Starting phenix.real_space_refine on Wed Sep 17 16:01:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zqc_60382/09_2025/8zqc_60382.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zqc_60382/09_2025/8zqc_60382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zqc_60382/09_2025/8zqc_60382.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zqc_60382/09_2025/8zqc_60382.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zqc_60382/09_2025/8zqc_60382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zqc_60382/09_2025/8zqc_60382.map" } resolution = 3.4 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= 0.000 sd= 0.007 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: 5 Type Number sf(0) Gaussians P 99 5.49 5 S 27 5.16 5 C 5784 2.51 5 N 1703 2.21 5 O 2067 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9680 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7612 Classifications: {'peptide': 930} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 907} Chain breaks: 3 Chain: "B" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 1167 Classifications: {'RNA': 55} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 8, 'rna3p_pur': 20, 'rna3p_pyr': 20} Link IDs: {'rna2p': 15, 'rna3p': 39} Chain: "C" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 542 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "D" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 359 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Time building chain proxies: 2.65, per 1000 atoms: 0.27 Number of scatterers: 9680 At special positions: 0 Unit cell: (84.48, 104.94, 126.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 P 99 15.00 O 2067 8.00 N 1703 7.00 C 5784 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: 1.13 Conformation dependent library (CDL) restraints added in 311.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1774 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 6 sheets defined 51.1% alpha, 10.2% beta 20 base pairs and 52 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 15 through 47 Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 64 through 76 removed outlier: 4.171A pdb=" N SER A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N CYS A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 98 Processing helix chain 'A' and resid 106 through 115 removed outlier: 3.741A pdb=" N LEU A 110 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 171 removed outlier: 4.232A pdb=" N ALA A 148 " --> pdb=" O LYS A 144 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ASN A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LYS A 153 " --> pdb=" O LYS A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 182 Processing helix chain 'A' and resid 186 through 229 removed outlier: 3.519A pdb=" N LEU A 190 " --> pdb=" O ASN A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 251 removed outlier: 3.991A pdb=" N LEU A 251 " --> pdb=" O ARG A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 272 removed outlier: 3.654A pdb=" N ALA A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS A 266 " --> pdb=" O GLN A 262 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG A 269 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS A 270 " --> pdb=" O LYS A 266 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE A 272 " --> pdb=" O TRP A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 275 No H-bonds generated for 'chain 'A' and resid 273 through 275' Processing helix chain 'A' and resid 284 through 295 removed outlier: 3.727A pdb=" N HIS A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 298 No H-bonds generated for 'chain 'A' and resid 296 through 298' Processing helix chain 'A' and resid 301 through 319 removed outlier: 3.758A pdb=" N LEU A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LYS A 308 " --> pdb=" O TYR A 304 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N GLU A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ASP A 310 " --> pdb=" O PHE A 306 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 436 Processing helix chain 'A' and resid 452 through 458 Processing helix chain 'A' and resid 459 through 462 removed outlier: 3.866A pdb=" N THR A 462 " --> pdb=" O LEU A 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 459 through 462' Processing helix chain 'A' and resid 469 through 474 Processing helix chain 'A' and resid 537 through 565 removed outlier: 3.806A pdb=" N LYS A 541 " --> pdb=" O ASN A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 605 