Starting phenix.real_space_refine on Tue Mar 11 14:30:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3j9d_6239/03_2025/3j9d_6239.cif Found real_map, /net/cci-nas-00/data/ceres_data/3j9d_6239/03_2025/3j9d_6239.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/3j9d_6239/03_2025/3j9d_6239.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3j9d_6239/03_2025/3j9d_6239.map" model { file = "/net/cci-nas-00/data/ceres_data/3j9d_6239/03_2025/3j9d_6239.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3j9d_6239/03_2025/3j9d_6239.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.013 sd= 0.220 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 Zn 1 6.06 5 S 32 5.16 5 C 3891 2.51 5 N 1057 2.21 5 O 1105 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6086 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 746, 6085 Classifications: {'peptide': 746} Link IDs: {'CIS': 14, 'PCIS': 2, 'PTRANS': 28, 'TRANS': 701} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1310 SG CYS A 162 20.064 54.313 30.963 1.00 92.09 S ATOM 3290 SG CYS A 617 23.647 56.157 31.648 1.00 70.99 S ATOM 5217 SG CYS A 851 20.362 53.869 34.614 1.00 39.61 S Time building chain proxies: 3.95, per 1000 atoms: 0.65 Number of scatterers: 6086 At special positions: 0 Unit cell: (84.84, 107.06, 81.81, 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) Zn 1 29.99 S 32 16.00 O 1105 8.00 N 1057 7.00 C 3891 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: 1.79 Conformation dependent library (CDL) restraints added in 811.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" NE2 HIS A 164 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 162 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 617 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 851 " Number of angles added : 3 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1414 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 8 sheets defined 35.9% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 40 through 43 Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 74 through 85 Processing helix chain 'A' and resid 103 through 110 Processing helix chain 'A' and resid 144 through 148 removed outlier: 4.027A pdb=" N THR A 147 " --> pdb=" O LYS A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 161 Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 166 through 176 Processing helix chain 'A' and resid 412 through 416 removed outlier: 3.544A pdb=" N ASP A 415 " --> pdb=" O ASN A 412 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE A 416 " --> pdb=" O LEU A 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 412 through 416' Processing helix chain 'A' and resid 461 through 476 Processing helix chain 'A' and resid 484 through 488 removed outlier: 3.506A pdb=" N ILE A 487 " --> pdb=" O MET A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 527 Processing helix chain 'A' and resid 557 through 562 Processing helix chain 'A' and resid 589 through 596 Processing helix chain 'A' and resid 599 through 607 removed outlier: 3.917A pdb=" N ARG A 606 " --> pdb=" O GLU A 602 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG A 607 " --> pdb=" O ILE A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 638 removed outlier: 3.598A pdb=" N THR A 621 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 641 No H-bonds generated for 'chain 'A' and resid 639 through 641' Processing helix chain 'A' and resid 669 through 682 WARNING: missing atoms! Processing helix chain 'A' and resid 690 through 704 removed outlier: 3.817A pdb=" N MET A 704 " --> pdb=" O ARG A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 713 removed outlier: 3.851A pdb=" N LEU A 710 " --> pdb=" O GLY A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 725 Processing helix chain 'A' and resid 732 through 737 removed outlier: 3.998A pdb=" N ILE A 736 " --> pdb=" O VAL A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 741 Processing helix chain 'A' and resid 742 through 747 removed outlier: 4.454A pdb=" N PHE A 746 " --> pdb=" O LEU A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 791 removed outlier: 4.407A pdb=" N GLU A 791 " --> pdb=" O ILE A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 795 Processing helix chain 'A' and resid 798 through 804 Processing helix chain 'A' and resid 808 through 822 removed outlier: 4.476A pdb=" N LYS A 812 " --> pdb=" O GLU A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 837 Processing helix chain 'A' and resid 839 through 851 Processing helix chain 'A' and resid 882 through 892 Processing helix chain 'A' and resid 897 through 899 No H-bonds generated for 'chain 'A' and resid 897 through 899' Processing helix chain 'A' and resid 953 through 960 Processing sheet with id=A, first strand: chain 'A' and resid 130 through 133 removed outlier: 10.664A pdb=" N PHE A 23 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N GLY A 5 " --> pdb=" O PHE A 23 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N ILE A 25 " --> pdb=" O GLY A 5 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 4 " --> pdb=" O LEU A 942 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP A 938 " --> pdb=" O VAL A 8 " (cutoff:3.500A) Processing sheet with id=B, first strand: chain 'A' and resid 33 through 34 removed outlier: 3.864A pdb=" N ARG A 37 " --> pdb=" O VAL A 34 " (cutoff:3.500A) Processing sheet with id=C, first strand: chain 'A' and resid 70 through 71 Processing sheet with id=D, first strand: chain 'A' and resid 87 through 90 Processing sheet with id=E, first strand: chain 'A' and resid 149 through 150 removed outlier: 6.508A pdb=" N ILE A 871 " --> pdb=" O LEU A 901 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY A 903 " --> pdb=" O ILE A 871 " (cutoff:3.500A) Processing sheet with id=F, first strand: chain 'A' and resid 180 through 184 Processing sheet with id=G, first strand: chain 'A' and resid 409 through 410 Processing sheet with id=H, first strand: chain 'A' and resid 760 through 765 197 hydrogen bonds defined for protein. 