Starting phenix.real_space_refine on Fri Oct 10 13:23:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q75_18204/10_2025/8q75_18204.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q75_18204/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8q75_18204/10_2025/8q75_18204.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q75_18204/10_2025/8q75_18204.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8q75_18204/10_2025/8q75_18204.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q75_18204/10_2025/8q75_18204.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 1.87, per 1000 atoms: 0.32 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: 0.57 Conformation dependent library (CDL) restraints added in 389.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.23 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: 1.09 Time building geometry restraints manager: 0.78 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: 3.390 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: 0.020 Extract box with map and model: 0.150 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.460 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.730 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.021 0.002 ARG A 265 TYR 0.009 0.001 TYR A 689 PHE 0.019 0.001 PHE A 710 TRP 0.026 0.002 TRP A 935 HIS 0.004 0.001 HIS A 633 Details of bonding type rmsd covalent geometry : bond 0.00563 ( 5980) covalent geometry : angle 1.55665 ( 8123) hydrogen bonds : bond 0.20669 ( 274) hydrogen bonds : angle 7.54221 ( 774) *********************** 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 : 0.237 Fit side-chains revert: symmetry clash 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 295 MET cc_start: 0.7880 (tpt) cc_final: 0.7676 (mmm) REVERT: A 299 MET cc_start: 0.6834 (tmm) cc_final: 0.6557 (tmm) REVERT: A 300 ILE cc_start: 0.8149 (tp) cc_final: 0.7886 (mm) REVERT: A 303 PHE cc_start: 0.8640 (m-80) cc_final: 0.8424 (m-80) 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 753 THR cc_start: 0.8499 (m) cc_final: 0.8296 (m) 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: 0.0965 time to fit residues: 15.6914 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 : 0.228 ------------------------------------------------------------------------------- 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 49 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 20.0000 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.0020 overall best weight: 1.5994 ------------------------------------------------------------------------------- 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 = 0.3971 r_free = 0.3971 target = 0.118063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.077774 restraints weight = 15937.150| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 4.39 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5980 Z= 0.225 Angle : 0.854 11.537 8123 Z= 0.432 Chirality : 0.049 0.170 963 Planarity : 0.007 0.073 1028 Dihedral : 6.509 43.802 820 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 18.45 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 : 0.41 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.13 (0.30), residues: 772 helix: -0.00 (0.26), residues: 383 sheet: -2.25 (0.65), residues: 55 loop : -3.03 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 931 TYR 0.011 0.001 TYR A 906 PHE 0.017 0.001 PHE A 710 TRP 0.014 0.001 TRP A 935 HIS 0.010 0.001 HIS A 749 Details of bonding type rmsd covalent geometry : bond 0.00497 ( 5980) covalent geometry : angle 0.85367 ( 8123) hydrogen bonds : bond 0.04939 ( 274) hydrogen bonds : angle 5.77442 ( 774) *********************** 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 103 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 MET cc_start: 0.6699 (tmm) cc_final: 0.6399 (tmm) REVERT: A 300 ILE cc_start: 0.7958 (tp) cc_final: 0.7745 (mm) REVERT: A 319 MET cc_start: 0.9037 (mtt) cc_final: 0.8705 (mtp) REVERT: A 391 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8812 (tpp) REVERT: A 446 LEU cc_start: 0.9471 (mt) cc_final: 0.9199 (mm) REVERT: A 558 TRP cc_start: 0.8374 (t60) cc_final: 0.8139 (t60) REVERT: A 610 MET cc_start: 0.7668 (mmt) cc_final: 0.7333 (mmp) REVERT: A 613 THR cc_start: 0.9438 (m) cc_final: 0.9109 (p) REVERT: A 630 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8050 (tm-30) REVERT: A 659 PHE cc_start: 0.8755 (p90) cc_final: 0.8052 (p90) REVERT: A 705 MET cc_start: 0.7131 (ppp) cc_final: 0.6768 (ppp) REVERT: A 860 ASP cc_start: 0.9273 (m-30) cc_final: 0.8945 (m-30) REVERT: A 903 ARG cc_start: 0.5876 (tpt170) cc_final: 0.5291 (mmm160) outliers start: 14 outliers