removed outlier: 3.531A pdb=" N GLY A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 611 removed outlier: 3.574A pdb=" N PHE A 610 " --> pdb=" O LEU A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 635 Processing helix chain 'A' and resid 638 through 657 removed outlier: 3.517A pdb=" N PHE A 642 " --> pdb=" O THR A 638 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE A 657 " --> pdb=" O ILE A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 666 Processing helix chain 'A' and resid 679 through 700 Processing helix chain 'A' and resid 715 through 743 removed outlier: 3.668A pdb=" N GLN A 719 " --> pdb=" O PHE A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 770 removed outlier: 4.115A pdb=" N ARG A 769 " --> pdb=" O ASP A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 789 removed outlier: 3.815A pdb=" N GLU A 789 " --> pdb=" O GLU A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 3.536A pdb=" N GLN A 804 " --> pdb=" O HIS A 801 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU A 805 " --> pdb=" O SER A 802 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 801 through 805' Processing helix chain 'A' and resid 835 through 850 Processing helix chain 'A' and resid 881 through 890 Processing helix chain 'A' and resid 908 through 916 removed outlier: 3.608A pdb=" N LEU A 916 " --> pdb=" O GLN A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 951 removed outlier: 4.089A pdb=" N ARG A 947 " --> pdb=" O GLU A 943 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N THR A 948 " --> pdb=" O ILE A 944 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ASN A 949 " --> pdb=" O GLY A 945 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL A 950 " --> pdb=" O ALA A 946 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN A 951 " --> pdb=" O ARG A 947 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 338 through 339 removed outlier: 4.921A pdb=" N PHE A 439 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU A 13 " --> pdb=" O LYS A 372 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS A 372 " --> pdb=" O GLU A 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 379 through 383 Processing sheet with id=AA3, first strand: chain 'A' and resid 509 through 510 removed outlier: 6.955A pdb=" N ILE A 497 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N GLU A 529 " --> pdb=" O MET A 495 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N MET A 495 " --> pdb=" O GLU A 529 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 748 " --> pdb=" O ARG A 481 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLU A 752 " --> pdb=" O VAL A 485 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 814 through 815 Processing sheet with id=AA5, first strand: chain 'A' and resid 857 through 858 Processing sheet with id=AA6, first strand: chain 'A' and resid 861 through 863 removed outlier: 3.653A pdb=" N GLY A 920 " --> pdb=" O LEU A 862 " (cutoff:3.500A) 380 hydrogen bonds defined for protein. 1092 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 53 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 52 stacking parallelities Total time for adding SS restraints: 1.92 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2276 1.33 - 1.45: 2497 1.45 - 1.57: 5065 1.57 - 1.69: 195 1.69 - 1.81: 39 Bond restraints: 10072 Sorted by residual: bond pdb=" N PHE A 670 " pdb=" CA PHE A 670 " ideal model delta sigma weight residual 1.462 1.481 -0.019 1.36e-02 5.41e+03 2.02e+00 bond pdb=" CA VAL A 580 " pdb=" CB VAL A 580 " ideal model delta sigma weight residual 1.540 1.558 -0.018 1.36e-02 5.41e+03 1.81e+00 bond pdb=" O5' A B -8 " pdb=" C5' A B -8 " ideal model delta sigma weight residual 1.420 1.439 -0.019 1.50e-02 4.44e+03 1.55e+00 bond pdb=" CB GLU A 317 " pdb=" CG GLU A 317 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.48e+00 bond pdb=" C LEU A 567 " pdb=" N GLU A 568 " ideal model delta sigma weight residual 1.332 1.316 0.017 1.40e-02 5.10e+03 1.44e+00 ... (remaining 10067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 13636 1.72 - 3.44: 311 3.44 - 5.17: 46 5.17 - 6.89: 18 6.89 - 8.61: 4 Bond angle restraints: 14015 Sorted by residual: angle pdb=" CA LYS A 180 " pdb=" CB LYS A 180 " pdb=" CG LYS A 180 " ideal model delta sigma weight residual 114.10 120.80 -6.70 2.00e+00 2.50e-01 1.12e+01 angle pdb=" N LYS A 674 " pdb=" CA LYS A 674 " pdb=" C LYS A 674 " ideal model delta sigma weight residual 110.80 117.66 -6.86 2.13e+00 2.20e-01 1.04e+01 angle pdb=" C4' A B -8 " pdb=" C3' A B -8 " pdb=" O3' A B -8 " ideal model delta sigma weight residual 113.00 108.51 4.49 1.50e+00 4.44e-01 8.98e+00 angle pdb=" N LEU A 98 " pdb=" CA LEU A 98 " pdb=" C LEU A 98 " ideal model delta sigma weight residual 110.35 106.23 4.12 1.38e+00 5.25e-01 8.92e+00 angle pdb=" N VAL A 580 " pdb=" CA VAL A 580 " pdb=" C VAL A 580 " ideal model delta sigma weight residual 109.34 115.29 -5.95 2.08e+00 2.31e-01 8.19e+00 ... (remaining 14010 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.84: 5502 34.84 - 69.68: 501 69.68 - 104.52: 40 104.52 - 139.36: 4 139.36 - 174.21: 2 Dihedral angle restraints: 6049 sinusoidal: 3314 harmonic: 2735 Sorted by residual: dihedral pdb=" O4' U B -32 " pdb=" C1' U B -32 " pdb=" N1 U B -32 " pdb=" C2 U B -32 " ideal model delta sinusoidal sigma weight residual -128.00 46.21 -174.21 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' G B -11 " pdb=" C1' G B -11 " pdb=" N9 G B -11 " pdb=" C4 G B -11 " ideal model delta sinusoidal sigma weight residual 70.00 -2.59 72.59 1 2.00e+01 2.50e-03 1.68e+01 dihedral pdb=" O4' A B -18 " pdb=" C1' A B -18 " pdb=" N9 A B -18 " pdb=" C4 A B -18 " ideal model delta sinusoidal sigma weight residual 70.00 -1.28 71.28 1 2.00e+01 2.50e-03 1.63e+01 ... (remaining 6046 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1237 0.046 - 0.092: 291 0.092 - 0.138: 42 0.138 - 0.184: 6 0.184 - 0.229: 3 Chirality restraints: 1579 Sorted by residual: chirality pdb=" C3' A B -8 " pdb=" C4' A B -8 " pdb=" O3' A B -8 " pdb=" C2' A B -8 " both_signs ideal model delta sigma weight residual False -2.48 -2.71 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" C1' U B 5 " pdb=" O4' U B 5 " pdb=" C2' U B 5 " pdb=" N1 U B 5 " both_signs ideal model delta sigma weight residual False 2.47 2.28 0.19 2.00e-01 2.50e+01 8.95e-01 chirality pdb=" C1' G B -36 " pdb=" O4' G B -36 " pdb=" C2' G B -36 " pdb=" N9 G B -36 " both_signs ideal model delta sigma weight residual False 2.46 2.27 0.19 2.00e-01 2.50e+01 8.59e-01 ... (remaining 1576 not shown) Planarity restraints: 1438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 806 " 0.065 5.00e-02 4.00e+02 9.82e-02 1.54e+01 pdb=" N PRO A 807 " -0.170 5.00e-02 4.00e+02 pdb=" CA PRO A 807 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 807 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A B -31 " 0.035 2.00e-02 2.50e+03 1.61e-02 7.12e+00 pdb=" N9 A B -31 " -0.037 2.00e-02 2.50e+03 pdb=" C8 A B -31 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A B -31 " 0.003 2.00e-02 2.50e+03 pdb=" C5 A B -31 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A B -31 " 0.007 2.00e-02 2.50e+03 pdb=" N6 A B -31 " 0.006 2.00e-02 2.50e+03 pdb=" N1 A B -31 " 0.004 2.00e-02 2.50e+03 pdb=" C2 A B -31 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A B -31 " -0.005 2.00e-02 2.50e+03 pdb=" C4 A B -31 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C B 1 " 0.028 2.00e-02 2.50e+03 1.54e-02 5.31e+00 pdb=" N1 C B 1 " -0.036 2.00e-02 2.50e+03 pdb=" C2 C B 1 " -0.002 2.00e-02 2.50e+03 pdb=" O2 C B 1 " 0.000 2.00e-02 2.50e+03 pdb=" N3 C B 1 " 0.000 2.00e-02 2.50e+03 pdb=" C4 C B 1 " 0.002 2.00e-02 2.50e+03 pdb=" N4 C B 1 " 0.008 2.00e-02 2.50e+03 pdb=" C5 C B 1 " 0.003 2.00e-02 2.50e+03 pdb=" C6 C B 1 " -0.004 2.00e-02 2.50e+03 ... (remaining 1435 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1030 2.74 - 3.28: 9166 3.28 - 3.82: 17008 3.82 - 4.36: 18905 4.36 - 4.90: 30721 Nonbonded interactions: 76830 Sorted by model distance: nonbonded pdb=" OG SER A 125 " pdb=" N4 DC D 1 " model vdw 2.198 3.120 nonbonded pdb=" OD1 ASN A 124 " pdb=" N SER A 125 " model vdw 2.210 3.120 nonbonded pdb=" OH TYR A 107 " pdb=" NZ LYS A 144 " model vdw 2.221 3.120 nonbonded pdb=" O SER A 892 " pdb=" OG SER A 892 " model vdw 2.237 3.040 nonbonded pdb=" OP2 G B -15 " pdb=" N2 G B -15 " model vdw 2.245 3.120 ... (remaining 76825 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.440 Find NCS groups from input model: 0.040 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10072 Z= 0.198 Angle : 0.659 8.609 14015 Z= 0.353 Chirality : 0.040 0.229 1579 Planarity : 0.004 0.098 1438 Dihedral : 22.960 174.205 4275 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.29 % Favored : 93.60 % Rotamer: Outliers : 0.83 % Allowed : 33.06 % Favored : 66.