 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: -0.57 (0.26), residues: 1038 helix: 1.09 (0.22), residues: 572 sheet: -2.39 (0.71), residues: 43 loop : -2.30 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 884 HIS 0.003 0.001 HIS A 114 PHE 0.009 0.001 PHE A 506 TYR 0.020 0.002 TYR A 155 ARG 0.003 0.000 ARG A 432 Details of bonding type rmsd hydrogen bonds : bond 0.04994 ( 402) hydrogen bonds : angle 3.68378 ( 1155) covalent geometry : bond 0.00365 (10454) covalent geometry : angle 0.57387 (14362) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 103 time to evaluate : 1.074 Fit side-chains revert: symmetry clash REVERT: A 48 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7379 (pm20) REVERT: A 117 TYR cc_start: 0.8586 (t80) cc_final: 0.8256 (t80) REVERT: A 131 TYR cc_start: 0.6897 (t80) cc_final: 0.6508 (t80) REVERT: A 180 GLU cc_start: 0.7951 (tp30) cc_final: 0.7638 (tp30) REVERT: A 591 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8455 (tt) REVERT: A 882 MET cc_start: 0.8071 (mmm) cc_final: 0.7820 (mmt) REVERT: A 962 ASP cc_start: 0.7859 (OUTLIER) cc_final: 0.7332 (p0) REVERT: A 1006 TYR cc_start: 0.6574 (m-80) cc_final: 0.6078 (m-80) REVERT: A 1050 ASP cc_start: 0.7890 (OUTLIER) cc_final: 0.7619 (p0) outliers start: 45 outliers final: 32 residues processed: 138 average time/residue: 0.2286 time to fit residues: 44.9544 Evaluate side-chains 129 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 93 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 791 PHE Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 945 VAL Chi-restraints excluded: chain A residue 962 ASP Chi-restraints excluded: chain A residue 970 GLN Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1044 ILE Chi-restraints excluded: chain A residue 1050 ASP Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1070 ASP Chi-restraints excluded: chain A residue 1105 ASN Chi-restraints excluded: chain A residue 1108 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 95 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 60 optimal weight: 10.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 794 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.145871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.120895 restraints weight = 15256.569| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.50 r_work: 0.3575 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 10454 Z= 0.237 Angle : 0.662 6.474 14362 Z= 0.350 Chirality : 0.045 0.207 1589 Planarity : 0.004 0.052 1558 Dihedral : 18.986 164.452 2141 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.21 % Favored : 89.79 % Rotamer: Outliers : 5.16 % Allowed : 29.08 % Favored : 65.75 % 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: -0.96 (0.26), residues: 1038 helix: 0.74 (0.22), residues: 578 sheet: -2.82 (0.67), residues: 41 loop : -2.46 (0.27), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 884 HIS 0.004 0.001 HIS A 787 PHE 0.014 0.002 PHE A 443 TYR 0.022 0.002 TYR A 965 ARG 0.004 0.000 ARG A 432 Details of bonding type rmsd hydrogen bonds : bond 0.05932 ( 402) hydrogen bonds : angle 3.94243 ( 1155) covalent geometry : bond 0.00537 (10454) covalent geometry : angle 0.66222 (14362) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 96 time to evaluate : 1.057 Fit side-chains revert: symmetry clash REVERT: A 102 TYR cc_start: 0.8280 (m-80) cc_final: 0.7873 (m-80) REVERT: A 180 GLU cc_start: 0.7958 (tp30) cc_final: 0.7674 (tp30) REVERT: A 591 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8462 (tt) REVERT: A 882 MET cc_start: 0.8075 (mmm) cc_final: 0.7812 (mmt) REVERT: A 1006 TYR cc_start: 0.6716 (m-80) cc_final: 0.6189 (m-80) REVERT: A 1048 ARG cc_start: 0.7588 (mmm-85) cc_final: 0.7319 (mmm-85) outliers start: 49 outliers final: 38 residues processed: 137 average time/residue: 0.2473 time to fit residues: 48.1806 Evaluate side-chains 128 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 89 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 791 PHE Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 945 VAL Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1044 ILE Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1067 PHE Chi-restraints excluded: chain A residue 1070 ASP Chi-restraints excluded: chain A residue 1105 ASN Chi-restraints excluded: chain A residue 1108 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 48 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 7 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 43 optimal weight: 8.