Starting phenix.real_space_refine on Tue May 13 08:00:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wcs_37448/05_2025/8wcs_37448.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wcs_37448/05_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_37448/05_2025/8wcs_37448.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wcs_37448/05_2025/8wcs_37448.map" model { file = "/net/cci-nas-00/data/ceres_data/8wcs_37448/05_2025/8wcs_37448.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wcs_37448/05_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-5687/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: 6.26, per 1000 atoms: 0.62 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: 2.50 Conformation dependent library (CDL) restraints added in 1.3 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: 3.26 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: 3.13 Time building geometry restraints manager: 2.98 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: 3.320 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 27.820 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.980 ------------------------------------------------------------------------------- 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 : 1.084 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: 0.2179 time to fit residues: 33.3361 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 : 1.082 ------------------------------------------------------------------------------- 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 = 52)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.132100 restraints weight = 15198.032| |-----------------------------------------------------------------------------| 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: 0.7531 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= 0.114 Angle : 0.531 6.805 14362 Z= 0.285 Chirality : 0.039 0.212 1589 Planarity : 0.003 0.045 1558 Dihedral : 18.996 170.382 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: 0.40 (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 0.04613 ( 402) hydrogen bonds : angle 3.86097 ( 1155) covalent geometry : bond 0.00229 (10454) covalent geometry : angle 0.53051 (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 : 1.102 Fit side-chains revert: symmetry clash REVERT: A 97 MET cc_start: 0.8021 (ptm) cc_final: 0.7710 (ptm) REVERT: A 313 LYS cc_start: 0.8538 (pttp) cc_final: 0.8140 (pttp) REVERT: A 329 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8095 (mp-120) REVERT: A 330 SER cc_start: 0.8537 (m) cc_final: 0.7987 (t) REVERT: A 591 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8368 (tt) REVERT: A 884 TRP cc_start: 0.8495 (t60) cc_final: 0.7966 (t-100) outliers start: 30 outliers final: 14 residues processed: 128 average time/residue: 0.2059 time to fit residues: 38.2823 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 : 1.055 ------------------------------------------------------------------------------- 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: 4.9990 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 107 optimal weight: 10.9990 chunk 69 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 9 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1081 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.155119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.129147 restraints weight = 15287.996| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.63 r_work: 0.3669 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10454 Z= 0.125 Angle : 0.539 6.575 14362 Z= 0.288 Chirality : 0.039 0.209 1589 Planarity : 0.003 0.048 1558 Dihedral : 18.861 168.805 2141 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 3.16 % Allowed : 29.93 % Favored : 66.91 % 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: -0.72 (0.26), residues: 1038 helix: 0.89 (0.22), residues: 562 sheet: -2.02 (0.74), residues: 40 loop : -2.23 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 884 HIS 0.004 0.001 HIS A 114 PHE 0.009 0.001 PHE A 506 TYR 0.019 0.001 TYR A 155 ARG 0.003 0.000 ARG A 432 Details of bonding type rmsd hydrogen bonds : bond 0.04523 ( 402) hydrogen bonds : angle 3.65907 ( 1155) covalent geometry : bond 0.00265 (10454) covalent geometry : angle 0.53874 (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 126 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 96 time to evaluate : 0.972 Fit side-chains revert: symmetry clash REVERT: A 329 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.7913 (mp10) REVERT: A 591 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8426 (tt) REVERT: A 1008 ASP cc_start: 0.7599 (t0) cc_final: 0.7323 (t0) outliers start: 30 outliers final: 20 residues processed: 118 average time/residue: 0.2176 time to fit residues: 36.9267 Evaluate side-chains 111 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 