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.38 (0.28), residues: 922 helix: 1.86 (0.26), residues: 425 sheet: 0.44 (0.46), residues: 126 loop : -1.84 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 668 TYR 0.011 0.001 TYR A 92 PHE 0.017 0.002 PHE A 325 TRP 0.016 0.002 TRP A 382 HIS 0.012 0.001 HIS A 376 Details of bonding type rmsd covalent geometry : bond 0.00424 (10072) covalent geometry : angle 0.65917 (14015) hydrogen bonds : bond 0.11553 ( 433) hydrogen bonds : angle 4.65810 ( 1196) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 134 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 138 average time/residue: 0.1346 time to fit residues: 24.5097 Evaluate side-chains 68 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 886 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.4980 chunk 100 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 0.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN A 294 GLN A 429 GLN A 768 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.088228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.063429 restraints weight = 32468.020| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 4.12 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10072 Z= 0.155 Angle : 0.616 11.526 14015 Z= 0.326 Chirality : 0.038 0.218 1579 Planarity : 0.004 0.065 1438 Dihedral : 22.731 178.144 2336 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.88 % Favored : 95.01 % Rotamer: Outliers : 4.38 % Allowed : 28.67 % Favored : 66.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.67 (0.28), residues: 922 helix: 2.15 (0.26), residues: 425 sheet: 0.55 (0.51), residues: 113 loop : -1.66 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 226 TYR 0.010 0.001 TYR A 107 PHE 0.010 0.001 PHE A 552 TRP 0.014 0.001 TRP A 382 HIS 0.008 0.001 HIS A 376 Details of bonding type rmsd covalent geometry : bond 0.00340 (10072) covalent geometry : angle 0.61639 (14015) hydrogen bonds : bond 0.04152 ( 433) hydrogen bonds : angle 3.73975 ( 1196) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 66 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.9140 (mtm) cc_final: 0.8826 (mtt) REVERT: A 280 TRP cc_start: 0.7428 (m-10) cc_final: 0.7224 (m-10) REVERT: A 479 GLN cc_start: 0.8847 (tm-30) cc_final: 0.8611 (tm-30) REVERT: A 501 ASN cc_start: 0.8900 (OUTLIER) cc_final: 0.7890 (t0) REVERT: A 709 GLU cc_start: 0.8994 (mm-30) cc_final: 0.8214 (mt-10) REVERT: A 805 LEU cc_start: 0.9603 (OUTLIER) cc_final: 0.9399 (mp) outliers start: 37 outliers final: 13 residues processed: 100 average time/residue: 0.1382 time to fit residues: 18.2781 Evaluate side-chains 72 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 TYR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 776 HIS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 840 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 34 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 98 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 30 optimal weight: 20.0000 chunk 58 optimal weight: 5.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.083995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.058355 restraints weight = 33614.364| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 4.22 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10072 Z= 0.232 Angle : 0.634 8.962 14015 Z= 0.338 Chirality : 0.040 0.182 1579 Planarity : 0.004 0.059 1438 Dihedral : 22.730 176.386 2334 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.10 % Favored : 94.79 % Rotamer: Outliers : 4.03 % Allowed : 29.03 % Favored : 66.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.65 (0.28), residues: 922 helix: 2.10 (0.26), residues: 427 sheet: 0.47 (0.48), residues: 114 loop : -1.62 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 226 TYR 0.011 0.002 TYR A 594 PHE 0.013 0.001 PHE A 715 TRP 0.014 0.002 TRP A 382 HIS 0.010 0.001 HIS A 376 Details of bonding type rmsd covalent geometry : bond 0.00509 (10072) covalent geometry : angle 0.63428 (14015) hydrogen bonds : bond 0.04522 ( 433) hydrogen bonds : angle 3.84180 ( 1196) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 54 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.9181 (mtm) cc_final: 0.8915 (mtt) REVERT: A 121 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.7250 (ptt-90) REVERT: A 130 PRO cc_start: 0.7804 (Cg_endo) cc_final: 0.7290 (Cg_exo) REVERT: A 154 MET cc_start: 0.8932 (tpp) cc_final: 0.8548 (ttm) REVERT: A 479 GLN cc_start: 0.8867 (tm-30) cc_final: 0.8548 (tm-30) REVERT: A 639 ARG cc_start: 0.8313 (mmt90) cc_final: 0.8054 (mmt-90) outliers start: 34 outliers final: 17 residues processed: 83 average time/residue: 0.1185 time to fit residues: 13.6566 Evaluate side-chains 66 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 