528 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: 1.72 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.54: 6038 1.54 - 1.90: 179 1.90 - 2.25: 3 2.25 - 2.61: 0 2.61 - 2.96: 1 Bond restraints: 6221 Sorted by residual: bond pdb=" SD MET A 771 " pdb=" CE MET A 771 " ideal model delta sigma weight residual 1.791 2.960 -1.169 2.50e-02 1.60e+03 2.19e+03 bond pdb=" CD2 TYR A 465 " pdb=" CE2 TYR A 465 " ideal model delta sigma weight residual 1.382 2.067 -0.685 3.00e-02 1.11e+03 5.21e+02 bond pdb=" CD1 TYR A 465 " pdb=" CE1 TYR A 465 " ideal model delta sigma weight residual 1.382 2.059 -0.677 3.00e-02 1.11e+03 5.10e+02 bond pdb=" CE1 TYR A 465 " pdb=" CZ TYR A 465 " ideal model delta sigma weight residual 1.378 1.812 -0.434 2.40e-02 1.74e+03 3.27e+02 bond pdb=" CE2 TYR A 465 " pdb=" CZ TYR A 465 " ideal model delta sigma weight residual 1.378 1.801 -0.423 2.40e-02 1.74e+03 3.11e+02 ... (remaining 6216 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.72: 8251 5.72 - 11.43: 154 11.43 - 17.15: 13 17.15 - 22.86: 1 22.86 - 28.58: 1 Bond angle restraints: 8420 Sorted by residual: angle pdb=" N HIS A 16 " pdb=" CA HIS A 16 " pdb=" C HIS A 16 " ideal model delta sigma weight residual 111.11 95.49 15.62 1.20e+00 6.94e-01 1.70e+02 angle pdb=" CG MET A 771 " pdb=" SD MET A 771 " pdb=" CE MET A 771 " ideal model delta sigma weight residual 100.90 129.48 -28.58 2.20e+00 2.07e-01 1.69e+02 angle pdb=" C HIS A 653 " pdb=" N PRO A 654 " pdb=" CA PRO A 654 " ideal model delta sigma weight residual 119.84 104.48 15.36 1.25e+00 6.40e-01 1.51e+02 angle pdb=" N VAL A 27 " pdb=" CA VAL A 27 " pdb=" C VAL A 27 " ideal model delta sigma weight residual 112.29 122.07 -9.78 9.40e-01 1.13e+00 1.08e+02 angle pdb=" N GLU A 715 " pdb=" CA GLU A 715 " pdb=" C GLU A 715 " ideal model delta sigma weight residual 113.18 99.89 13.29 1.33e+00 5.65e-01 9.99e+01 ... (remaining 8415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 3047 17.68 - 35.36: 463 35.36 - 53.04: 191 53.04 - 70.72: 47 70.72 - 88.40: 8 Dihedral angle restraints: 3756 sinusoidal: 1560 harmonic: 2196 Sorted by residual: dihedral pdb=" CA VAL A 27 " pdb=" C VAL A 27 " pdb=" N GLY A 28 " pdb=" CA GLY A 28 " ideal model delta harmonic sigma weight residual 0.00 38.21 -38.21 0 5.00e+00 4.00e-02 5.84e+01 dihedral pdb=" CA HIS A 38 " pdb=" C HIS A 38 " pdb=" N ASP A 39 " pdb=" CA ASP A 39 " ideal model delta harmonic sigma weight residual -180.00 -145.72 -34.28 0 5.00e+00 4.00e-02 4.70e+01 dihedral pdb=" CA SER A 55 " pdb=" C SER A 55 " pdb=" N ILE A 56 " pdb=" CA ILE A 56 " ideal model delta harmonic sigma weight residual -180.00 -148.27 -31.73 0 5.00e+00 4.00e-02 4.03e+01 ... (remaining 3753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 749 0.101 - 0.203: 160 0.203 - 0.304: 17 0.304 - 0.405: 2 0.405 - 0.506: 1 Chirality restraints: 929 Sorted by residual: chirality pdb=" CA ASN A 63 " pdb=" N ASN A 63 " pdb=" C ASN A 63 " pdb=" CB ASN A 63 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.41e+00 chirality pdb=" CA ASN A 128 " pdb=" N ASN A 128 " pdb=" C ASN A 128 " pdb=" CB ASN A 128 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CB ILE A 670 " pdb=" CA ILE A 670 " pdb=" CG1 ILE A 670 " pdb=" CG2 ILE A 670 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.36e+00 ... (remaining 926 not shown) Planarity restraints: 1078 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 618 " -0.018 2.00e-02 2.50e+03 3.60e-02 1.29e+01 pdb=" C PRO A 618 " 0.062 2.00e-02 2.50e+03 pdb=" O PRO A 618 " -0.023 2.00e-02 2.50e+03 pdb=" N THR A 619 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 653 " 0.057 5.00e-02 4.00e+02 8.58e-02 1.18e+01 pdb=" N PRO A 654 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO A 654 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 654 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 16 " 0.016 2.00e-02 2.50e+03 3.34e-02 1.11e+01 pdb=" C HIS A 16 " -0.058 2.00e-02 2.50e+03 pdb=" O HIS A 16 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU A 17 " 0.019 2.00e-02 2.50e+03 ... (remaining 1075 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 158 2.61 - 3.18: 5710 3.18 - 3.75: 9704 3.75 - 4.33: 13753 4.33 - 4.90: 21601 Nonbonded interactions: 50926 Sorted by model distance: nonbonded pdb=" O ASN A 47 " pdb=" ND2 ASN A 47 " model vdw 2.034 3.120 nonbonded pdb=" O PHE A 803 " pdb=" N LYS A 805 " model vdw 2.131 3.120 nonbonded pdb=" NE ARG A 74 " pdb=" OD2 ASP A 114 " model vdw 2.162 3.120 nonbonded pdb=" N GLU A 184 " pdb=" OE1 GLU A 184 " model vdw 2.234 3.120 nonbonded pdb=" OG1 THR A 506 " pdb=" N THR A 507 " model vdw 2.247 3.120 ... (remaining 50921 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: 0.140 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: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.580 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 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 : 0.027 1.169 6221 Z= 1.945 Angle : 2.044 28.578 8420 Z= 1.291 Chirality : 0.083 0.506 929 Planarity : 0.009 0.086 1078 Dihedral : 20.567 88.397 2342 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 23.66 Ramachandran Plot: Outliers : 2.16 % Allowed : 8.22 % Favored : 89.62 % Rotamer: Outliers : 24.92 % Allowed : 16.97 % Favored : 58.