final: 10 residues processed: 96 average time/residue: 0.0844 time to fit residues: 10.8198 Evaluate side-chains 86 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.225 ------------------------------------------------------------------------------- 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 391 MET 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 67 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 14 optimal weight: 0.1980 chunk 40 optimal weight: 0.6980 chunk 74 optimal weight: 0.0030 chunk 71 optimal weight: 0.4980 chunk 12 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 overall best weight: 0.3990 ------------------------------------------------------------------------------- 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 = 0.4007 r_free = 0.4007 target = 0.120823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.080742 restraints weight = 15657.233| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 4.39 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5980 Z= 0.145 Angle : 0.782 11.733 8123 Z= 0.388 Chirality : 0.046 0.165 963 Planarity : 0.006 0.068 1028 Dihedral : 6.173 48.159 816 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 1.30 % Allowed : 10.62 % Favored : 88.08 % Rotamer: Outliers : 2.66 % Allowed : 15.00 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.80 (0.30), residues: 772 helix: 0.11 (0.26), residues: 392 sheet: -1.74 (0.71), residues: 47 loop : -2.79 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 694 TYR 0.013 0.001 TYR A 570 PHE 0.014 0.001 PHE A 710 TRP 0.011 0.001 TRP A 335 HIS 0.004 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 5980) covalent geometry : angle 0.78191 ( 8123) hydrogen bonds : bond 0.04134 ( 274) hydrogen bonds : angle 5.33761 ( 774) *********************** 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 105 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 MET cc_start: 0.6681 (tmm) cc_final: 0.6225 (tmm) REVERT: A 300 ILE cc_start: 0.7973 (tp) cc_final: 0.7478 (mm) REVERT: A 319 MET cc_start: 0.9035 (mtt) cc_final: 0.8680 (mtp) REVERT: A 403 GLU cc_start: 0.9014 (tp30) cc_final: 0.8601 (tp30) REVERT: A 446 LEU cc_start: 0.9430 (mt) cc_final: 0.9165 (mm) REVERT: A 558 TRP cc_start: 0.8330 (t60) cc_final: 0.7933 (t60) REVERT: A 630 GLU cc_start: 0.8632 (tm-30) cc_final: 0.7958 (tm-30) REVERT: A 650 LYS cc_start: 0.8592 (tptt) cc_final: 0.8247 (tptt) REVERT: A 705 MET cc_start: 0.6905 (ppp) cc_final: 0.6546 (ppp) REVERT: A 860 ASP cc_start: 0.9246 (m-30) cc_final: 0.8984 (m-30) REVERT: A 903 ARG cc_start: 0.5739 (tpt170) cc_final: 0.5108 (mmm160) outliers start: 17 outliers final: 12 residues processed: 99 average time/residue: 0.0716 time to fit residues: 9.8311 Evaluate side-chains 85 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.234 ------------------------------------------------------------------------------- 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 321 LEU Chi-restraints excluded: chain A residue 335 TRP Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 392 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 906 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 18 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 58 optimal weight: 20.0000 chunk 12 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 7 optimal weight: 0.0570 chunk 34 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 overall best weight: 0.7902 ------------------------------------------------------------------------------- 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 = 0.4006 r_free = 0.4006 target = 0.120517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.080217 restraints weight = 15838.691| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 4.42 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5980 Z= 0.148 Angle : 0.761 10.983 8123 Z= 0.377 Chirality : 0.046 0.161 963 Planarity : 0.005 0.051 1028 Dihedral : 6.029 44.090 816 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 1.17 % Allowed : 11.14 % Favored : 87.69 % Rotamer: Outliers : 3.75 % Allowed : 15.94 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.71 (0.30), residues: 772 helix: 0.25 (0.26), residues: 389 sheet: -1.69 (0.70), residues: 47 loop : -2.81 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 931 TYR 0.010 0.001 TYR A 366 PHE 0.011 0.001 PHE A 710 TRP 0.009 0.001 TRP A 335 HIS 0.003 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 5980) covalent geometry : angle 0.76086 ( 8123) hydrogen bonds : bond 0.03750 ( 274) hydrogen bonds : angle 5.11498 ( 774) *********************** 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 101 