48 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 29 TYR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 776 HIS Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 840 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 1 optimal weight: 0.5980 chunk 12 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 26 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.085284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.059976 restraints weight = 33361.130| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 4.19 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10072 Z= 0.157 Angle : 0.578 8.717 14015 Z= 0.306 Chirality : 0.038 0.196 1579 Planarity : 0.003 0.053 1438 Dihedral : 22.616 178.394 2334 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.66 % Favored : 95.23 % Rotamer: Outliers : 4.38 % Allowed : 28.79 % Favored : 66.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.83 (0.29), residues: 922 helix: 2.30 (0.26), residues: 429 sheet: 0.52 (0.48), residues: 115 loop : -1.61 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 79 TYR 0.008 0.001 TYR A 652 PHE 0.011 0.001 PHE A 832 TRP 0.012 0.001 TRP A 382 HIS 0.006 0.001 HIS A 376 Details of bonding type rmsd covalent geometry : bond 0.00339 (10072) covalent geometry : angle 0.57793 (14015) hydrogen bonds : bond 0.04006 ( 433) hydrogen bonds : angle 3.62183 ( 1196) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 54 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.9152 (mtm) cc_final: 0.8934 (mtt) REVERT: A 154 MET cc_start: 0.8964 (tpp) cc_final: 0.8572 (ttm) REVERT: A 407 LYS cc_start: 0.9305 (OUTLIER) cc_final: 0.8978 (tptp) REVERT: A 431 ARG cc_start: 0.8417 (mtp-110) cc_final: 0.7814 (ptm160) REVERT: A 479 GLN cc_start: 0.8841 (tm-30) cc_final: 0.8346 (tm-30) outliers start: 37 outliers final: 17 residues processed: 84 average time/residue: 0.1252 time to fit residues: 14.4120 Evaluate side-chains 68 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 29 TYR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 776 HIS Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 936 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 46 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 78 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 GLN A 634 HIS ** A 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.083256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.057896 restraints weight = 33978.957| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 4.22 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10072 Z= 0.200 Angle : 0.603 8.402 14015 Z= 0.321 Chirality : 0.039 0.183 1579 Planarity : 0.003 0.049 1438 Dihedral : 22.603 175.781 2334 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.88 % Favored : 95.01 % Rotamer: Outliers : 4.38 % Allowed : 28.67 % Favored : 66.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.82 (0.28), residues: 922 helix: 2.39 (0.26), residues: 422 sheet: 0.45 (0.47), residues: 115 loop : -1.65 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 758 TYR 0.009 0.001 TYR A 594 PHE 0.010 0.001 PHE A 626 TRP 0.011 0.001 TRP A 382 HIS 0.006 0.001 HIS A 376 Details of bonding type rmsd covalent geometry : bond 0.00433 (10072) covalent geometry : angle 0.60321 (14015) hydrogen bonds : bond 0.04273 ( 433) hydrogen bonds : angle 3.69828 ( 1196) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 46 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.9236 (mtm) cc_final: 0.8997 (mtt) REVERT: A 154 MET cc_start: 0.9005 (tpp) cc_final: 0.8568 (ttm) REVERT: A 407 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.8944 (tptp) REVERT: A 479 GLN cc_start: 0.8848 (tm-30) cc_final: 0.8396 (tm-30) REVERT: A 501 ASN cc_start: 0.8785 (OUTLIER) cc_final: 0.7981 (t0) REVERT: A 583 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7500 (ptm160) REVERT: A 810 MET cc_start: 0.9321 (mmt) cc_final: 0.9100 (mmt) outliers start: 37 outliers final: 23 residues processed: 79 average time/residue: 0.1115 time to fit residues: 12.3881 Evaluate side-chains 70 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 44 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 29 TYR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 634 HIS Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 776 HIS Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 936 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 37 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 92 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 