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 1.82 % Twisted Proline : 0.00 % Twisted General : 0.84 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.64 (0.29), residues: 742 helix: -3.11 (0.25), residues: 222 sheet: -2.97 (0.37), residues: 153 loop : -1.54 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.004 TRP A 107 HIS 0.015 0.003 HIS A 653 PHE 0.036 0.005 PHE A 23 TYR 0.038 0.005 TYR A 827 ARG 0.007 0.001 ARG A 709 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 144 time to evaluate : 0.728 Fit side-chains TARDY: cannot create tardy model for: "SER A 671 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 15 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8628 (tt0) REVERT: A 22 GLU cc_start: 0.9444 (tt0) cc_final: 0.9192 (tt0) REVERT: A 56 ILE cc_start: 0.9492 (OUTLIER) cc_final: 0.9055 (tp) REVERT: A 118 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9292 (mt) REVERT: A 119 LYS cc_start: 0.9358 (OUTLIER) cc_final: 0.8890 (tttp) REVERT: A 156 GLU cc_start: 0.7009 (pt0) cc_final: 0.4953 (tt0) REVERT: A 168 MET cc_start: 0.9255 (OUTLIER) cc_final: 0.9017 (tpp) REVERT: A 413 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9118 (mt) REVERT: A 467 GLN cc_start: 0.8661 (mt0) cc_final: 0.8316 (tt0) REVERT: A 486 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.8949 (mtmt) REVERT: A 501 LYS cc_start: 0.7210 (OUTLIER) cc_final: 0.6839 (mmtp) REVERT: A 529 LYS cc_start: 0.8998 (tttm) cc_final: 0.8794 (ttpt) REVERT: A 540 ARG cc_start: 0.8091 (ptp90) cc_final: 0.7401 (ptm-80) REVERT: A 552 SER cc_start: 0.9261 (t) cc_final: 0.8927 (p) REVERT: A 576 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.8985 (mt) REVERT: A 577 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.8520 (ttm170) REVERT: A 584 GLN cc_start: 0.9327 (OUTLIER) cc_final: 0.8569 (tt0) REVERT: A 606 ARG cc_start: 0.9541 (OUTLIER) cc_final: 0.9340 (mtp-110) REVERT: A 625 THR cc_start: 0.9687 (OUTLIER) cc_final: 0.9347 (m) REVERT: A 627 GLU cc_start: 0.9489 (OUTLIER) cc_final: 0.8786 (tm-30) REVERT: A 638 GLN cc_start: 0.9522 (OUTLIER) cc_final: 0.9246 (mt0) REVERT: A 641 VAL cc_start: 0.9394 (t) cc_final: 0.9065 (m) REVERT: A 681 ILE cc_start: 0.9537 (OUTLIER) cc_final: 0.9256 (mp) REVERT: A 687 ARG cc_start: 0.9119 (ttm110) cc_final: 0.8892 (ttm-80) REVERT: A 692 TYR cc_start: 0.9546 (m-80) cc_final: 0.9315 (m-80) REVERT: A 704 MET cc_start: 0.9360 (OUTLIER) cc_final: 0.9106 (mmm) REVERT: A 733 VAL cc_start: 0.9325 (OUTLIER) cc_final: 0.8975 (t) REVERT: A 758 GLN cc_start: 0.8957 (mt0) cc_final: 0.8575 (mt0) REVERT: A 769 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7055 (pm20) REVERT: A 784 CYS cc_start: 0.8758 (OUTLIER) cc_final: 0.7992 (p) REVERT: A 818 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8847 (tp) REVERT: A 819 LYS cc_start: 0.9273 (OUTLIER) cc_final: 0.8966 (tttp) REVERT: A 842 LEU cc_start: 0.9503 (OUTLIER) cc_final: 0.9251 (tp) REVERT: A 879 GLU cc_start: 0.8813 (tp30) cc_final: 0.8510 (tm-30) REVERT: A 934 LYS cc_start: 0.9317 (OUTLIER) cc_final: 0.8385 (ttmt) REVERT: A 959 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9286 (mt) outliers start: 166 outliers final: 72 residues processed: 273 average time/residue: 0.2283 time to fit residues: 76.9789 Evaluate side-chains 210 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 113 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 16 HIS Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 486 LYS Chi-restraints excluded: chain A residue 501 LYS Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 584 GLN Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 606 ARG Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 638 GLN Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 679 ASP Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 704 MET Chi-restraints excluded: chain A residue 708 GLU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 757 ARG Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 769 GLU Chi-restraints excluded: chain A residue 784 CYS Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 819 LYS Chi-restraints excluded: chain A residue 823 ASN Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 839 LYS Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 856 ASP Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 929 LYS Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 956 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 961 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 HIS ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 HIS A 947 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.102293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.086086 restraints weight = 8780.304| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 1.63 r_work: 0.2741 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 1.165 6221 Z= 1.641 Angle : 0.898 28.890 8420 Z= 0.458 Chirality : 0.048 0.175 929 Planarity : 0.005 0.052 1078 Dihedral : 15.035 59.699 1033 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.67 % Allowed : 7.55 % Favored : 91.78 % Rotamer: Outliers : 11.86 % Allowed : 20.72 % Favored : 67.