301 MET Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 329 GLN 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 772 VAL 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 66 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 329 GLN A 970 GLN A1081 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.154922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.129109 restraints weight = 15055.999| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.60 r_work: 0.3670 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10454 Z= 0.118 Angle : 0.525 6.957 14362 Z= 0.280 Chirality : 0.039 0.189 1589 Planarity : 0.003 0.048 1558 Dihedral : 18.760 170.065 2141 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 3.48 % Allowed : 29.08 % 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: -0.44 (0.26), residues: 1038 helix: 1.19 (0.22), residues: 562 sheet: -1.93 (0.74), residues: 42 loop : -2.20 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 884 HIS 0.003 0.001 HIS A 114 PHE 0.008 0.001 PHE A 506 TYR 0.019 0.001 TYR A 155 ARG 0.002 0.000 ARG A 432 Details of bonding type rmsd hydrogen bonds : bond 0.04331 ( 402) hydrogen bonds : angle 3.53208 ( 1155) covalent geometry : bond 0.00250 (10454) covalent geometry : angle 0.52509 (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 132 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 99 time to evaluate : 1.011 Fit side-chains revert: symmetry clash REVERT: A 591 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8448 (tt) REVERT: A 884 TRP cc_start: 0.8449 (t60) cc_final: 0.7937 (t-100) REVERT: A 1006 TYR cc_start: 0.6513 (m-80) cc_final: 0.6177 (m-80) outliers start: 33 outliers final: 23 residues processed: 123 average time/residue: 0.2131 time to fit residues: 38.0320 Evaluate side-chains 116 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.989 ------------------------------------------------------------------------------- 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 230 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 316 THR 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 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 25 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 38 optimal weight: 0.2980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 970 GLN A1081 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.153546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.127710 restraints weight = 15250.881| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.61 r_work: 0.3654 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10454 Z= 0.137 Angle : 0.545 7.728 14362 Z= 0.289 Chirality : 0.040 0.195 1589 Planarity : 0.003 0.047 1558 Dihedral : 18.774 166.817 2141 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 4.74 % Allowed : 27.92 % Favored : 67.33 % 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: 1.21 (0.22), residues: 571 sheet: -2.00 (0.74), residues: 42 loop : -2.25 (0.28), residues: 425 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 0.009 0.001 PHE A 506 TYR 0.019 0.001 TYR A 155 ARG 0.002 0.000 ARG A 432 Details of bonding type rmsd hydrogen bonds : bond 0.04643 ( 402) hydrogen bonds : angle 3.57122 ( 1155) covalent geometry : bond 0.00297 (10454) covalent geometry : angle 0.54525 (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 152 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 107 time to evaluate : 0.971 Fit side-chains REVERT: A 88 TRP cc_start: 0.2598 (OUTLIER) cc_final: 0.2285 (t60) REVERT: A 400 LYS cc_start: 0.7576 (OUTLIER) cc_final: 0.7014 (mmtm) REVERT: A 591 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8430 (tt) REVERT: A 884 TRP cc_start: 0.8449 (t60) cc_final: 0.7900 (t-100) REVERT: A 962 ASP cc_start: 0.7852 (OUTLIER) cc_final: 0.7297 (p0) REVERT: A 1006 TYR cc_start: 0.6525 (m-80) cc_final: 0.6032 (m-80) REVERT: A 1050 ASP cc_start: 0.7711 (OUTLIER) cc_final: 0.7464 (p0) outliers start: 45 outliers final: 29 residues processed: 142 average time/residue: 0.2208 time to fit residues: 44.2215 Evaluate side-chains 126 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 92 time to evaluate : 0.953 ------------------------------------------------------------------------------- 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 276 ILE 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 400 LYS 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 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 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 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 1053 LEU Chi-restraints excluded: chain A residue 1070 ASP 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: 8.9990 chunk 53 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 61 optimal weight: 0.7980 chunk 87 optimal weight: 0.0370 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 