61 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 73 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 HIS A 505 ASN ** A 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.081796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.056429 restraints weight = 34137.373| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 4.19 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.030 10072 Z= 0.256 Angle : 0.629 8.594 14015 Z= 0.335 Chirality : 0.040 0.187 1579 Planarity : 0.003 0.049 1438 Dihedral : 22.700 175.611 2334 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.42 % Favored : 94.47 % Rotamer: Outliers : 4.62 % Allowed : 29.15 % Favored : 66.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.77 (0.28), residues: 922 helix: 2.31 (0.26), residues: 420 sheet: 0.33 (0.47), residues: 115 loop : -1.56 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 121 TYR 0.010 0.001 TYR A 594 PHE 0.010 0.001 PHE A 204 TRP 0.011 0.001 TRP A 382 HIS 0.007 0.001 HIS A 634 Details of bonding type rmsd covalent geometry : bond 0.00554 (10072) covalent geometry : angle 0.62913 (14015) hydrogen bonds : bond 0.04547 ( 433) hydrogen bonds : angle 3.82904 ( 1196) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 44 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.9231 (mtm) cc_final: 0.9022 (mtt) REVERT: A 125 SER cc_start: 0.9594 (OUTLIER) cc_final: 0.9328 (m) REVERT: A 407 LYS cc_start: 0.9336 (OUTLIER) cc_final: 0.8984 (tptp) REVERT: A 479 GLN cc_start: 0.8854 (tm-30) cc_final: 0.8404 (tm-30) REVERT: A 489 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8624 (mt) REVERT: A 501 ASN cc_start: 0.8749 (OUTLIER) cc_final: 0.7952 (t0) REVERT: A 583 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7484 (ptm160) outliers start: 39 outliers final: 25 residues processed: 80 average time/residue: 0.1129 time to fit residues: 12.6193 Evaluate side-chains 71 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 41 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 29 TYR Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 634 HIS Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 776 HIS Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 936 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 71 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 GLN A 634 HIS A 907 GLN A 912 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.083596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.058040 restraints weight = 34070.700| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 4.28 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10072 Z= 0.139 Angle : 0.572 8.398 14015 Z= 0.303 Chirality : 0.037 0.196 1579 Planarity : 0.003 0.047 1438 Dihedral : 22.576 177.847 2332 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.88 % Favored : 95.01 % Rotamer: Outliers : 3.55 % Allowed : 29.98 % Favored : 66.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.92 (0.29), residues: 922 helix: 2.48 (0.26), residues: 422 sheet: 0.63 (0.48), residues: 113 loop : -1.66 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 758 TYR 0.007 0.001 TYR A 8 PHE 0.012 0.001 PHE A 626 TRP 0.011 0.001 TRP A 382 HIS 0.005 0.001 HIS A 634 Details of bonding type rmsd covalent geometry : bond 0.00297 (10072) covalent geometry : angle 0.57209 (14015) hydrogen bonds : bond 0.03928 ( 433) hydrogen bonds : angle 3.55508 ( 1196) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 47 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 SER cc_start: 0.9549 (OUTLIER) cc_final: 0.9290 (m) REVERT: A 154 MET cc_start: 0.8968 (tpp) cc_final: 0.8492 (ttm) REVERT: A 407 LYS cc_start: 0.9339 (OUTLIER) cc_final: 0.9009 (tptp) REVERT: A 479 GLN cc_start: 0.8826 (tm-30) cc_final: 0.8360 (tm-30) REVERT: A 501 ASN cc_start: 0.8712 (OUTLIER) cc_final: 0.7826 (t0) REVERT: A 583 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7597 (ptm160) REVERT: A 717 ASN cc_start: 0.9374 (OUTLIER) cc_final: 0.8949 (m110) REVERT: A 777 ARG cc_start: 0.8345 (tpp80) cc_final: 0.7982 (ttm170) outliers start: 30 outliers final: 15 residues processed: 74 average time/residue: 0.1256 time to fit residues: 12.7300 Evaluate side-chains 64 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 44 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 29 TYR Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 634 HIS Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 776 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 38 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 