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.153624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.127592 restraints weight = 15437.619| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.64 r_work: 0.3653 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10454 Z= 0.114 Angle : 0.544 6.431 14362 Z= 0.290 Chirality : 0.040 0.210 1589 Planarity : 0.003 0.055 1558 Dihedral : 18.834 170.323 2141 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 3.69 % Allowed : 31.40 % Favored : 64.91 % 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: -0.51 (0.26), residues: 1038 helix: 1.20 (0.22), residues: 578 sheet: -2.70 (0.67), residues: 45 loop : -2.39 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 884 HIS 0.003 0.001 HIS A 114 PHE 0.009 0.001 PHE A 241 TYR 0.018 0.001 TYR A 155 ARG 0.002 0.000 ARG A 707 Details of bonding type rmsd hydrogen bonds : bond 0.04357 ( 402) hydrogen bonds : angle 3.62959 ( 1155) covalent geometry : bond 0.00237 (10454) covalent geometry : angle 0.54369 (14362) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 106 time to evaluate : 1.119 Fit side-chains revert: symmetry clash REVERT: A 36 ARG cc_start: 0.8135 (ptt90) cc_final: 0.7834 (ptm160) REVERT: A 102 TYR cc_start: 0.8187 (m-80) cc_final: 0.7758 (m-80) REVERT: A 131 TYR cc_start: 0.6784 (t80) cc_final: 0.6477 (t80) REVERT: A 856 GLU cc_start: 0.7311 (tp30) cc_final: 0.7105 (tp30) REVERT: A 882 MET cc_start: 0.8054 (mmm) cc_final: 0.7825 (mmt) REVERT: A 1006 TYR cc_start: 0.6572 (m-80) cc_final: 0.6188 (m-80) REVERT: A 1038 LYS cc_start: 0.6106 (tptp) cc_final: 0.5774 (mmmm) outliers start: 35 outliers final: 31 residues processed: 130 average time/residue: 0.2418 time to fit residues: 45.9588 Evaluate side-chains 126 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 95 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 791 PHE Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 1044 ILE Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1067 PHE Chi-restraints excluded: chain A residue 1105 ASN Chi-restraints excluded: chain A residue 1108 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 54 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 73 optimal weight: 0.0040 chunk 38 optimal weight: 0.0870 chunk 50 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 chunk 71 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.151862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.126606 restraints weight = 15050.229| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.53 r_work: 0.3619 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10454 Z= 0.126 Angle : 0.555 6.769 14362 Z= 0.295 Chirality : 0.040 0.214 1589 Planarity : 0.003 0.051 1558 Dihedral : 18.770 166.868 2141 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 3.58 % Allowed : 31.93 % Favored : 64.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.27), residues: 1038 helix: 1.27 (0.22), residues: 578 sheet: -2.61 (0.67), residues: 45 loop : -2.35 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 884 HIS 0.003 0.001 HIS A 114 PHE 0.019 0.001 PHE A 676 TYR 0.019 0.001 TYR A 155 ARG 0.002 0.000 ARG A1095 Details of bonding type rmsd hydrogen bonds : bond 0.04437 ( 402) hydrogen bonds : angle 3.61931 ( 1155) covalent geometry : bond 0.00273 (10454) covalent geometry : angle 0.55522 (14362) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 98 time to evaluate : 1.115 Fit side-chains revert: symmetry clash REVERT: A 36 ARG cc_start: 0.8139 (ptt90) cc_final: 0.7810 (ptm160) REVERT: A 102 TYR cc_start: 0.8177 (m-80) cc_final: 0.7763 (m-80) REVERT: A 131 TYR cc_start: 0.6806 (t80) cc_final: 0.6485 (t80) REVERT: A 882 MET cc_start: 0.8039 (mmm) cc_final: 0.7760 (mmt) REVERT: A 1006 TYR cc_start: 0.6582 (m-80) cc_final: 0.6134 (m-80) outliers start: 34 outliers final: 32 residues processed: 124 average time/residue: 0.2254 time to fit residues: 40.1564 Evaluate side-chains 127 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 95 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 791 PHE Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 945 VAL Chi-restraints excluded: chain A residue 1044 ILE Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1067 PHE Chi-restraints excluded: chain A residue 1105 ASN Chi-restraints excluded: chain A residue 1108 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 29 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 100 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 70 optimal weight: 0.0020 chunk 23 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 chunk 9 optimal weight: 6.9990 chunk 78 optimal weight: 0.3980 chunk 106 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 overall best weight: 0.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 ASN ** 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 = 0.4067 r_free = 0.4067 target = 0.154911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.129058 restraints weight = 15183.093| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.63 r_work: 0.3649 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10454 Z= 0.108 Angle : 0.543 7.359 14362 Z= 0.289 Chirality : 0.040 0.215 1589 Planarity : 0.003 0.052 1558 Dihedral : 18.679 169.461 2141 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 3.27 % Allowed : 32.03 % Favored : 64.