Starting phenix.real_space_refine on Sun Apr 27 14:34:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q75_18204/04_2025/8q75_18204.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q75_18204/04_2025/8q75_18204.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q75_18204/04_2025/8q75_18204.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q75_18204/04_2025/8q75_18204.map" model { file = "/net/cci-nas-00/data/ceres_data/8q75_18204/04_2025/8q75_18204.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q75_18204/04_2025/8q75_18204.cif" } resolution = 3.2 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= -0.002 sd= 0.047 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: 7 Type Number sf(0) Gaussians Al 1 5.89 5 Mg 1 5.21 5 S 34 5.16 5 C 3760 2.51 5 N 975 2.21 5 O 1095 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 5870 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 774, 5864 Classifications: {'peptide': 774} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 738} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' MG': 1, 'ALF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.02, per 1000 atoms: 0.68 Number of scatterers: 5870 At special positions: 0 Unit cell: (78.208, 84.864, 135.616, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 34 16.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1095 8.00 N 975 7.00 C 3760 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: 1.50 Conformation dependent library (CDL) restraints added in 853.6 milliseconds 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1430 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 6 sheets defined 51.7% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 197 through 210 removed outlier: 3.692A pdb=" N ILE A 201 " --> pdb=" O SER A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 246 removed outlier: 4.465A pdb=" N LEU A 240 " --> pdb=" O GLY A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 293 removed outlier: 3.547A pdb=" N PHE A 286 " --> pdb=" O TRP A 282 " (cutoff:3.500A) Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 296 through 300 Processing helix chain 'A' and resid 302 through 309 Processing helix chain 'A' and resid 316 through 332 Proline residue: A 328 - end of helix Processing helix chain 'A' and resid 334 through 345 Processing helix chain 'A' and resid 351 through 377 removed outlier: 3.708A pdb=" N LEU A 355 " --> pdb=" O ASN A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 406 removed outlier: 3.634A pdb=" N SER A 389 " --> pdb=" O PHE A 385 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A 393 " --> pdb=" O SER A 389 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER A 394 " --> pdb=" O ALA A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 421 removed outlier: 3.905A pdb=" N ALA A 421 " --> pdb=" O LEU A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 515 Processing helix chain 'A' and resid 516 through 531 Processing helix chain 'A' and resid 537 through 562 removed outlier: 3.680A pdb=" N PHE A 545 " --> pdb=" O ARG A 541 " (cutoff:3.500A) Proline residue: A 548 - end of helix removed outlier: 3.798A pdb=" N LEU A 556 " --> pdb=" O VAL A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 567 Processing helix chain 'A' and resid 571 through 575 Processing helix chain 'A' and resid 580 through 597 removed outlier: 3.640A pdb=" N LEU A 593 " --> pdb=" O GLY A 589 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N CYS A 597 " --> pdb=" O LEU A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 609 Processing helix chain 'A' and resid 611 through 620 removed outlier: 6.266A pdb=" N ALA A 617 " --> pdb=" O THR A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 633 removed outlier: 4.030A pdb=" N HIS A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 675 Processing helix chain 'A' and resid 680 through 697 Processing helix chain 'A' and resid 721 through 725 Processing helix chain 'A' and resid 731 through 738 removed outlier: 3.722A pdb=" N PHE A 738 " --> pdb=" O LEU A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 793 Processing helix chain 'A' and resid 804 through 816 Processing helix chain 'A' and resid 825 through 839 Processing helix chain 'A' and resid 851 through 859 removed outlier: 4.615A pdb=" N ALA A 855 " --> pdb=" O ASN A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 876 Processing helix chain 'A' and resid 885 through 897 removed outlier: 3.937A pdb=" N ILE A 889 " --> pdb=" O LEU A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 915 removed outlier: 4.551A pdb=" N TYR A 912 " --> pdb=" O TRP A 908 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ASN A 913 " --> pdb=" O ALA A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 922 Processing helix chain 'A' and resid 923 through 929 removed outlier: 4.444A pdb=" N PHE A 927 " --> pdb=" O VAL A 923 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 948 removed