66 optimal weight: 0.0170 chunk 94 optimal weight: 0.8980 chunk 60 optimal weight: 7.9990 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.155940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.130088 restraints weight = 15016.262| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 2.59 r_work: 0.3686 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10454 Z= 0.105 Angle : 0.514 6.424 14362 Z= 0.274 Chirality : 0.038 0.197 1589 Planarity : 0.003 0.048 1558 Dihedral : 18.670 171.441 2141 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 3.16 % Allowed : 29.50 % Favored : 67.33 % 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: -0.17 (0.27), residues: 1038 helix: 1.46 (0.23), residues: 567 sheet: -1.89 (0.75), residues: 42 loop : -2.20 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 884 HIS 0.004 0.001 HIS A 972 PHE 0.010 0.001 PHE A 241 TYR 0.018 0.001 TYR A 155 ARG 0.002 0.000 ARG A 432 Details of bonding type rmsd hydrogen bonds : bond 0.04000 ( 402) hydrogen bonds : angle 3.47892 ( 1155) covalent geometry : bond 0.00214 (10454) covalent geometry : angle 0.51416 (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 134 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 0.998 Fit side-chains revert: symmetry clash REVERT: A 36 ARG cc_start: 0.8106 (ptt90) cc_final: 0.7820 (ptm160) REVERT: A 131 TYR cc_start: 0.6723 (t80) cc_final: 0.6446 (t80) REVERT: A 591 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8443 (tt) REVERT: A 884 TRP cc_start: 0.8447 (t60) cc_final: 0.7983 (t-100) REVERT: A 962 ASP cc_start: 0.7865 (OUTLIER) cc_final: 0.7336 (p0) REVERT: A 1006 TYR cc_start: 0.6508 (m-80) cc_final: 0.6064 (m-80) REVERT: A 1050 ASP cc_start: 0.7715 (OUTLIER) cc_final: 0.7464 (p0) outliers start: 30 outliers final: 22 residues processed: 126 average time/residue: 0.2399 time to fit residues: 43.5486 Evaluate side-chains 120 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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 301 MET Chi-restraints excluded: chain A residue 316 THR 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 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 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 962 ASP 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 1053 LEU 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: 0.9980 chunk 94 optimal weight: 0.9990 chunk 31 optimal weight: 0.3980 chunk 58 optimal weight: 0.0020 chunk 2 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 74 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.157969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.132110 restraints weight = 15345.308| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.65 r_work: 0.3706 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.1865 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= 0.097 Angle : 0.504 6.404 14362 Z= 0.267 Chirality : 0.038 0.200 1589 Planarity : 0.003 0.045 1558 Dihedral : 18.558 171.676 2141 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 3.69 % Allowed : 29.40 % Favored : 66.91 % 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: -0.05 (0.27), residues: 1038 helix: 1.57 (0.23), residues: 570 sheet: -1.71 (0.77), residues: 42 loop : -2.20 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 884 HIS 0.002 0.000 HIS A 795 PHE 0.017 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 0.03733 ( 402) hydrogen bonds : angle 3.40058 ( 1155) covalent geometry : bond 0.00197 (10454) covalent geometry : angle 0.50431 (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 146 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 111 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: A 131 TYR cc_start: 0.6755 (t80) cc_final: 0.6547 (t80) REVERT: A 396 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7486 (pp20) REVERT: A 591 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8429 (tt) REVERT: A 884 TRP cc_start: 0.8393 (t60) cc_final: 0.7984 (t-100) REVERT: A 962 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7316 (p0) REVERT: A 1006 TYR cc_start: 0.6484 (m-80) cc_final: 0.6043 (m-80) REVERT: A 1050 ASP cc_start: 0.7690 (OUTLIER) cc_final: 0.7420 (p0) outliers start: 35 outliers final: 25 residues processed: 141 average time/residue: 0.2137 time to fit residues: 43.0816 Evaluate side-chains 130 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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 230 THR 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 396 GLU Chi-restraints excluded: chain A residue 495 LEU 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 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 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 962 ASP Chi-restraints excluded: chain A residue 986 ILE Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1050 