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 1.96 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.29), residues: 742 helix: -1.40 (0.31), residues: 223 sheet: -2.21 (0.37), residues: 150 loop : -1.62 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 61 HIS 0.010 0.002 HIS A 658 PHE 0.020 0.002 PHE A 796 TYR 0.025 0.002 TYR A 62 ARG 0.005 0.001 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 143 time to evaluate : 0.663 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "SER A 671 " (corrupted residue). Skipping it. REVERT: A 22 GLU cc_start: 0.8948 (tt0) cc_final: 0.8704 (tt0) REVERT: A 56 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8721 (tp) REVERT: A 156 GLU cc_start: 0.5197 (pt0) cc_final: 0.4472 (tt0) REVERT: A 168 MET cc_start: 0.8876 (tmm) cc_final: 0.8625 (tpp) REVERT: A 487 ILE cc_start: 0.9370 (pt) cc_final: 0.9147 (pt) REVERT: A 501 LYS cc_start: 0.7244 (OUTLIER) cc_final: 0.7014 (mmtp) REVERT: A 540 ARG cc_start: 0.7914 (ptp90) cc_final: 0.7443 (ptm-80) REVERT: A 560 GLU cc_start: 0.7930 (tp30) cc_final: 0.7588 (tt0) REVERT: A 592 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7493 (tm-30) REVERT: A 687 ARG cc_start: 0.8443 (ttm110) cc_final: 0.8226 (ttm-80) REVERT: A 692 TYR cc_start: 0.8929 (m-80) cc_final: 0.8178 (m-80) REVERT: A 704 MET cc_start: 0.9109 (mpp) cc_final: 0.8760 (mmp) REVERT: A 733 VAL cc_start: 0.8950 (OUTLIER) cc_final: 0.8509 (t) REVERT: A 798 SER cc_start: 0.8707 (m) cc_final: 0.8311 (p) REVERT: A 810 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8138 (mt0) REVERT: A 819 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8385 (tttm) REVERT: A 879 GLU cc_start: 0.7793 (tp30) cc_final: 0.7530 (tm-30) outliers start: 79 outliers final: 44 residues processed: 208 average time/residue: 0.1802 time to fit residues: 48.9914 Evaluate side-chains 160 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 111 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 16 HIS Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 501 LYS Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 658 HIS Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 810 GLN Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 819 LYS Chi-restraints excluded: chain A residue 823 ASN Chi-restraints excluded: chain A residue 856 ASP Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 956 THR Chi-restraints excluded: chain A residue 961 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 68 optimal weight: 0.4980 chunk 20 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 ASN ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 GLN A 735 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.104119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.087959 restraints weight = 8894.231| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 1.63 r_work: 0.2778 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 1.165 6221 Z= 1.638 Angle : 0.805 28.728 8420 Z= 0.411 Chirality : 0.047 0.177 929 Planarity : 0.004 0.043 1078 Dihedral : 11.663 59.708 908 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.67 % Allowed : 7.82 % Favored : 91.51 % Rotamer: Outliers : 8.86 % Allowed : 24.02 % Favored : 67.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 1.96 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.29), residues: 742 helix: -0.53 (0.33), residues: 219 sheet: -2.12 (0.36), residues: 144 loop : -1.63 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.004 0.001 HIS A 658 PHE 0.016 0.002 PHE A 796 TYR 0.021 0.002 TYR A 62 ARG 0.007 0.000 ARG A 597 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 130 time to evaluate : 0.629 Fit side-chains TARDY: cannot create tardy model for: "SER A 671 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 16 HIS cc_start: 0.5187 (OUTLIER) cc_final: 0.4976 (t70) REVERT: A 22 GLU cc_start: 0.8934 (tt0) cc_final: 0.8671 (tt0) REVERT: A 156 GLU cc_start: 0.5292 (pt0) cc_final: 0.4471 (tt0) REVERT: A 168 MET cc_start: 0.8786 (tmm) cc_final: 0.8563 (tpp) REVERT: A 177 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8177 (mt-10) REVERT: A 540 ARG cc_start: 0.7919 (ptp90) cc_final: 0.7412 (ptm-80) REVERT: A 686 ARG cc_start: 0.8959 (ttm-80) cc_final: 0.8679 (mtt-85) REVERT: A 687 ARG cc_start: 0.8372 (ttm110) cc_final: 0.8169 (ttm-80) REVERT: A 692 TYR cc_start: 0.8964 (m-80) cc_final: 0.8198 (m-80) REVERT: A 704 MET cc_start: 0.9086 (mpp) cc_final: 0.8853 (mmp) REVERT: A 793 MET cc_start: 0.8812 (mmm) cc_final: 0.8544 (mmm) REVERT: A 798 SER cc_start: 0.8594 (m) cc_final: 0.8254 (p) REVERT: A 810 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.8193 (mt0) REVERT: A 819 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8258 (tttm) REVERT: A 844 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7936 (mt-10) outliers start: 59 outliers final: 38 residues processed: 176 average time/residue: 0.1806 time to fit residues: 41.6313 Evaluate side-chains 161 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 119 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 16 HIS Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 810 GLN Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 819 LYS Chi-restraints excluded: chain A residue 823 ASN Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 856 ASP Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 956 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 15 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 7 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 ASN A 474 ASN ** A 541 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 = 0.3089 r_free = 0.3089 target = 0.103602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.087360 restraints weight = 9068.101| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 1.64 r_work: 0.2768 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 1.166 6221 Z= 1.643 Angle : 0.797 28.357 8420 Z= 0.405 Chirality : 0.047 0.184 929 Planarity : 0.004 0.031 1078 Dihedral : 10.513 59.514 884 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.67 % Allowed : 7.55 % Favored : 91.78 % Rotamer: Outliers : 8.11 % Allowed : 25.68 % Favored : 66.