outlier: 3.996A pdb=" N ALA A 943 " --> pdb=" O ALA A 939 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 216 through 218 Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 453 removed outlier: 3.706A pdb=" N VAL A 507 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE A 506 " --> pdb=" O ILE A 468 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 472 through 474 Processing sheet with id=AA4, first strand: chain 'A' and resid 621 through 623 removed outlier: 6.856A pdb=" N ALA A 864 " --> pdb=" O LEU A 880 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N LEU A 863 " --> pdb=" O VAL A 843 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N MET A 845 " --> pdb=" O LEU A 863 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ILE A 865 " --> pdb=" O MET A 845 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N GLY A 847 " --> pdb=" O ILE A 865 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR A 842 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA A 637 " --> pdb=" O THR A 842 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LYS A 636 " --> pdb=" O SER A 796 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ILE A 798 " --> pdb=" O LYS A 636 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE A 638 " --> pdb=" O ILE A 798 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 652 through 653 Processing sheet with id=AA6, first strand: chain 'A' and resid 717 through 720 274 hydrogen bonds defined for protein. 774 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.66 Time building geometry restraints manager: 1.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 999 1.32 - 1.44: 1434 1.44 - 1.56: 3489 1.56 - 1.69: 0 1.69 - 1.81: 58 Bond restraints: 5980 Sorted by residual: bond pdb=" CA LYS A 642 " pdb=" C LYS A 642 " ideal model delta sigma weight residual 1.526 1.450 0.076 9.20e-03 1.18e+04 6.81e+01 bond pdb=" CA ASP A 641 " pdb=" C ASP A 641 " ideal model delta sigma weight residual 1.524 1.458 0.066 1.31e-02 5.83e+03 2.51e+01 bond pdb=" F1 ALF A1001 " pdb="AL ALF A1001 " ideal model delta sigma weight residual 1.684 1.783 -0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" F3 ALF A1001 " pdb="AL ALF A1001 " ideal model delta sigma weight residual 1.685 1.783 -0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" F2 ALF A1001 " pdb="AL ALF A1001 " ideal model delta sigma weight residual 1.685 1.783 -0.098 2.00e-02 2.50e+03 2.39e+01 ... (remaining 5975 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.19: 8117 14.19 - 28.38: 4 28.38 - 42.56: 0 42.56 - 56.75: 0 56.75 - 70.94: 2 Bond angle restraints: 8123 Sorted by residual: angle pdb=" F1 ALF A1001 " pdb="AL ALF A1001 " pdb=" F2 ALF A1001 " ideal model delta sigma weight residual 108.68 179.62 -70.94 3.00e+00 1.11e-01 5.59e+02 angle pdb=" F3 ALF A1001 " pdb="AL ALF A1001 " pdb=" F4 ALF A1001 " ideal model delta sigma weight residual 109.63 179.75 -70.12 3.00e+00 1.11e-01 5.46e+02 angle pdb=" N ILE A 902 " pdb=" CA ILE A 902 " pdb=" C ILE A 902 " ideal model delta sigma weight residual 113.71 105.97 7.74 9.50e-01 1.11e+00 6.64e+01 angle pdb=" N THR A 753 " pdb=" CA THR A 753 " pdb=" C THR A 753 " ideal model delta sigma weight residual 114.62 106.58 8.04 1.14e+00 7.69e-01 4.98e+01 angle pdb=" F2 ALF A1001 " pdb="AL ALF A1001 " pdb=" F4 ALF A1001 " ideal model delta sigma weight residual 110.21 89.95 20.26 3.00e+00 1.11e-01 4.56e+01 ... (remaining 8118 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 3234 17.92 - 35.84: 301 35.84 - 53.76: 43 53.76 - 71.69: 16 71.69 - 89.61: 7 Dihedral angle restraints: 3601 sinusoidal: 1380 harmonic: 2221 Sorted by residual: dihedral pdb=" CA PHE A 293 " pdb=" C PHE A 293 " pdb=" N SER A 294 " pdb=" CA SER A 294 " ideal model delta harmonic sigma weight residual 180.00 -140.20 -39.80 0 5.00e+00 4.00e-02 6.34e+01 dihedral pdb=" CA ARG A 758 " pdb=" C ARG A 758 " pdb=" N THR A 759 " pdb=" CA THR A 759 " ideal model delta harmonic sigma weight residual 180.00 145.31 34.69 0 5.00e+00 4.00e-02 4.81e+01 dihedral pdb=" CA GLU A 752 " pdb=" C GLU A 752 " pdb=" N THR A 753 " pdb=" CA THR A 753 " ideal model delta harmonic sigma weight residual 180.00 148.27 31.73 0 5.00e+00 4.00e-02 4.03e+01 ... (remaining 3598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 747 0.056 - 0.113: 180 0.113 - 0.169: 27 0.169 - 0.225: 8 0.225 - 0.282: 1 Chirality restraints: 963 Sorted by residual: chirality pdb=" CA ARG A 758 " pdb=" N ARG A 758 " pdb=" C ARG A 758 " pdb=" CB ARG A 758 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CA VAL A 311 " pdb=" N VAL A 311 " pdb=" C VAL A 311 " pdb=" CB VAL A 311 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.96e-01 chirality pdb=" CG LEU A 954 " pdb=" CB LEU A 954 " pdb=" CD1 LEU A 954 " pdb=" CD2 LEU A 954 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.72e-01 ... (remaining 960 not shown) Planarity restraints: 1028 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 