ASP Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1067 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 54 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 38 optimal weight: 0.0870 chunk 50 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 61 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- 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 = 0.4088 r_free = 0.4088 target = 0.157184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.131284 restraints weight = 15165.632| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 2.63 r_work: 0.3693 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1919 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= 0.104 Angle : 0.516 8.816 14362 Z= 0.270 Chirality : 0.038 0.208 1589 Planarity : 0.003 0.044 1558 Dihedral : 18.537 170.767 2141 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 3.90 % Allowed : 29.72 % 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: -0.06 (0.27), residues: 1038 helix: 1.60 (0.23), residues: 570 sheet: -1.88 (0.74), residues: 44 loop : -2.24 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 884 HIS 0.002 0.000 HIS A 114 PHE 0.010 0.001 PHE A 676 TYR 0.018 0.001 TYR A 155 ARG 0.002 0.000 ARG A 432 Details of bonding type rmsd hydrogen bonds : bond 0.03884 ( 402) hydrogen bonds : angle 3.40653 ( 1155) covalent geometry : bond 0.00216 (10454) covalent geometry : angle 0.51608 (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 141 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 104 time to evaluate : 1.025 Fit side-chains REVERT: A 88 TRP cc_start: 0.2548 (OUTLIER) cc_final: 0.2228 (t60) REVERT: A 131 TYR cc_start: 0.6806 (t80) cc_final: 0.6585 (t80) REVERT: A 400 LYS cc_start: 0.7569 (OUTLIER) cc_final: 0.7089 (mmtm) REVERT: A 591 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8450 (tt) REVERT: A 884 TRP cc_start: 0.8387 (t60) cc_final: 0.7986 (t-100) REVERT: A 962 ASP cc_start: 0.7883 (OUTLIER) cc_final: 0.7337 (p0) REVERT: A 1006 TYR cc_start: 0.6464 (m-80) cc_final: 0.6082 (m-80) REVERT: A 1050 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.7354 (p0) outliers start: 37 outliers final: 28 residues processed: 133 average time/residue: 0.2149 time to fit residues: 41.3287 Evaluate side-chains 132 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 99 time to evaluate : 0.992 ------------------------------------------------------------------------------- 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 230 THR 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 495 LEU 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 687 HIS Chi-restraints excluded: chain A residue 696 MET 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 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 962 ASP Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 986 ILE Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1050 ASP Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1067 PHE Chi-restraints excluded: chain A residue 1102 CYS 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: 0.0030 chunk 6 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 78 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 overall best weight: 2.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.149743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.123444 restraints weight = 15420.858| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.67 r_work: 0.3601 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10454 Z= 0.196 Angle : 0.631 7.712 14362 Z= 0.329 Chirality : 0.043 0.221 1589 Planarity : 0.004 0.043 1558 Dihedral : 18.879 163.868 2141 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 3.69 % Allowed : 30.14 % 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: -0.56 (0.26), residues: 1038 helix: 1.17 (0.22), residues: 575 sheet: -2.48 (0.70), residues: 45 loop : -2.42 (0.27), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 884 HIS 0.003 0.001 HIS A 114 PHE 0.014 0.002 PHE A 443 TYR 0.021 0.002 TYR A 965 ARG 0.007 0.000 ARG A 304 Details of bonding type rmsd hydrogen bonds : bond 0.05474 ( 402) hydrogen bonds : angle 3.74900 ( 1155) covalent geometry : bond 0.00442 (10454) covalent geometry : angle 0.63133 (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 136 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 101 time to evaluate : 1.125 Fit side-chains REVERT: A 88 TRP cc_start: 0.2512 (OUTLIER) cc_final: 0.2234 (t60) REVERT: A 102 TYR cc_start: 0.8239 (m-80) cc_final: 0.7877 (m-80) REVERT: A 131 TYR cc_start: 0.6827 (t80) cc_final: 0.6464 (t80) REVERT: A 400 LYS cc_start: 0.7570 (OUTLIER) cc_final: 0.7083 (mmtm) REVERT: A 591 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8447 (tt) REVERT: A 1006 TYR cc_start: 0.6682 (m-80) cc_final: 0.6174 (m-80) REVERT: A 1050 ASP cc_start: 0.7782 (OUTLIER) cc_final: 0.7540 (p0) outliers start: 35 outliers final: 