37 optimal weight: 0.0970 chunk 54 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 57 optimal weight: 0.0970 chunk 90 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 overall best weight: 0.5776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 GLN A 538 GLN A 630 ASN A 634 HIS A 701 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.085356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.060354 restraints weight = 34162.902| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 4.24 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10072 Z= 0.119 Angle : 0.564 8.299 14015 Z= 0.298 Chirality : 0.037 0.324 1579 Planarity : 0.003 0.046 1438 Dihedral : 22.488 177.890 2332 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.56 % Favored : 95.34 % Rotamer: Outliers : 3.20 % Allowed : 30.09 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.04 (0.28), residues: 922 helix: 2.64 (0.26), residues: 419 sheet: 0.74 (0.48), residues: 110 loop : -1.63 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 758 TYR 0.007 0.001 TYR A 39 PHE 0.015 0.001 PHE A 552 TRP 0.010 0.001 TRP A 382 HIS 0.017 0.001 HIS A 634 Details of bonding type rmsd covalent geometry : bond 0.00250 (10072) covalent geometry : angle 0.56407 (14015) hydrogen bonds : bond 0.03620 ( 433) hydrogen bonds : angle 3.44385 ( 1196) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 47 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 SER cc_start: 0.9487 (OUTLIER) cc_final: 0.9241 (m) REVERT: A 154 MET cc_start: 0.8959 (tpp) cc_final: 0.8623 (ttm) REVERT: A 248 MET cc_start: 0.8946 (mmt) cc_final: 0.8147 (mmm) REVERT: A 407 LYS cc_start: 0.9331 (OUTLIER) cc_final: 0.9016 (tptp) REVERT: A 479 GLN cc_start: 0.8836 (tm-30) cc_final: 0.8322 (tm-30) REVERT: A 489 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8624 (mt) REVERT: A 501 ASN cc_start: 0.8712 (OUTLIER) cc_final: 0.7851 (t0) REVERT: A 583 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7635 (ptm160) REVERT: A 639 ARG cc_start: 0.7977 (mmt180) cc_final: 0.7520 (mpt180) REVERT: A 717 ASN cc_start: 0.9299 (OUTLIER) cc_final: 0.8913 (m110) REVERT: A 777 ARG cc_start: 0.8356 (tpp80) cc_final: 0.7997 (ttm170) outliers start: 27 outliers final: 14 residues processed: 72 average time/residue: 0.1183 time to fit residues: 11.8168 Evaluate side-chains 64 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 44 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 29 TYR Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 776 HIS Chi-restraints excluded: chain A residue 861 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 54 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 80 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 ASN A 701 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.084407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.059392 restraints weight = 33999.371| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 4.24 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10072 Z= 0.148 Angle : 0.573 10.701 14015 Z= 0.302 Chirality : 0.038 0.281 1579 Planarity : 0.003 0.047 1438 Dihedral : 22.479 176.401 2332 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.88 % Favored : 95.01 % Rotamer: Outliers : 3.32 % Allowed : 29.74 % Favored : 66.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.04 (0.28), residues: 922 helix: 2.60 (0.26), residues: 420 sheet: 0.77 (0.48), residues: 110 loop : -1.60 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 758 TYR 0.008 0.001 TYR A 627 PHE 0.015 0.001 PHE A 552 TRP 0.009 0.001 TRP A 382 HIS 0.004 0.001 HIS A 701 Details of bonding type rmsd covalent geometry : bond 0.00321 (10072) covalent geometry : angle 0.57281 (14015) hydrogen bonds : bond 0.03723 ( 433) hydrogen bonds : angle 3.49929 ( 1196) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 48 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 SER cc_start: 0.9498 (OUTLIER) cc_final: 0.9258 (m) REVERT: A 154 MET cc_start: 0.9009 (tpp) cc_final: 0.8625 (ttm) REVERT: A 201 MET cc_start: 0.8279 (tpp) cc_final: 0.8040 (tpp) REVERT: A 248 MET cc_start: 0.8961 (mmt) cc_final: 0.8170 (mmm) REVERT: A 407 LYS cc_start: 0.9338 (OUTLIER) cc_final: 0.9005 (tptp) REVERT: A 428 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8450 (tt) REVERT: A 479 GLN cc_start: 0.8814 (tm-30) cc_final: 0.8353 (tm-30) REVERT: A 489 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8631 (mt) REVERT: A 501 ASN cc_start: 0.8726 (OUTLIER) cc_final: 0.7865 (t0) REVERT: A 583 