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 1.96 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.29), residues: 742 helix: -0.42 (0.34), residues: 226 sheet: -2.01 (0.37), residues: 134 loop : -1.76 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 107 HIS 0.005 0.001 HIS A 658 PHE 0.017 0.001 PHE A 796 TYR 0.022 0.002 TYR A 62 ARG 0.004 0.000 ARG A 597 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 122 time to evaluate : 0.734 Fit side-chains TARDY: cannot create tardy model for: "SER A 671 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 22 GLU cc_start: 0.9005 (tt0) cc_final: 0.8750 (tt0) REVERT: A 106 GLN cc_start: 0.8403 (mm-40) cc_final: 0.8042 (mt0) REVERT: A 156 GLU cc_start: 0.5787 (pt0) cc_final: 0.4994 (mt-10) REVERT: A 168 MET cc_start: 0.8766 (tmm) cc_final: 0.8537 (tpp) REVERT: A 177 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8188 (mt-10) REVERT: A 183 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8321 (mm-40) REVERT: A 540 ARG cc_start: 0.7952 (ptp90) cc_final: 0.7447 (ptm-80) REVERT: A 687 ARG cc_start: 0.8380 (ttm110) cc_final: 0.8138 (ttm-80) REVERT: A 692 TYR cc_start: 0.9011 (m-80) cc_final: 0.8261 (m-80) REVERT: A 704 MET cc_start: 0.9088 (mpp) cc_final: 0.8886 (mmp) REVERT: A 793 MET cc_start: 0.8826 (mmm) cc_final: 0.8463 (mmm) REVERT: A 798 SER cc_start: 0.8687 (m) cc_final: 0.8325 (p) REVERT: A 810 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.7858 (mt0) REVERT: A 819 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8275 (tttm) REVERT: A 844 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7986 (mt-10) REVERT: A 934 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8685 (ttmt) outliers start: 54 outliers final: 39 residues processed: 163 average time/residue: 0.1828 time to fit residues: 39.0169 Evaluate side-chains 154 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 110 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 16 HIS Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 810 GLN Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 819 LYS Chi-restraints excluded: chain A residue 823 ASN Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 856 ASP Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 956 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 12 optimal weight: 0.2980 chunk 2 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 ASN A 474 ASN ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 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 = 0.3147 r_free = 0.3147 target = 0.107699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.091471 restraints weight = 8873.699| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 1.66 r_work: 0.2835 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 1.164 6221 Z= 1.631 Angle : 0.744 28.584 8420 Z= 0.379 Chirality : 0.045 0.180 929 Planarity : 0.004 0.034 1078 Dihedral : 10.091 59.800 883 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.67 % Allowed : 7.28 % Favored : 92.05 % Rotamer: Outliers : 7.21 % Allowed : 25.38 % Favored : 67.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 1.96 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.29), residues: 742 helix: -0.12 (0.35), residues: 225 sheet: -1.97 (0.40), residues: 124 loop : -1.77 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.003 0.001 HIS A 38 PHE 0.016 0.001 PHE A 796 TYR 0.021 0.001 TYR A 62 ARG 0.002 0.000 ARG A 757 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 130 time to evaluate : 0.715 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "SER A 671 " (corrupted residue). Skipping it. REVERT: A 22 GLU cc_start: 0.8945 (tt0) cc_final: 0.8714 (tt0) REVERT: A 38 HIS cc_start: 0.8149 (OUTLIER) cc_final: 0.7761 (p90) REVERT: A 106 GLN cc_start: 0.8342 (mm-40) cc_final: 0.8067 (mt0) REVERT: A 119 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.7555 (tttp) REVERT: A 156 GLU cc_start: 0.5791 (pt0) cc_final: 0.4601 (mp0) REVERT: A 168 MET cc_start: 0.8727 (tmm) cc_final: 0.8503 (tpp) REVERT: A 183 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8283 (mm-40) REVERT: A 540 ARG cc_start: 0.8011 (ptp90) cc_final: 0.7476 (ptm-80) REVERT: A 562 GLN cc_start: 0.8876 (mm110) cc_final: 0.8673 (mm-40) REVERT: A 687 ARG cc_start: 0.8428 (ttm110) cc_final: 0.8160 (ttm-80) REVERT: A 692 TYR cc_start: 0.8966 (m-80) cc_final: 0.8189 (m-80) REVERT: A 750 ASP cc_start: 0.8609 (p0) cc_final: 0.8407 (p0) REVERT: A 789 TYR cc_start: 0.9249 (t80) cc_final: 0.8975 (t80) REVERT: A 798 SER cc_start: 0.8691 (m) cc_final: 0.8286 (p) REVERT: A 810 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.7822 (mt0) REVERT: A 844 GLU cc_start: 0.8236 (mm-30) cc_final: 0.8019 (mt-10) REVERT: A 875 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.7913 (tm-30) REVERT: A 878 ASP cc_start: 0.7679 (t0) cc_final: 0.7204 (t0) REVERT: A 886 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.6965 (ttt90) outliers start: 48 outliers final: 35 residues processed: 168 average time/residue: 0.1753 time to fit residues: 38.9832 Evaluate side-chains 156 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 115 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 810 GLN Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 823 ASN Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 856 ASP Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 886 ARG Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 956 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 7 optimal weight: 0.5980 chunk 5 optimal weight: 0.0870 chunk 16 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 ASN A 485 HIS ** A 541 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 = 0.3140 r_free = 0.3140 target = 0.107163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.090525 restraints weight = 8767.611| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 1.68 r_work: 0.2826 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 1.163 6221 Z= 1.635 Angle : 0.755 28.542 8420 Z= 0.385 Chirality : 0.045 0.175 929 Planarity : 0.004 0.035 1078 Dihedral : 9.772 59.983 875 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.67 % Allowed : 7.14 % Favored : 92.18 % Rotamer: Outliers : 8.11 % Allowed : 25.68 % Favored : 66.