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 299 MET cc_start: 0.6659 (tmm) cc_final: 0.6152 (tmm) REVERT: A 300 ILE cc_start: 0.7948 (tp) cc_final: 0.7405 (mm) REVERT: A 319 MET cc_start: 0.9055 (mtt) cc_final: 0.8704 (mtp) REVERT: A 403 GLU cc_start: 0.9003 (tp30) cc_final: 0.8557 (tp30) REVERT: A 446 LEU cc_start: 0.9434 (mt) cc_final: 0.9153 (mm) REVERT: A 558 TRP cc_start: 0.8330 (t60) cc_final: 0.7947 (t60) REVERT: A 630 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8033 (tm-30) REVERT: A 705 MET cc_start: 0.7024 (ppp) cc_final: 0.6609 (ppp) REVERT: A 860 ASP cc_start: 0.9249 (m-30) cc_final: 0.9006 (m-30) REVERT: A 903 ARG cc_start: 0.5777 (tpt170) cc_final: 0.5154 (mmm160) outliers start: 24 outliers final: 15 residues processed: 92 average time/residue: 0.0796 time to fit residues: 9.8717 Evaluate side-chains 85 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.185 ------------------------------------------------------------------------------- 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 391 MET 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 17 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 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 = 0.4028 r_free = 0.4028 target = 0.120908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.080886 restraints weight = 16086.519| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 4.40 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5980 Z= 0.145 Angle : 0.757 10.676 8123 Z= 0.372 Chirality : 0.045 0.151 963 Planarity : 0.005 0.056 1028 Dihedral : 5.902 43.955 816 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 1.17 % Allowed : 10.75 % Favored : 88.08 % Rotamer: Outliers : 4.38 % Allowed : 16.56 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.57 (0.30), residues: 772 helix: 0.41 (0.27), residues: 391 sheet: -1.73 (0.68), residues: 50 loop : -2.80 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 694 TYR 0.011 0.001 TYR A 906 PHE 0.009 0.001 PHE A 659 TRP 0.009 0.001 TRP A 335 HIS 0.003 0.000 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 5980) covalent geometry : angle 0.75739 ( 8123) hydrogen bonds : bond 0.03604 ( 274) hydrogen bonds : angle 4.91864 ( 774) *********************** 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 101 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 73 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 MET cc_start: 0.6425 (tmm) cc_final: 0.6211 (tmm) REVERT: A 300 ILE cc_start: 0.7964 (tp) cc_final: 0.7657 (tp) REVERT: A 319 MET cc_start: 0.9046 (mtt) cc_final: 0.8729 (mtp) REVERT: A 403 GLU cc_start: 0.9006 (tp30) cc_final: 0.8524 (tp30) REVERT: A 446 LEU cc_start: 0.9425 (mt) cc_final: 0.9151 (mm) REVERT: A 558 TRP cc_start: 0.8324 (t60) cc_final: 0.7906 (t60) REVERT: A 630 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8037 (tm-30) REVERT: A 650 LYS cc_start: 0.8619 (tptt) cc_final: 0.8374 (tptt) REVERT: A 705 MET cc_start: 0.6993 (ppp) cc_final: 0.6563 (ppp) REVERT: A 838 MET cc_start: 0.8817 (tmm) cc_final: 0.8616 (tmm) REVERT: A 860 ASP cc_start: 0.9239 (m-30) cc_final: 0.9033 (m-30) REVERT: A 903 ARG cc_start: 0.5844 (tpt170) cc_final: 0.5243 (mmm160) outliers start: 28 outliers final: 18 residues processed: 90 average time/residue: 0.0790 time to fit residues: 9.6245 Evaluate side-chains 88 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.156 ------------------------------------------------------------------------------- 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 392 LEU Chi-restraints excluded: chain A residue 456 VAL 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 841 LEU 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 906 TYR Chi-restraints excluded: chain A residue 908 TRP Chi-restraints excluded: chain A residue 932 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 43 optimal weight: 0.0570 chunk 61 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 29 optimal weight: 0.0010 chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 overall best weight: 0.5504 ------------------------------------------------------------------------------- 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 = 0.4044 r_free = 0.4044 target = 0.122328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.082436 restraints weight = 15847.653| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 4.40 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3365 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= 0.132 Angle : 0.747 11.090 8123 Z= 0.365 Chirality : 0.045 0.196 963 Planarity : 0.005 0.062 1028 Dihedral : 5.777 42.580 816 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.91 % Allowed : 10.62 % Favored : 88.47 % Rotamer: Outliers : 3.75 % Allowed : 17.19 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.30), residues: 772 helix: 0.52 (0.27), residues: 391 sheet: -1.42 (0.72), residues: 47 loop : -2.63 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 694 TYR 0.011 0.001 TYR A 366 PHE 0.009 0.001 PHE A 659 TRP 0.009 0.001 TRP A 335 HIS 0.002 0.000 HIS A 749 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 5980) covalent geometry : angle 0.74712 ( 8123) hydrogen bonds : bond 0.03483 ( 274) hydrogen bonds : angle 4.74603 ( 774) *********************** 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 100 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 76 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 MET cc_start: 0.6367 (tmm) cc_final: 0.6089 (tmm) REVERT: A 319 MET cc_start: 0.9038 (mtt) cc_final: 0.8743 (mtp) REVERT: A 403 GLU cc_start: 0.8977 (tp30) cc_final: 0.8512 (tp30) REVERT: A 446 LEU cc_start: 0.9408 (mt) cc_final: 0.9129 (mm) REVERT: A 558 TRP cc_start: 0.8343 (t60) cc_final: 0.7911 (t60) REVERT: A 630 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8010 (tm-30) REVERT: A 650 LYS cc_start: 0.8609 (tptt) cc_final: 0.8350 (tptt) REVERT: A 705 MET cc_start: 0.6913 (ppp) cc_final: 0.6454 (ppp) REVERT: A 838 MET cc_start: 0.8787 (tmm) cc_final: 0.8577 (tmm) REVERT: A 903 ARG cc_start: 0.5823 (tpt170) cc_final: 0.5221 (mmm160) outliers start: 24 outliers final: 18 residues processed: 91 average time/residue: 0.0786 time to fit residues: 9.7217 Evaluate side-chains 89 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 392 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 511 HIS Chi-restraints excluded: chain A residue 523 GLN 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 841 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 28 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 52 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.118938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.078547 restraints weight = 15941.160| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 4.42 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5980 Z= 0.195 Angle : 0.769 12.140 8123 Z= 0.378 Chirality : 0.046 0.180 963 Planarity : 0.005 0.067 1028 Dihedral : 5.806 40.532 816 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.78 % Allowed : 10.88 % Favored : 88.34 % Rotamer: Outliers : 4.06 % Allowed : 17.19 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.30), residues: 772 helix: 0.47 (0.26), residues: 391 sheet: -1.35 (0.80), residues: 38 loop : -2.44 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 758 TYR 0.014 0.001 TYR A 366 PHE 0.010 0.001 PHE A 555 TRP 0.012 0.001 TRP A 935 HIS 0.002 0.001 HIS A 749 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 5980) covalent geometry : angle 0.76867 ( 8123) hydrogen bonds : bond 0.03625 ( 274) hydrogen bonds : angle 4.71810 ( 774) *********************** 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 99 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 73 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 MET cc_start: 0.6363 (tmm) cc_final: 0.6087 (tmm) REVERT: A 300 ILE cc_start: 0.7734 (tp) cc_final: 0.7379 (tp) REVERT: A 319 MET cc_start: 0.9039 (mtt) cc_final: 0.8771 (mtp) REVERT: A 353 ASP cc_start: 0.9121 (m-30) cc_final: 0.8825 (m-30) REVERT: A 403 GLU cc_start: 0.9018 (tp30) cc_final: 0.8544 (tp30) REVERT: A 441 GLU cc_start: 0.9168 (tp30) cc_final: 0.8832 (tp30) REVERT: A 446 LEU cc_start: 0.9422 (mt) cc_final: 0.9148 (mm) REVERT: A 558 TRP cc_start: 0.8361 (t60) cc_final: 0.7814 (t60) REVERT: A 630 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8051 (tm-30) REVERT: A 650 LYS cc_start: 0.8678 (tptt) cc_final: 0.8403 (tptt) REVERT: A 659 PHE cc_start: 0.9038 (OUTLIER) cc_final: 0.8302 (p90) REVERT: A 705 MET cc_start: 0.6944 (ppp) cc_final: 0.6616 (ppp) REVERT: A 780 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7895 (pttp) REVERT: A 903 ARG cc_start: 0.5775 (tpt170) cc_final: 0.5137 (mmm160) outliers start: 26 outliers final: 17 residues processed: 88 average time/residue: 0.0869 time to fit residues: 10.4486 Evaluate side-chains 91 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.233 ------------------------------------------------------------------------------- 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 368 VAL 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 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 780 LYS Chi-restraints excluded: chain A residue 841 LEU 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 932 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 