265 " 0.248 9.50e-02 1.11e+02 1.12e-01 9.01e+00 pdb=" NE ARG A 265 " -0.022 2.00e-02 2.50e+03 pdb=" CZ ARG A 265 " 0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG A 265 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG A 265 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 288 " -0.045 5.00e-02 4.00e+02 6.78e-02 7.37e+00 pdb=" N PRO A 289 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 289 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 289 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 680 " 0.043 5.00e-02 4.00e+02 6.47e-02 6.70e+00 pdb=" N PRO A 681 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 681 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 681 " 0.036 5.00e-02 4.00e+02 ... (remaining 1025 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 50 2.44 - 3.06: 4287 3.06 - 3.67: 9621 3.67 - 4.29: 13723 4.29 - 4.90: 21542 Nonbonded interactions: 49223 Sorted by model distance: nonbonded pdb=" OD2 ASP A 641 " pdb=" F2 ALF A1001 " model vdw 1.828 2.990 nonbonded pdb=" F2 ALF A1001 " pdb="MG MG A1002 " model vdw 1.895 2.120 nonbonded pdb=" OD2 ASP A 641 " pdb="MG MG A1002 " model vdw 1.913 2.170 nonbonded pdb=" OD2 ASP A 848 " pdb="MG MG A1002 " model vdw 2.029 2.170 nonbonded pdb=" O THR A 643 " pdb="MG MG A1002 " model vdw 2.030 2.170 ... (remaining 49218 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.470 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.600 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 5980 Z= 0.323 Angle : 1.557 70.940 8123 Z= 0.722 Chirality : 0.051 0.282 963 Planarity : 0.008 0.112 1028 Dihedral : 14.765 89.606 2171 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 20.97 Ramachandran Plot: Outliers : 1.55 % Allowed : 12.31 % Favored : 86.14 % Rotamer: Outliers : 0.62 % Allowed : 0.62 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % 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: -2.02 (0.31), residues: 772 helix: 0.19 (0.28), residues: 383 sheet: -2.68 (0.65), residues: 53 loop : -3.02 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 935 HIS 0.004 0.001 HIS A 633 PHE 0.019 0.001 PHE A 710 TYR 0.009 0.001 TYR A 689 ARG 0.021 0.002 ARG A 265 Details of bonding type rmsd hydrogen bonds : bond 0.20669 ( 274) hydrogen bonds : angle 7.54221 ( 774) covalent geometry : bond 0.00563 ( 5980) covalent geometry : angle 1.55665 ( 8123) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 123 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 HIS cc_start: 0.9504 (m-70) cc_final: 0.9288 (m-70) REVERT: A 299 MET cc_start: 0.6834 (tmm) cc_final: 0.6553 (tmm) REVERT: A 300 ILE cc_start: 0.8149 (tp) cc_final: 0.7888 (mm) REVERT: A 403 GLU cc_start: 0.9030 (tp30) cc_final: 0.8812 (tp30) REVERT: A 446 LEU cc_start: 0.9507 (mt) cc_final: 0.9241 (mm) REVERT: A 613 THR cc_start: 0.9447 (m) cc_final: 0.9087 (p) REVERT: A 630 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8178 (tm-30) REVERT: A 642 LYS cc_start: 0.9480 (OUTLIER) cc_final: 0.8974 (ttpp) REVERT: A 659 PHE cc_start: 0.8873 (p90) cc_final: 0.8284 (p90) REVERT: A 705 MET cc_start: 0.7363 (ppp) cc_final: 0.6989 (ppp) REVERT: A 766 ASP cc_start: 0.8177 (t70) cc_final: 0.7856 (t0) REVERT: A 860 ASP cc_start: 0.9382 (m-30) cc_final: 0.9060 (m-30) outliers start: 4 outliers final: 0 residues processed: 126 average time/residue: 0.1933 time to fit residues: 31.6424 Evaluate side-chains 82 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 642 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 1.9990 chunk 58 optimal weight: 20.0000 chunk 32 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 36 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.118596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.078807 restraints weight = 15586.588| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 4.32 r_work: 0.3095 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5980 Z= 0.200 Angle : 0.851 11.979 8123 Z= 0.429 Chirality : 0.049 0.172 963 Planarity : 0.007 0.070 1028 Dihedral : 6.516 43.643 820 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 1.55 % Allowed : 11.66 % Favored : 86.79 % Rotamer: Outliers : 2.19 % Allowed : 11.88 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.54 % 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: -2.06 (0.30), residues: 772 helix: 0.02 (0.26), residues: 384 sheet: -2.12 (0.67), residues: 53 loop : -2.99 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 935 HIS 0.009 0.002 HIS A 749 PHE 0.017 0.002 PHE A 710 TYR 0.011 0.001 TYR A 906 ARG 0.010 0.001 ARG A 931 Details of bonding type rmsd hydrogen bonds : bond 0.04789 ( 274) hydrogen bonds : angle 5.71938 ( 774) covalent geometry : bond 0.00444 ( 5980) covalent geometry : angle 0.85126 ( 8123) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 MET cc_start: 0.6824 (tmm) cc_final: 0.6500 (tmm) REVERT: A 300 ILE cc_start: 0.8072 (tp) cc_final: 0.7732 (mm) REVERT: A 319 MET