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.27), residues: 1038 helix: 1.37 (0.22), residues: 577 sheet: -2.42 (0.68), residues: 45 loop : -2.30 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 884 HIS 0.003 0.001 HIS A 114 PHE 0.015 0.001 PHE A 241 TYR 0.019 0.001 TYR A 155 ARG 0.002 0.000 ARG A 432 Details of bonding type rmsd hydrogen bonds : bond 0.04058 ( 402) hydrogen bonds : angle 3.55327 ( 1155) covalent geometry : bond 0.00221 (10454) covalent geometry : angle 0.54347 (14362) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 1.046 Fit side-chains revert: symmetry clash REVERT: A 36 ARG cc_start: 0.8170 (ptt90) cc_final: 0.7853 (ptm160) REVERT: A 102 TYR cc_start: 0.8166 (m-80) cc_final: 0.7820 (m-80) REVERT: A 131 TYR cc_start: 0.6787 (t80) cc_final: 0.6491 (t80) REVERT: A 396 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7536 (pp20) REVERT: A 884 TRP cc_start: 0.8389 (t60) cc_final: 0.7911 (t-100) REVERT: A 1006 TYR cc_start: 0.6574 (m-80) cc_final: 0.6171 (m-80) REVERT: A 1038 LYS cc_start: 0.6020 (tptp) cc_final: 0.5746 (mmmm) outliers start: 31 outliers final: 29 residues processed: 124 average time/residue: 0.2281 time to fit residues: 40.3175 Evaluate side-chains 126 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 96 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 687 HIS Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 791 PHE Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 1044 ILE Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1067 PHE Chi-restraints excluded: chain A residue 1105 ASN Chi-restraints excluded: chain A residue 1108 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 6.9990 chunk 65 optimal weight: 0.0870 chunk 29 optimal weight: 0.0870 chunk 106 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 25 optimal weight: 0.7980 chunk 2 optimal weight: 6.9990 chunk 39 optimal weight: 0.1980 chunk 93 optimal weight: 7.9990 overall best weight: 1.2338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 ASN ** 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 = 0.4057 r_free = 0.4057 target = 0.154166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.128230 restraints weight = 15336.169| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.63 r_work: 0.3637 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10454 Z= 0.119 Angle : 0.563 8.019 14362 Z= 0.296 Chirality : 0.040 0.222 1589 Planarity : 0.003 0.050 1558 Dihedral : 18.658 167.802 2141 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 3.27 % Allowed : 32.46 % Favored : 64.28 % 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: -0.27 (0.27), residues: 1038 helix: 1.38 (0.22), residues: 577 sheet: -2.40 (0.69), residues: 45 loop : -2.27 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 884 HIS 0.003 0.001 HIS A 114 PHE 0.014 0.001 PHE A 676 TYR 0.019 0.001 TYR A 155 ARG 0.002 0.000 ARG A 432 Details of bonding type rmsd hydrogen bonds : bond 0.04183 ( 402) hydrogen bonds : angle 3.56163 ( 1155) covalent geometry : bond 0.00257 (10454) covalent geometry : angle 0.56314 (14362) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 1.004 Fit side-chains revert: symmetry clash REVERT: A 36 ARG cc_start: 0.8184 (ptt90) cc_final: 0.7874 (ptm160) REVERT: A 131 TYR cc_start: 0.6780 (t80) cc_final: 0.6536 (t80) REVERT: A 396 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7556 (pp20) REVERT: A 884 TRP cc_start: 0.8381 (t60) cc_final: 0.7891 (t-100) REVERT: A 1006 TYR cc_start: 0.6596 (m-80) cc_final: 0.6197 (m-80) REVERT: A 1038 LYS cc_start: 0.6042 (tptp) cc_final: 0.5749 (mmmm) outliers start: 31 outliers final: 30 residues processed: 125 average time/residue: 0.2385 time to fit residues: 42.5714 Evaluate side-chains 130 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 99 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 687 HIS Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 791 PHE Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 945 VAL Chi-restraints excluded: chain A residue 1044 ILE Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1067 PHE Chi-restraints excluded: chain A residue 1105 ASN Chi-restraints excluded: chain A residue 1108 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 58 optimal weight: 0.0870 chunk 45 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 98 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 ASN ** 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 = 0.4033 r_free = 0.4033 target = 0.152072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.126078 restraints weight = 15278.992| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.62 r_work: 0.3607 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10454 Z= 0.147 Angle : 0.594 11.354 14362 Z= 0.311 Chirality : 0.041 0.229 1589 Planarity : 0.003 0.049 1558 Dihedral : 18.730 165.452 2141 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 3.48 % Allowed : 32.35 % Favored : 64.17 % 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: -0.41 (0.27), residues: 1038 helix: 1.28 (0.22), residues: 579 sheet: -2.53 (0.68), residues: 45 loop : -2.35 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 884 HIS 0.002 0.001 HIS A 114 PHE 0.012 0.001 PHE A 676 TYR 0.019 0.001 TYR A 155 ARG 0.002 0.000 ARG A 432 Details of bonding type rmsd hydrogen bonds : bond 0.04651 ( 402) hydrogen bonds : angle 3.65471 ( 1155) covalent geometry : bond 0.00327 (10454) covalent geometry : angle 0.59380 (14362) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4706.23 seconds wall clock time: 82 minutes 47.91 seconds (4967.91 seconds total)