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 1.96 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.29), residues: 742 helix: -0.06 (0.35), residues: 227 sheet: -1.98 (0.41), residues: 114 loop : -1.76 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 107 HIS 0.004 0.001 HIS A 658 PHE 0.013 0.001 PHE A 632 TYR 0.017 0.001 TYR A 62 ARG 0.003 0.000 ARG A 597 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 118 time to evaluate : 0.691 Fit side-chains TARDY: cannot create tardy model for: "SER A 671 " (corrupted residue). Skipping it. REVERT: A 22 GLU cc_start: 0.8996 (tt0) cc_final: 0.8746 (tt0) REVERT: A 38 HIS cc_start: 0.8088 (OUTLIER) cc_final: 0.7610 (p90) REVERT: A 106 GLN cc_start: 0.8329 (mm-40) cc_final: 0.7959 (mt0) REVERT: A 119 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.7587 (tttp) REVERT: A 156 GLU cc_start: 0.5662 (pt0) cc_final: 0.4551 (mp0) REVERT: A 168 MET cc_start: 0.8734 (tmm) cc_final: 0.8497 (tpp) REVERT: A 183 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8297 (mm-40) REVERT: A 540 ARG cc_start: 0.8042 (ptp90) cc_final: 0.7470 (ptm-80) REVERT: A 599 ASP cc_start: 0.7399 (t0) cc_final: 0.6474 (t0) REVERT: A 603 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8564 (mt) REVERT: A 658 HIS cc_start: 0.7156 (m170) cc_final: 0.6854 (m90) REVERT: A 672 GLN cc_start: 0.9140 (OUTLIER) cc_final: 0.8801 (mt0) REVERT: A 687 ARG cc_start: 0.8453 (ttm110) cc_final: 0.8183 (ttm-80) REVERT: A 692 TYR cc_start: 0.8965 (m-80) cc_final: 0.8133 (m-80) REVERT: A 750 ASP cc_start: 0.8526 (p0) cc_final: 0.8322 (p0) REVERT: A 789 TYR cc_start: 0.9271 (t80) cc_final: 0.8924 (t80) REVERT: A 798 SER cc_start: 0.8715 (m) cc_final: 0.8336 (p) REVERT: A 810 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.7846 (mt0) REVERT: A 844 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7914 (mt-10) REVERT: A 875 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.7961 (tm-30) REVERT: A 886 ARG cc_start: 0.9040 (OUTLIER) cc_final: 0.6909 (ttt90) outliers start: 54 outliers final: 41 residues processed: 159 average time/residue: 0.1767 time to fit residues: 36.9923 Evaluate side-chains 164 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 115 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 672 GLN Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 757 ARG Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 810 GLN Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 823 ASN Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 856 ASP Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 886 ARG Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 956 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 39 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 ASN ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.109365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.092669 restraints weight = 8793.731| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.70 r_work: 0.2859 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 1.163 6221 Z= 1.631 Angle : 0.725 28.568 8420 Z= 0.369 Chirality : 0.044 0.173 929 Planarity : 0.004 0.037 1078 Dihedral : 9.347 59.594 874 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.67 % Allowed : 7.41 % Favored : 91.91 % Rotamer: Outliers : 7.96 % Allowed : 25.38 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 1.96 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.29), residues: 742 helix: 0.15 (0.35), residues: 225 sheet: -1.80 (0.42), residues: 114 loop : -1.75 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 107 HIS 0.003 0.001 HIS A 658 PHE 0.015 0.001 PHE A 796 TYR 0.018 0.001 TYR A 62 ARG 0.003 0.000 ARG A 597 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 128 time to evaluate : 0.659 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "SER A 671 " (corrupted residue). Skipping it. REVERT: A 16 HIS cc_start: 0.4892 (OUTLIER) cc_final: 0.3661 (t-90) REVERT: A 22 GLU cc_start: 0.8972 (tt0) cc_final: 0.8738 (tt0) REVERT: A 38 HIS cc_start: 0.8131 (OUTLIER) cc_final: 0.7614 (p90) REVERT: A 102 ASP cc_start: 0.7195 (p0) cc_final: 0.6979 (p0) REVERT: A 106 GLN cc_start: 0.8296 (mm-40) cc_final: 0.7987 (mt0) REVERT: A 110 LYS cc_start: 0.8722 (ptmt) cc_final: 0.8377 (ttpp) REVERT: A 119 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.7516 (tttp) REVERT: A 156 GLU cc_start: 0.6400 (pt0) cc_final: 0.5155 (mp0) REVERT: A 168 MET cc_start: 0.8698 (tmm) cc_final: 0.8468 (tpp) REVERT: A 183 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.8260 (mm-40) REVERT: A 599 ASP cc_start: 0.7267 (t0) cc_final: 0.6427 (t0) REVERT: A 672 GLN cc_start: 0.9157 (OUTLIER) cc_final: 0.8835 (mt0) REVERT: A 687 ARG cc_start: 0.8508 (ttm110) cc_final: 0.8197 (ttm-80) REVERT: A 692 TYR cc_start: 0.8937 (m-80) cc_final: 0.8115 (m-80) REVERT: A 750 ASP cc_start: 0.8429 (p0) cc_final: 0.8163 (p0) REVERT: A 758 GLN cc_start: 0.8281 (mt0) cc_final: 0.8005 (mt0) REVERT: A 789 TYR cc_start: 0.9208 (t80) cc_final: 0.8865 (t80) REVERT: A 798 SER cc_start: 0.8745 (m) cc_final: 0.8339 (p) REVERT: A 810 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.7877 (mt0) REVERT: A 844 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7798 (mt-10) outliers start: 53 outliers final: 40 residues processed: 169 average time/residue: 0.1749 time to fit residues: 38.8896 Evaluate side-chains 161 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 115 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 16 HIS Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 672 GLN Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 757 ARG Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 810 GLN Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 823 ASN Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 856 ASP Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 924 SER Chi-restraints excluded: chain A residue 956 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 6 optimal weight: 0.5980 chunk 3 optimal weight: 7.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 ASN ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.108962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.092241 restraints weight = 8781.885| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.70 r_work: 0.2842 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 1.163 6221 Z= 1.634 Angle : 0.735 28.504 8420 Z= 0.373 Chirality : 0.045 0.170 929 Planarity : 0.004 0.037 1078 Dihedral : 9.300 59.938 874 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.54 % Allowed : 7.55 % Favored : 91.91 % Rotamer: Outliers : 7.21 % Allowed : 25.53 % Favored : 67.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 1.96 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.29), residues: 742 helix: 0.14 (0.35), residues: 226 sheet: -1.66 (0.42), residues: 114 loop : -1.71 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 107 HIS 0.012 0.001 HIS A 658 PHE 0.015 0.001 PHE A 796 TYR 0.019 0.001 TYR A 62 ARG 0.004 0.000 ARG A 886 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 124 time to evaluate : 0.642 Fit side-chains TARDY: cannot create tardy model for: "SER A 671 " (corrupted residue). Skipping it. REVERT: A 16 HIS cc_start: 0.4964 (OUTLIER) cc_final: 0.3672 (t-90) REVERT: A 22 GLU cc_start: 0.8981 (tt0) cc_final: 0.8765 (tt0) REVERT: A 38 HIS cc_start: 0.8123 (OUTLIER) cc_final: 0.7699 (p90) REVERT: A 119 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.7517 (tttp) REVERT: A 156 GLU cc_start: 0.6487 (pt0) cc_final: 0.5641 (mt-10) REVERT: A 183 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.8270 (mm-40) REVERT: A 597 ARG cc_start: 0.7661 (ttm-80) cc_final: 0.7447 (ptp-110) REVERT: A 687 ARG cc_start: 0.8519 (ttm110) cc_final: 0.8200 (ttm-80) REVERT: A 692 TYR cc_start: 0.8966 (m-80) cc_final: 0.8191 (m-80) REVERT: A 750 ASP cc_start: 0.8432 (p0) cc_final: 0.8212 (p0) REVERT: A 758 GLN cc_start: 0.8228 (mt0) cc_final: 0.7987 (mt0) REVERT: A 789 TYR cc_start: 0.9216 (t80) cc_final: 0.8813 (t80) REVERT: A 798 SER cc_start: 0.8747 (m) cc_final: 0.8347 (p) REVERT: A 810 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.7866 (mt0) REVERT: A 844 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7830 (mt-10) outliers start: 48 outliers final: 38 residues processed: 161 average time/residue: 0.1647 time to fit residues: 35.4581 Evaluate side-chains 163 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 120 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 16 HIS Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 757 ARG Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 810 GLN Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 823 ASN Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 856 ASP Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 956 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 19 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 44 optimal weight: 0.5980 chunk 20 optimal weight: 0.4980 chunk 62 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 ASN A 474 ASN ** A 541 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 = 0.3214 r_free = 0.3214 target = 0.112469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.095686 restraints weight = 8728.019| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.75 r_work: 0.2877 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 1.162 6221 Z= 1.631 Angle : 0.732 28.529 8420 Z= 0.372 Chirality : 0.044 0.168 929 Planarity : 0.004 0.039 1078 Dihedral : 8.989 59.807 871 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.54 % Allowed : 7.14 % Favored : 92.32 % Rotamer: Outliers : 6.46 % Allowed : 26.73 % Favored : 66.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 1.96 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.30), residues: 742 helix: 0.29 (0.36), residues: 227 sheet: -1.42 (0.44), residues: 114 loop : -1.69 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 107 HIS 0.003 0.001 HIS A 38 PHE 0.015 0.001 PHE A 796 TYR 0.017 0.001 TYR A 49 ARG 0.004 0.000 ARG A 886 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 130 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER A 671 " (corrupted residue). Skipping it. REVERT: A 2 ASP cc_start: 0.8875 (t70) cc_final: 0.8630 (t0) REVERT: A 16 HIS cc_start: 0.4881 (OUTLIER) cc_final: 0.3634 (t-90) REVERT: A 22 GLU cc_start: 0.8961 (tt0) cc_final: 0.8756 (tt0) REVERT: A 38 HIS cc_start: 0.8024 (OUTLIER) cc_final: 0.7627 (p90) REVERT: A 110 LYS cc_start: 0.8737 (ptmt) cc_final: 0.8383 (ttpp) REVERT: A 119 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.7462 (tttp) REVERT: A 183 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8276 (mm-40) REVERT: A 687 ARG cc_start: 0.8549 (ttm110) cc_final: 0.8236 (ttm-80) REVERT: A 692 TYR cc_start: 0.8936 (m-80) cc_final: 0.8152 (m-80) REVERT: A 697 ILE cc_start: 0.8805 (mt) cc_final: 0.8536 (mt) REVERT: A 750 ASP cc_start: 0.8401 (p0) cc_final: 0.8193 (p0) REVERT: A 782 ASP cc_start: 0.7562 (t0) cc_final: 0.7178 (t0) REVERT: A 789 TYR cc_start: 0.9154 (t80) cc_final: 0.8781 (t80) REVERT: A 798 SER cc_start: 0.8776 (m) cc_final: 0.8334 (p) REVERT: A 810 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.8122 (mt0) REVERT: A 844 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7821 (mt-10) outliers start: 43 outliers final: 36 residues processed: 160 average time/residue: 0.1834 time to fit residues: 38.6618 Evaluate side-chains 162 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 121 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 16 HIS Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 757 ARG Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 810 GLN Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 823 ASN Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 856 ASP Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain A residue 878 ASP Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 917 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 2 optimal weight: 0.0170 chunk 12 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 72 optimal weight: 0.5980 chunk 18 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 overall best weight: 1.3022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 ASN ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 758 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.108799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.091783 restraints weight = 8858.521| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 1.78 r_work: 0.2833 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 1.163 6221 Z= 1.638 Angle : 0.750 28.450 8420 Z= 0.381 Chirality : 0.045 0.191 929 Planarity : 0.004 0.040 1078 Dihedral : 8.974 58.916 868 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.54 % Allowed : 7.55 % Favored : 91.91 % Rotamer: Outliers : 6.76 % Allowed : 27.03 % Favored : 66.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 1.96 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.30), residues: 742 helix: 0.28 (0.36), residues: 227 sheet: -1.28 (0.45), residues: 114 loop : -1.69 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.003 0.001 HIS A 38 PHE 0.014 0.001 PHE A 796 TYR 0.022 0.002 TYR A 62 ARG 0.004 0.000 ARG A 886 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 119 time to evaluate : 0.677 Fit side-chains TARDY: cannot create tardy model for: "SER A 671 " (corrupted residue). Skipping it. REVERT: A 2 ASP cc_start: 0.8930 (t70) cc_final: 0.8655 (t0) REVERT: A 16 HIS cc_start: 0.4981 (OUTLIER) cc_final: 0.4369 (t70) REVERT: A 22 GLU cc_start: 0.8971 (tt0) cc_final: 0.8761 (tt0) REVERT: A 38 HIS cc_start: 0.8138 (OUTLIER) cc_final: 0.7765 (p90) REVERT: A 119 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.7510 (tttp) REVERT: A 168 MET cc_start: 0.8686 (tmm) cc_final: 0.8436 (tpp) REVERT: A 183 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.8317 (mm-40) REVERT: A 540 ARG cc_start: 0.7985 (ptp90) cc_final: 0.7323 (ptm-80) REVERT: A 687 ARG cc_start: 0.8586 (ttm110) cc_final: 0.8262 (ttm-80) REVERT: A 692 TYR cc_start: 0.8994 (m-80) cc_final: 0.8273 (m-80) REVERT: A 750 ASP cc_start: 0.8433 (p0) cc_final: 0.8227 (p0) REVERT: A 782 ASP cc_start: 0.7663 (t0) cc_final: 0.7264 (t0) REVERT: A 789 TYR cc_start: 0.9170 (t80) cc_final: 0.8749 (t80) REVERT: A 798 SER cc_start: 0.8730 (m) cc_final: 0.8343 (p) REVERT: A 810 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8124 (mt0) REVERT: A 844 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7855 (mt-10) outliers start: 45 outliers final: 38 residues processed: 151 average time/residue: 0.1772 time to fit residues: 35.7229 Evaluate side-chains 158 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 115 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 16 HIS Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 757 ARG Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 810 GLN Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 823 ASN Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 856 ASP Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain A residue 878 ASP Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 924 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 28 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 ASN ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 758 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.109609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.092700 restraints weight = 8872.812| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 1.79 r_work: 0.2841 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 1.162 6221 Z= 1.636 Angle : 0.745 28.446 8420 Z= 0.378 Chirality : 0.045 0.184 929 Planarity : 0.004 0.040 1078 Dihedral : 9.003 58.627 868 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.54 % Allowed : 7.68 % Favored : 91.78 % Rotamer: Outliers : 6.76 % Allowed : 26.73 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 1.96 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.30), residues: 742 helix: 0.27 (0.36), residues: 227 sheet: -1.30 (0.45), residues: 114 loop : -1.68 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 107 HIS 0.003 0.001 HIS A 38 PHE 0.015 0.001 PHE A 796 TYR 0.018 0.001 TYR A 62 ARG 0.007 0.000 ARG A 597 =============================================================================== Job complete usr+sys time: 3144.59 seconds wall clock time: 54 minutes 31.45 seconds (3271.45 seconds total)