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7604 (ptm160) REVERT: A 639 ARG cc_start: 0.7967 (mmt180) cc_final: 0.7529 (mpt180) REVERT: A 717 ASN cc_start: 0.9324 (OUTLIER) cc_final: 0.8914 (m110) REVERT: A 758 ARG cc_start: 0.5449 (tmm160) cc_final: 0.4970 (ttp80) outliers start: 28 outliers final: 16 residues processed: 74 average time/residue: 0.1253 time to fit residues: 12.8260 Evaluate side-chains 68 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 45 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 29 TYR Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 776 HIS Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 861 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 66 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 98 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 ASN A 630 ASN A 634 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.081834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.056256 restraints weight = 34278.701| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 4.24 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 10072 Z= 0.228 Angle : 0.622 10.060 14015 Z= 0.330 Chirality : 0.040 0.266 1579 Planarity : 0.003 0.048 1438 Dihedral : 22.617 174.035 2332 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.42 % Favored : 94.47 % Rotamer: Outliers : 3.55 % Allowed : 29.50 % Favored : 66.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.85 (0.28), residues: 922 helix: 2.38 (0.26), residues: 421 sheet: 0.59 (0.48), residues: 114 loop : -1.63 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 758 TYR 0.009 0.001 TYR A 594 PHE 0.016 0.001 PHE A 552 TRP 0.011 0.001 TRP A 244 HIS 0.005 0.001 HIS A 631 Details of bonding type rmsd covalent geometry : bond 0.00496 (10072) covalent geometry : angle 0.62180 (14015) hydrogen bonds : bond 0.04357 ( 433) hydrogen bonds : angle 3.78299 ( 1196) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 42 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 125 SER cc_start: 0.9545 (OUTLIER) cc_final: 0.9293 (m) REVERT: A 407 LYS cc_start: 0.9334 (OUTLIER) cc_final: 0.8980 (tptp) REVERT: A 479 GLN cc_start: 0.8851 (tm-30) cc_final: 0.8411 (tm-30) REVERT: A 489 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8552 (mt) REVERT: A 501 ASN cc_start: 0.8715 (OUTLIER) cc_final: 0.7857 (t0) REVERT: A 581 MET cc_start: 0.8505 (ttt) cc_final: 0.7884 (ppp) REVERT: A 583 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7533 (ptm160) REVERT: A 639 ARG cc_start: 0.7953 (mmt180) cc_final: 0.7707 (mmt180) REVERT: A 717 ASN cc_start: 0.9411 (OUTLIER) cc_final: 0.8979 (m-40) REVERT: A 758 ARG cc_start: 0.5526 (tmm160) cc_final: 0.5098 (tmm160) REVERT: A 777 ARG cc_start: 0.8336 (tpp80) cc_final: 0.7889 (mtp85) outliers start: 30 outliers final: 21 residues processed: 69 average time/residue: 0.1187 time to fit residues: 11.4332 Evaluate side-chains 68 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 41 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 29 TYR Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 634 HIS Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 861 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.3980 chunk 16 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 85 optimal weight: 0.4980 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 GLN A 505 ASN ** A 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.084882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.059997 restraints weight = 33878.745| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 4.20 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10072 Z= 0.126 Angle : 0.579 8.803 14015 Z= 0.305 Chirality : 0.038 0.261 1579 Planarity : 0.003 0.047 1438 Dihedral : 22.523 176.949 2332 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.66 % Favored : 95.23 % Rotamer: Outliers : 3.20 % Allowed : 30.09 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.00 (0.29), residues: 922 helix: 2.53 (0.26), residues: 423 sheet: 0.68 (0.48), residues: 115 loop : -1.62 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 226 TYR 0.009 0.001 TYR A 229 PHE 0.014 0.001 PHE A 552 TRP 0.011 0.001 TRP A 382 HIS 0.009 0.001 HIS A 631 Details of bonding type rmsd covalent geometry : bond 0.00265 (10072) covalent geometry : angle 0.57907 (14015) hydrogen bonds : bond 0.03752 ( 433) hydrogen bonds : angle 3.49384 ( 1196) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2037.41 seconds wall clock time: 35 minutes 59.24 seconds (2159.24 seconds total)