cc_start: 0.9184 (mtt) cc_final: 0.8888 (mtp) REVERT: A 446 LEU cc_start: 0.9445 (mt) cc_final: 0.9214 (mm) REVERT: A 558 TRP cc_start: 0.8528 (t60) cc_final: 0.8306 (t60) REVERT: A 610 MET cc_start: 0.7785 (mmt) cc_final: 0.7539 (mmp) REVERT: A 613 THR cc_start: 0.9404 (m) cc_final: 0.9147 (p) REVERT: A 630 GLU cc_start: 0.8852 (tm-30) cc_final: 0.8258 (tm-30) REVERT: A 659 PHE cc_start: 0.8782 (p90) cc_final: 0.8060 (p90) REVERT: A 705 MET cc_start: 0.7251 (ppp) cc_final: 0.6874 (ppp) REVERT: A 860 ASP cc_start: 0.9409 (m-30) cc_final: 0.9135 (m-30) REVERT: A 903 ARG cc_start: 0.6099 (tpt170) cc_final: 0.5537 (mmm160) outliers start: 14 outliers final: 9 residues processed: 99 average time/residue: 0.2015 time to fit residues: 26.8061 Evaluate side-chains 85 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 335 TRP Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 523 GLN Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 935 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 33 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 913 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 = 0.3958 r_free = 0.3958 target = 0.117340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.077557 restraints weight = 15869.808| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 4.38 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 5980 Z= 0.206 Angle : 0.804 10.989 8123 Z= 0.405 Chirality : 0.047 0.158 963 Planarity : 0.006 0.065 1028 Dihedral : 6.342 47.044 816 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 1.30 % Allowed : 12.05 % Favored : 86.66 % Rotamer: Outliers : 3.59 % Allowed : 15.16 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.54 % 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: -1.88 (0.30), residues: 772 helix: 0.12 (0.26), residues: 386 sheet: -1.72 (0.71), residues: 47 loop : -2.89 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 935 HIS 0.004 0.001 HIS A 189 PHE 0.014 0.001 PHE A 710 TYR 0.015 0.002 TYR A 906 ARG 0.004 0.001 ARG A 694 Details of bonding type rmsd hydrogen bonds : bond 0.04336 ( 274) hydrogen bonds : angle 5.44115 ( 774) covalent geometry : bond 0.00459 ( 5980) covalent geometry : angle 0.80443 ( 8123) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 266 GLU cc_start: 0.9003 (tm-30) cc_final: 0.8700 (tm-30) REVERT: A 299 MET cc_start: 0.6752 (tmm) cc_final: 0.6422 (tmm) REVERT: A 300 ILE cc_start: 0.8035 (tp) cc_final: 0.7616 (mm) REVERT: A 319 MET cc_start: 0.9060 (mtt) cc_final: 0.8725 (mtp) REVERT: A 403 GLU cc_start: 0.9017 (tp30) cc_final: 0.8624 (tp30) REVERT: A 446 LEU cc_start: 0.9465 (mt) cc_final: 0.9202 (mm) REVERT: A 558 TRP cc_start: 0.8416 (t60) cc_final: 0.7871 (t60) REVERT: A 610 MET cc_start: 0.7799 (mmt) cc_final: 0.7486 (mmp) REVERT: A 613 THR cc_start: 0.9402 (m) cc_final: 0.9073 (p) REVERT: A 630 GLU cc_start: 0.8673 (tm-30) cc_final: 0.8032 (tm-30) REVERT: A 650 LYS cc_start: 0.8657 (tptt) cc_final: 0.8447 (tptt) REVERT: A 705 MET cc_start: 0.7105 (ppp) cc_final: 0.6709 (ppp) REVERT: A 860 ASP cc_start: 0.9262 (m-30) cc_final: 0.8971 (m-30) REVERT: A 903 ARG cc_start: 0.5871 (tpt170) cc_final: 0.5288 (mmm160) outliers start: 23 outliers final: 15 residues processed: 94 average time/residue: 0.1625 time to fit residues: 20.9833 Evaluate side-chains 91 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 335 TRP Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 523 GLN Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain A residue 914 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 72 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 3 optimal weight: 50.0000 chunk 25 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 6 optimal weight: 30.0000 chunk 13 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 52 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 913 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 = 0.3920 r_free = 0.3920 target = 0.114793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.074315 restraints weight = 16455.946| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 4.40 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 5980 Z= 0.304 Angle : 0.846 10.171 8123 Z= 0.429 Chirality : 0.049 0.162 963 Planarity : 0.005 0.051 1028 Dihedral : 6.456 42.860 816 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 1.04 % Allowed : 11.79 % Favored : 87.18 % Rotamer: Outliers : 5.00 % Allowed : 16.09 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.54 % 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: -2.02 (0.29), residues: 772 helix: 0.01 (0.26), residues: 380 sheet: -1.72 (0.70), residues: 48 loop : -2.93 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 935 HIS 0.003 0.001 HIS A 189 PHE 0.013 0.002 PHE A 555 TYR 0.018 0.002 TYR A 906 ARG 0.005 0.001 ARG A 931 Details of bonding type rmsd hydrogen bonds : bond 0.04400 ( 274) hydrogen bonds : angle 5.45459 ( 774) covalent geometry : bond 0.00671 ( 5980) covalent geometry : angle 0.84625 ( 8123) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 72 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 MET cc_start: 0.6826 (tmm) cc_final: 0.6390 (tmm) REVERT: A 300 ILE cc_start: 0.8109 (tp) cc_final: 0.7792 (tp) REVERT: A 319 MET cc_start: 0.9035 (mtt) cc_final: 0.8739 (mtp) REVERT: A 391 MET cc_start: 0.9062 (tpp) cc_final: 0.8828 (tpp) REVERT: A 397 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9188 (mt) REVERT: A 403 GLU cc_start: 0.9008 (tp30) cc_final: 0.8535 (tp30) REVERT: A 446 LEU cc_start: 0.9483 (mt) cc_final: 0.9238 (mm) REVERT: A 630 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8089 (tm-30) REVERT: A 650 LYS cc_start: 0.8763 (tptt) cc_final: 0.8546 (tptt) REVERT: A 705 MET cc_start: 0.7285 (ppp) cc_final: 0.6857 (ppp) REVERT: A 780 LYS cc_start: 0.8338 (pttp) cc_final: 0.8068 (ptpp) REVERT: A 860 ASP cc_start: 0.9226 (m-30) cc_final: 0.8874 (m-30) REVERT: A 903 ARG cc_start: 0.5878 (tpt170) cc_final: 0.5233 (mmm160) outliers start: 32 outliers final: 21 residues processed: 92 average time/residue: 0.1715 time to fit residues: 21.1684 Evaluate side-chains 92 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 335 TRP Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 523 GLN Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 902 ILE Chi-restraints excluded: chain A residue 906 TYR Chi-restraints excluded: chain A residue 914 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 28 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 0 optimal weight: 40.0000 chunk 37 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 5 optimal weight: 8.9990 chunk 3 optimal weight: 50.0000 chunk 10 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 913 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.117660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.077630 restraints weight = 15808.114| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 4.37 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5980 Z= 0.171 Angle : 0.779 10.611 8123 Z= 0.385 Chirality : 0.046 0.158 963 Planarity : 0.005 0.059 1028 Dihedral : 6.231 45.436 816 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 1.30 % Allowed : 10.36 % Favored : 88.34 % Rotamer: Outliers : 4.84 % Allowed : 16.88 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % 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: -1.70 (0.30), residues: 772 helix: 0.13 (0.26), residues: 394 sheet: -1.59 (0.71), residues: 47 loop : -2.67 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 335 HIS 0.003 0.000 HIS A 189 PHE 0.011 0.001 PHE A 337 TYR 0.017 0.001 TYR A 906 ARG 0.003 0.001 ARG A 694 Details of bonding type rmsd hydrogen bonds : bond 0.03865 ( 274) hydrogen bonds : angle 5.08841 ( 774) covalent geometry : bond 0.00383 ( 5980) covalent geometry : angle 0.77950 ( 8123) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 81 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 MET cc_start: 0.6709 (tmm) cc_final: 0.6413 (tmm) REVERT: A 300 ILE cc_start: 0.7999 (tp) cc_final: 0.7723 (tp) REVERT: A 319 MET cc_start: 0.9023 (mtt) cc_final: 0.8739 (mtp) REVERT: A 403 GLU cc_start: 0.8977 (tp30) cc_final: 0.8505 (tp30) REVERT: A 446 LEU cc_start: 0.9467 (mt) cc_final: 0.9204 (mm) REVERT: A 476 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7574 (tm-30) REVERT: A 538 LEU cc_start: 0.8931 (tp) cc_final: 0.8673 (tp) REVERT: A 558 TRP cc_start: 0.8430 (t60) cc_final: 0.7881 (t60) REVERT: A 613 THR cc_start: 0.9373 (m) cc_final: 0.9055 (p) REVERT: A 630 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8002 (tm-30) REVERT: A 705 MET cc_start: 0.7098 (ppp) cc_final: 0.6661 (ppp) REVERT: A 860 ASP cc_start: 0.9204 (m-30) cc_final: 0.8914 (m-30) REVERT: A 903 ARG cc_start: 0.5694 (tpt170) cc_final: 0.5076 (mmm160) outliers start: 31 outliers final: 17 residues processed: 98 average time/residue: 0.1654 time to fit residues: 22.0438 Evaluate side-chains 93 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 335 TRP Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 511 HIS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 523 GLN Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain A residue 906 TYR Chi-restraints excluded: chain A residue 908 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 27 optimal weight: 0.2980 chunk 28 optimal weight: 0.9990 chunk 2 optimal weight: 50.0000 chunk 51 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 chunk 56 optimal weight: 0.4980 chunk 57 optimal weight: 2.9990 chunk 0 optimal weight: 40.0000 chunk 1 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.117773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.077371 restraints weight = 15943.443| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 4.43 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5980 Z= 0.172 Angle : 0.776 10.933 8123 Z= 0.384 Chirality : 0.046 0.197 963 Planarity : 