52 optimal weight: 10.0000 chunk 44 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 0 optimal weight: 40.0000 chunk 70 optimal weight: 0.7980 chunk 3 optimal weight: 20.0000 chunk 21 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.4001 r_free = 0.4001 target = 0.120017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.079678 restraints weight = 15781.316| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 4.31 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5980 Z= 0.165 Angle : 0.765 12.727 8123 Z= 0.374 Chirality : 0.046 0.187 963 Planarity : 0.005 0.069 1028 Dihedral : 5.830 42.166 816 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.78 % Allowed : 11.14 % Favored : 88.08 % Rotamer: Outliers : 4.22 % Allowed : 17.97 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.31), residues: 772 helix: 0.51 (0.27), residues: 391 sheet: -1.19 (0.80), residues: 38 loop : -2.38 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 532 TYR 0.012 0.001 TYR A 366 PHE 0.012 0.001 PHE A 337 TRP 0.009 0.001 TRP A 335 HIS 0.002 0.000 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 5980) covalent geometry : angle 0.76545 ( 8123) hydrogen bonds : bond 0.03517 ( 274) hydrogen bonds : angle 4.62835 ( 774) *********************** 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 101 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 74 time to evaluate : 0.261 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: 0.6070 (tmm) REVERT: A 300 ILE cc_start: 0.7600 (tp) cc_final: 0.7235 (tp) REVERT: A 319 MET cc_start: 0.9037 (mtt) cc_final: 0.8754 (mtp) REVERT: A 353 ASP cc_start: 0.9097 (m-30) cc_final: 0.8811 (m-30) REVERT: A 403 GLU cc_start: 0.8991 (tp30) cc_final: 0.8505 (tp30) REVERT: A 441 GLU cc_start: 0.9128 (tp30) cc_final: 0.8789 (tp30) REVERT: A 446 LEU cc_start: 0.9415 (mt) cc_final: 0.9139 (mm) REVERT: A 558 TRP cc_start: 0.8380 (t60) cc_final: 0.7813 (t60) REVERT: A 630 GLU cc_start: 0.8667 (tm-30) cc_final: 0.8017 (tm-30) REVERT: A 659 PHE cc_start: 0.9096 (OUTLIER) cc_final: 0.8381 (p90) REVERT: A 705 MET cc_start: 0.6907 (ppp) cc_final: 0.6357 (ppp) REVERT: A 903 ARG cc_start: 0.5625 (tpt170) cc_final: 0.4977 (mmm160) outliers start: 27 outliers final: 19 residues processed: 91 average time/residue: 0.0805 time to fit residues: 9.9121 Evaluate side-chains 92 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.233 ------------------------------------------------------------------------------- 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 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 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 746 VAL Chi-restraints excluded: chain A residue 841 LEU 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 932 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 36 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 3 optimal weight: 20.0000 chunk 17 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 0 optimal weight: 40.0000 chunk 35 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4026 r_free = 0.4026 target = 0.121484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.080719 restraints weight = 15909.075| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 4.37 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5980 Z= 0.140 Angle : 0.774 14.018 8123 Z= 0.373 Chirality : 0.046 0.188 963 Planarity : 0.005 0.069 1028 Dihedral : 5.742 40.902 816 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.78 % Allowed : 11.40 % Favored : 87.82 % Rotamer: Outliers : 3.44 % Allowed : 18.59 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.31), residues: 772 helix: 0.70 (0.27), residues: 386 sheet: -1.08 (0.79), residues: 38 loop : -2.32 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 931 TYR 0.013 0.001 TYR A 366 PHE 0.011 0.001 PHE A 337 TRP 0.009 0.001 TRP A 335 HIS 0.002 0.000 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 5980) covalent geometry : angle 0.77412 ( 8123) hydrogen bonds : bond 0.03383 ( 274) hydrogen bonds : angle 4.53412 ( 774) *********************** 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 98 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 MET cc_start: 0.6334 (tmm) cc_final: 0.5981 (tmm) REVERT: A 300 ILE cc_start: 0.7459 (tp) cc_final: 0.7065 (tp) REVERT: A 319 MET cc_start: 0.9051 (mtt) cc_final: 0.8762 (mtp) REVERT: A 353 ASP cc_start: 0.9063 (m-30) cc_final: 0.8759 (m-30) REVERT: A 403 GLU cc_start: 0.8993 (tp30) cc_final: 0.8510 (tp30) REVERT: A 441 GLU cc_start: 0.9073 (tp30) cc_final: 0.8743 (tp30) REVERT: A 446 LEU cc_start: 0.9374 (mt) cc_final: 0.9094 (mm) REVERT: A 630 GLU cc_start: 0.8652 (tm-30) cc_final: 