24 residues processed: 130 average time/residue: 0.2326 time to fit residues: 43.5706 Evaluate side-chains 125 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 0.955 ------------------------------------------------------------------------------- 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 306 SER 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 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 687 HIS Chi-restraints excluded: chain A residue 696 MET 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 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 1050 ASP Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1067 PHE 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: 3.9990 chunk 29 optimal weight: 0.0170 chunk 106 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 overall best weight: 1.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 767 ASN A 794 ASN A 970 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.153269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.127084 restraints weight = 15292.600| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.62 r_work: 0.3624 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2098 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= 0.126 Angle : 0.581 11.773 14362 Z= 0.301 Chirality : 0.040 0.222 1589 Planarity : 0.003 0.048 1558 Dihedral : 18.756 168.177 2141 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 3.06 % Allowed : 31.30 % Favored : 65.65 % 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: -0.37 (0.27), residues: 1038 helix: 1.26 (0.22), residues: 578 sheet: -2.45 (0.70), residues: 45 loop : -2.26 (0.28), residues: 415 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 0.009 0.001 PHE A 241 TYR 0.017 0.001 TYR A 155 ARG 0.003 0.000 ARG A 304 Details of bonding type rmsd hydrogen bonds : bond 0.04554 ( 402) hydrogen bonds : angle 3.67434 ( 1155) covalent geometry : bond 0.00273 (10454) covalent geometry : angle 0.58081 (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 129 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 1.079 Fit side-chains REVERT: A 88 TRP cc_start: 0.2421 (OUTLIER) cc_final: 0.2155 (t60) REVERT: A 102 TYR cc_start: 0.8196 (m-80) cc_final: 0.7821 (m-80) REVERT: A 131 TYR cc_start: 0.6740 (t80) cc_final: 0.6446 (t80) REVERT: A 400 LYS cc_start: 0.7574 (OUTLIER) cc_final: 0.7093 (mmtm) REVERT: A 591 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8383 (tt) REVERT: A 884 TRP cc_start: 0.8416 (t60) cc_final: 0.7901 (t-100) REVERT: A 1006 TYR cc_start: 0.6653 (m-80) cc_final: 0.6243 (m-80) REVERT: A 1050 ASP cc_start: 0.7738 (OUTLIER) cc_final: 0.7514 (p0) outliers start: 29 outliers final: 23 residues processed: 124 average time/residue: 0.2186 time to fit residues: 38.6627 Evaluate side-chains 124 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.979 ------------------------------------------------------------------------------- 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 306 SER 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 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 736 LEU Chi-restraints excluded: chain A residue 738 SER 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 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 1050 ASP Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1067 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 58 optimal weight: 0.0570 chunk 45 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 36 optimal weight: 0.0000 chunk 43 optimal weight: 8.9990 chunk 97 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.5704 ------------------------------------------------------------------------------- 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 = 0.4094 r_free = 0.4094 target = 0.157495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.131649 restraints weight = 15063.964| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 2.60 r_work: 0.3703 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10454 Z= 0.103 Angle : 0.548 10.972 14362 Z= 0.283 Chirality : 0.039 0.228 1589 Planarity : 0.003 0.049 1558 Dihedral : 18.567 172.498 2141 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 2.21 % Allowed : 31.93 % Favored : 65.86 % 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: -0.16 (0.27), residues: 1038 helix: 1.51 (0.23), residues: 571 sheet: -2.04 (0.72), residues: 44 loop : -2.27 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 884 HIS 0.003 0.000 HIS A 114 PHE 0.010 0.001 PHE A 241 TYR 0.018 0.001 TYR A 155 ARG 0.002 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.03782 ( 402) hydrogen bonds : angle 3.54491 ( 1155) covalent geometry : bond 0.00213 (10454) covalent geometry : angle 0.54776 (14362) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4276.25 seconds wall clock time: 75 minutes 38.09 seconds (4538.09 seconds total)