0.005 0.061 1028 Dihedral : 6.120 44.190 816 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.91 % Allowed : 11.01 % Favored : 88.08 % Rotamer: Outliers : 4.38 % Allowed : 18.12 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % 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: -1.52 (0.30), residues: 772 helix: 0.33 (0.26), residues: 388 sheet: -1.46 (0.71), residues: 47 loop : -2.63 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 335 HIS 0.002 0.000 HIS A 749 PHE 0.009 0.001 PHE A 337 TYR 0.015 0.001 TYR A 906 ARG 0.003 0.000 ARG A 931 Details of bonding type rmsd hydrogen bonds : bond 0.03683 ( 274) hydrogen bonds : angle 4.97250 ( 774) covalent geometry : bond 0.00385 ( 5980) covalent geometry : angle 0.77568 ( 8123) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 81 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 MET cc_start: 0.6465 (tmm) cc_final: 0.5968 (tmm) REVERT: A 300 ILE cc_start: 0.8014 (tp) cc_final: 0.7670 (tp) REVERT: A 319 MET cc_start: 0.9043 (mtt) cc_final: 0.8751 (mtp) REVERT: A 403 GLU cc_start: 0.9006 (tp30) cc_final: 0.8535 (tp30) REVERT: A 441 GLU cc_start: 0.9191 (tp30) cc_final: 0.8725 (tm-30) REVERT: A 446 LEU cc_start: 0.9456 (mt) cc_final: 0.9193 (mm) REVERT: A 538 LEU cc_start: 0.8924 (tp) cc_final: 0.8667 (tp) REVERT: A 558 TRP cc_start: 0.8437 (t60) cc_final: 0.7873 (t60) REVERT: A 613 THR cc_start: 0.9367 (m) cc_final: 0.9054 (p) REVERT: A 630 GLU cc_start: 0.8676 (tm-30) cc_final: 0.8015 (tm-30) REVERT: A 705 MET cc_start: 0.7060 (ppp) cc_final: 0.6600 (ppp) REVERT: A 860 ASP cc_start: 0.9187 (m-30) cc_final: 0.8921 (m-30) REVERT: A 903 ARG cc_start: 0.5598 (tpt170) cc_final: 0.4981 (mmm160) outliers start: 28 outliers final: 20 residues processed: 98 average time/residue: 0.1552 time to fit residues: 20.8321 Evaluate side-chains 97 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 335 TRP Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 511 HIS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 523 GLN Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain A residue 906 TYR Chi-restraints excluded: chain A residue 932 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.1980 chunk 45 optimal weight: 0.0470 chunk 2 optimal weight: 40.0000 chunk 22 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 58 optimal weight: 20.0000 chunk 10 optimal weight: 0.9980 overall best weight: 0.8480 ------------------------------------------------------------------------------- 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 = 0.3999 r_free = 0.3999 target = 0.119301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.079741 restraints weight = 16087.743| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 4.31 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5980 Z= 0.152 Angle : 0.784 10.348 8123 Z= 0.385 Chirality : 0.046 0.189 963 Planarity : 0.005 0.067 1028 Dihedral : 6.038 44.232 816 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.91 % Allowed : 10.75 % Favored : 88.34 % Rotamer: Outliers : 4.84 % Allowed : 18.12 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -1.26 (0.30), residues: 772 helix: 0.47 (0.26), residues: 389 sheet: -1.28 (0.80), residues: 37 loop : -2.40 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 335 HIS 0.002 0.001 HIS A 749 PHE 0.010 0.001 PHE A 337 TYR 0.014 0.001 TYR A 906 ARG 0.002 0.000 ARG A 532 Details of bonding type rmsd hydrogen bonds : bond 0.03584 ( 274) hydrogen bonds : angle 4.79357 ( 774) covalent geometry : bond 0.00338 ( 5980) covalent geometry : angle 0.78428 ( 8123) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 82 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 MET cc_start: 0.6403 (tmm) cc_final: 0.6099 (tmm) REVERT: A 300 ILE cc_start: 0.7945 (tp) cc_final: 0.7644 (tp) REVERT: A 319 MET cc_start: 0.9041 (mtt) cc_final: 0.8749 (mtp) REVERT: A 403 GLU cc_start: 0.8980 (tp30) cc_final: 0.8499 (tp30) REVERT: A 441 GLU cc_start: 0.9159 (tp30) cc_final: 0.8739 (tp30) REVERT: A 446 LEU cc_start: 0.9448 (mt) cc_final: 0.9182 (mm) REVERT: A 558 TRP cc_start: 0.8439 (t60) cc_final: 0.7857 (t60) REVERT: A 613 THR cc_start: 0.9309 (OUTLIER) cc_final: 0.9033 (p) REVERT: A 630 GLU cc_start: 0.8671 (tm-30) cc_final: 0.8023 (tm-30) REVERT: A 705 MET cc_start: 0.7106 (ppp) cc_final: 0.6620 (ppp) REVERT: A 860 ASP cc_start: 0.9223 (m-30) cc_final: 0.9001 (m-30) REVERT: A 903 ARG cc_start: 0.5610 (tpt170) cc_final: 0.4998 (mmm160) outliers start: 31 outliers final: 24 residues processed: 102 average time/residue: 0.1682 time to fit residues: 23.2300 Evaluate side-chains 102 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 77 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 335 TRP Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 511 HIS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 523 GLN Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 780 LYS Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain A residue 902 ILE Chi-restraints excluded: chain A residue 906 TYR Chi-restraints excluded: chain A residue 908 TRP Chi-restraints excluded: chain A residue 932 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 66 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 52 optimal weight: 0.0070 chunk 39 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 overall best weight: 0.9202 ------------------------------------------------------------------------------- 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 = 0.3997 r_free = 0.3997 target = 0.119694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.079782 restraints weight = 15733.585| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 4.35 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5980 Z= 0.157 Angle : 0.785 12.917 8123 Z= 0.387 Chirality : 0.046 0.188 963 Planarity : 0.005 0.070 1028 Dihedral : 6.062 43.136 816 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 1.04 % Allowed : 10.49 % Favored : 88.47 % Rotamer: Outliers : 4.84 % Allowed : 18.91 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -1.22 (0.30), residues: 772 helix: 0.58 (0.27), residues: 387 sheet: -1.09 (0.73), residues: 47 loop : -2.50 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 335 HIS 0.002 0.000 HIS A 189 PHE 0.009 0.001 PHE A 337 TYR 0.016 0.001 TYR A 906 ARG 0.003 0.000 ARG A 758 Details of bonding type rmsd hydrogen bonds : bond 0.03472 ( 274) hydrogen bonds : angle 4.70892 ( 774) covalent geometry : bond 0.00351 ( 5980) covalent geometry : angle 0.78545 ( 8123) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 79 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 MET cc_start: 0.6405 (tmm) cc_final: 0.6102 (tmm) REVERT: A 300 ILE cc_start: 0.7883 (tp) cc_final: 0.7573 (tp) REVERT: A 319 MET cc_start: 0.9049 (mtt) cc_final: 0.8760 (mtp) REVERT: A 403 GLU cc_start: 0.9004 (tp30) cc_final: 0.8520 (tp30) REVERT: A 441 GLU cc_start: 0.9108 (tp30) cc_final: 0.8835 (tp30) REVERT: A 446 LEU cc_start: 0.9430 (mt) cc_final: 0.9167 (mm) REVERT: A 558 TRP cc_start: 0.8431 (t60) cc_final: 0.7828 (t60) REVERT: A 583 GLU cc_start: 0.8323 (mt-10) cc_final: 0.8110 (mt-10) REVERT: A 613 THR cc_start: 0.9307 (OUTLIER) cc_final: 0.9034 (p) REVERT: A 630 GLU cc_start: 0.8690 (tm-30) cc_final: 0.8034 (tm-30) REVERT: A 705 MET cc_start: 0.6993 (ppp) cc_final: 0.6513 (ppp) REVERT: A 860 ASP cc_start: 0.9201 (m-30) cc_final: 0.8981 (m-30) REVERT: A 903 ARG cc_start: 0.5540 (tpt170) cc_final: 0.4890 (mmm160) outliers start: 31 outliers final: 21 residues processed: 99 average time/residue: 0.1937 time to fit residues: 27.1859 Evaluate side-chains 99 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 335 TRP Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 511 HIS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 523 GLN Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain A residue 902 ILE Chi-restraints excluded: chain A residue 906 TYR Chi-restraints excluded: chain A residue 908 TRP Chi-restraints excluded: chain A residue 932 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 14 optimal weight: 0.5980 chunk 0 optimal weight: 40.0000 chunk 1 optimal weight: 8.9990 chunk 42 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4008 r_free = 0.4008 target = 0.120478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.079551 restraints weight = 15890.304| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 4.57 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5980 Z= 0.150 Angle : 0.792 12.978 8123 Z= 0.388 Chirality : 0.046 0.191 963 Planarity : 0.005 0.071 1028 Dihedral : 5.966 42.686 816 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.91 % Allowed : 11.14 % Favored : 87.95 % Rotamer: Outliers : 3.59 % Allowed : 20.00 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.31), residues: 772 helix: 0.72 (0.27), residues: 384 sheet: -0.88 (0.74), residues: 47 loop : -2.46 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 335 HIS 0.002 0.001 HIS A 189 PHE 0.009 0.001 PHE A 337 TYR 0.012 0.001 TYR A 906 ARG 0.002 0.000 ARG A 532 Details of bonding type rmsd hydrogen bonds : bond 0.03394 ( 274) hydrogen bonds : angle 4.64192 ( 774) covalent geometry : bond 0.00338 ( 5980) covalent geometry : angle 0.79155 ( 8123) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 MET cc_start: 0.6376 (tmm) cc_final: 0.6008 (tmm) REVERT: A 300 ILE cc_start: 0.7822 (tp) cc_final: 0.7466 (tp) REVERT: A 319 MET cc_start: 0.9067 (mtt) cc_final: 0.8784 (mtp) REVERT: A 403 GLU cc_start: 0.9005 (tp30) cc_final: 0.8523 (tp30) REVERT: A 441 GLU cc_start: 0.9061 (tp30) cc_final: 0.8784 (tp30) REVERT: A 446 LEU cc_start: 0.9414 (mt) cc_final: 0.9150 (mm) REVERT: A 558 TRP cc_start: 0.8428 (t60) cc_final: 0.7823 (t60) REVERT: A 583 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8127 (mt-10) REVERT: A 613 THR cc_start: 0.9276 (OUTLIER) cc_final: 0.9009 (p) REVERT: A 630 GLU cc_start: 0.8693 (tm-30) cc_final: 0.8029 (tm-30) REVERT: A 705 MET cc_start: 0.7509 (ppp) cc_final: 0.7086 (ppp) REVERT: A 860 ASP cc_start: 0.9199 (m-30) cc_final: 0.8983 (m-30) REVERT: A 903 ARG cc_start: 0.5544 (tpt170) cc_final: 0.4912 (mmm160) outliers start: 23 outliers final: 18 residues processed: 93 average time/residue: 0.1865 time to fit residues: 23.9728 Evaluate side-chains 99 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 335 TRP Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 511 HIS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 523 GLN Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain A residue 902 ILE Chi-restraints excluded: chain A residue 906 TYR Chi-restraints excluded: chain A residue 908 TRP Chi-restraints excluded: chain A residue 932 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 56 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 28 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 46 optimal weight: 0.2980 chunk 26 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.3998 r_free = 0.3998 target = 0.119950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.078923 restraints weight = 15834.175| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 4.54 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5980 Z= 0.166 Angle : 0.817 18.196 8123 Z= 0.395 Chirality : 0.046 0.189 963 Planarity : 0.005 0.071 1028 Dihedral : 5.995 42.317 816 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.78 % Allowed : 11.27 % Favored : 87.95 % Rotamer: Outliers : 3.12 % Allowed : 20.78 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -1.05 (0.31), residues: 772 helix: 0.78 (0.27), residues: 384 sheet: -1.19 (0.69), residues: 55 loop : -2.47 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 335 HIS 0.002 0.000 HIS A 749 PHE 0.014 0.001 PHE A 337 TYR 0.011 0.001 TYR A 906 ARG 0.002 0.000 ARG A 532 Details of bonding type rmsd hydrogen bonds : bond 0.03348 ( 274) hydrogen bonds : angle 4.60920 ( 774) covalent geometry : bond 0.00376 ( 5980) covalent geometry : angle 0.81670 ( 8123) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 MET cc_start: 0.6357 (tmm) cc_final: 0.5991 (tmm) REVERT: A 300 ILE cc_start: 0.7756 (tp) cc_final: 0.7405 (tp) REVERT: A 319 MET cc_start: 0.9071 (mtt) cc_final: 0.8787 (mtp) REVERT: A 403 GLU cc_start: 0.9010 (tp30) cc_final: 0.8533 (tp30) REVERT: A 441 GLU cc_start: 0.9029 (tp30) cc_final: 0.8786 (tp30) REVERT: A 446 LEU cc_start: 0.9417 (mt) cc_final: 0.9142 (mm) REVERT: A 558 TRP cc_start: 0.8443 (t60) cc_final: 0.7883 (t60) REVERT: A 583 GLU cc_start: 0.8337 (mt-10) cc_final: 0.8127 (mt-10) REVERT: A 613 THR cc_start: 0.9278 (OUTLIER) cc_final: 0.8973 (p) REVERT: A 630 GLU cc_start: 0.8690 (tm-30) cc_final: 0.8025 (tm-30) REVERT: A 705 MET cc_start: 0.7504 (ppp) cc_final: 0.7103 (ppp) REVERT: A 860 ASP cc_start: 0.9181 (m-30) cc_final: 0.8979 (m-30) REVERT: A 903 ARG cc_start: 0.5582 (tpt170) cc_final: 0.4965 (mmm160) outliers start: 20 outliers final: 18 residues processed: 86 average time/residue: 0.1549 time to fit residues: 18.5872 Evaluate side-chains 96 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 335 TRP Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 511 HIS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 523 GLN Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain A residue 902 ILE Chi-restraints excluded: chain A residue 906 TYR Chi-restraints excluded: chain A residue 908 TRP Chi-restraints excluded: chain A residue 932 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 34 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 25 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 51 optimal weight: 20.0000 chunk 67 optimal weight: 0.8980 chunk 5 optimal weight: 0.0870 chunk 13 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.121314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.080823 restraints weight = 16073.529| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 4.50 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5980 Z= 0.141 Angle : 0.804 17.682 8123 Z= 0.388 Chirality : 0.046 0.191 963 Planarity : 0.005 0.070 1028 Dihedral : 5.901 42.125 816 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.78 % Allowed : 11.27 % Favored : 87.95 % Rotamer: Outliers : 3.75 % Allowed : 20.00 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -0.99 (0.31), residues: 772 helix: 0.83 (0.27), residues: 383 sheet: -1.11 (0.69), residues: 55 loop : -2.44 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 335 HIS 0.002 0.000 HIS A 189 PHE 0.013 0.001 PHE A 337 TYR 0.011 0.001 TYR A 366 ARG 0.002 0.000 ARG A 694 Details of bonding type rmsd hydrogen bonds : bond 0.03282 ( 274) hydrogen bonds : angle 4.57568 ( 774) covalent geometry : bond 0.00317 ( 5980) covalent geometry : angle 0.80395 ( 8123) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3319.82 seconds wall clock time: 59 minutes 1.15 seconds (3541.15 seconds total)