0.7992 (tm-30) REVERT: A 705 MET cc_start: 0.6888 (ppp) cc_final: 0.6340 (ppp) REVERT: A 903 ARG cc_start: 0.5563 (tpt170) cc_final: 0.4913 (mmm160) outliers start: 22 outliers final: 18 residues processed: 89 average time/residue: 0.0767 time to fit residues: 9.2352 Evaluate side-chains 94 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.228 ------------------------------------------------------------------------------- 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 456 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 511 HIS 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 746 VAL Chi-restraints excluded: chain A residue 841 LEU 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 9 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 42 optimal weight: 0.0980 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 17 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 = 0.4036 r_free = 0.4036 target = 0.122197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.081825 restraints weight = 15953.927| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 4.46 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3952 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= 0.138 Angle : 0.773 15.091 8123 Z= 0.372 Chirality : 0.045 0.192 963 Planarity : 0.005 0.069 1028 Dihedral : 5.652 40.776 816 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.78 % Allowed : 11.01 % Favored : 88.21 % Rotamer: Outliers : 2.97 % Allowed : 18.91 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.31), residues: 772 helix: 0.72 (0.27), residues: 386 sheet: -1.41 (0.73), residues: 45 loop : -2.27 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 758 TYR 0.012 0.001 TYR A 366 PHE 0.014 0.001 PHE A 337 TRP 0.009 0.001 TRP A 335 HIS 0.002 0.000 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 5980) covalent geometry : angle 0.77279 ( 8123) hydrogen bonds : bond 0.03331 ( 274) hydrogen bonds : angle 4.49682 ( 774) ********************** 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 100 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 MET cc_start: 0.6204 (tmm) cc_final: 0.5904 (tmm) REVERT: A 300 ILE cc_start: 0.7336 (tp) cc_final: 0.6962 (tp) REVERT: A 319 MET cc_start: 0.9074 (mtt) cc_final: 0.8795 (mtp) REVERT: A 403 GLU cc_start: 0.8974 (tp30) cc_final: 0.8482 (tp30) REVERT: A 441 GLU cc_start: 0.9031 (tp30) cc_final: 0.8694 (tp30) REVERT: A 446 LEU cc_start: 0.9379 (mt) cc_final: 0.9093 (mm) REVERT: A 630 GLU cc_start: 0.8646 (tm-30) cc_final: 0.7980 (tm-30) REVERT: A 705 MET cc_start: 0.6972 (ppp) cc_final: 0.6425 (ppp) REVERT: A 903 ARG cc_start: 0.5621 (tpt170) cc_final: 0.4924 (mmm160) outliers start: 19 outliers final: 18 residues processed: 92 average time/residue: 0.0834 time to fit residues: 10.3140 Evaluate side-chains 93 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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 456 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 511 HIS 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 746 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 879 VAL 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 Chi-restraints excluded: chain A residue 954 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 72 optimal weight: 0.0870 chunk 18 optimal weight: 0.6980 chunk 4 optimal weight: 7.9990 chunk 42 optimal weight: 0.4980 chunk 58 optimal weight: 20.0000 chunk 20 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 24 optimal weight: 9.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.123158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.082677 restraints weight = 15904.715| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 4.43 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5980 Z= 0.133 Angle : 0.773 16.370 8123 Z= 0.371 Chirality : 0.046 0.191 963 Planarity : 0.005 0.069 1028 Dihedral : 5.564 38.957 816 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.78 % Allowed : 10.75 % Favored : 88.47 % Rotamer: Outliers : 2.97 % Allowed : 19.53 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.31), residues: 772 helix: 0.82 (0.27), residues: 384 sheet: -1.35 (0.72), residues: 45 loop : -2.22 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 758 TYR 0.010 0.001 TYR A 906 PHE 0.012 0.001 PHE A 337 TRP 0.026 0.001 TRP A 558 HIS 0.002 0.000 HIS A 749 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 5980) covalent geometry : angle 0.77251 ( 8123) hydrogen bonds : bond 0.03228 ( 274) hydrogen bonds : angle 4.44594 ( 774) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1602.12 seconds wall clock time: 28 minutes 22.20 seconds (1702.20 seconds total)