Starting phenix.real_space_refine on Fri Aug 7 10:17:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8i54_35191/08_2026/8i54_35191.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i54_35191/08_2026/8i54_35191.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8i54_35191/08_2026/8i54_35191.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i54_35191/08_2026/8i54_35191.map" model { file = "/net/cci-nas-00/data/ceres_data/8i54_35191/08_2026/8i54_35191.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i54_35191/08_2026/8i54_35191.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8i54_35191/08_2026/8i54_35191.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8i54_35191/08_2026/8i54_35191.cif" } resolution = 3.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1091 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 65 5.49 5 S 25 5.16 5 C 6474 2.51 5 N 1794 2.21 5 O 2203 1.98 5 H 9100 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19661 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 18269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1113, 18269 Classifications: {'peptide': 1113} Link IDs: {'PTRANS': 23, 'TRANS': 1089} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 690 Classifications: {'RNAv2': 33} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p_pur': 9, 'rna3p_pyr': 15} Link IDs: {'rna2p': 9, 'rna3p': 23} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 520 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "D" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 182 Classifications: {'DNA': 9} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 8} Time building chain proxies: 3.09, per 1000 atoms: 0.16 Number of scatterers: 19661 At special positions: 0 Unit cell: (103.87, 104.975, 141.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 25 16.00 P 65 15.00 O 2203 8.00 N 1794 7.00 C 6474 6.00 H 9100 1.00 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: 1.77 Conformation dependent library (CDL) restraints added in 506.7 milliseconds 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2136 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 4 sheets defined 33.4% alpha, 3.6% beta 10 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 3.01 Creating SS restraints... Processing helix chain 'A' and resid 52 through 63 removed outlier: 4.257A pdb=" N LYS A 58 " --> pdb=" O ASP A 54 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLN A 59 " --> pdb=" O GLU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 76 removed outlier: 3.735A pdb=" N ALA A 76 " --> pdb=" O LEU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 98 Processing helix chain 'A' and resid 103 through 109 Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 154 through 158 Processing helix chain 'A' and resid 172 through 188 removed outlier: 3.939A pdb=" N PHE A 179 " --> pdb=" O ILE A 175 " (cutoff:3.500A) Proline residue: A 180 - end of helix Processing helix chain 'A' and resid 194 through 199 removed outlier: 3.644A pdb=" N ALA A 199 " --> pdb=" O ALA A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 220 Processing helix chain 'A' and resid 225 through 236 removed outlier: 5.406A pdb=" N GLN A 231 " --> pdb=" O THR A 227 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N VAL A 232 " --> pdb=" O TYR A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 335 Processing helix chain 'A' and resid 338 through 345 removed outlier: 3.934A pdb=" N LEU A 343 " --> pdb=" O THR A 339 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN A 345 " --> pdb=" O ASP A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 431 through 436 removed outlier: 4.307A pdb=" N LYS A 434 " --> pdb=" O LYS A 431 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE A 436 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 450 Processing helix chain 'A' and resid 480 through 488 removed outlier: 3.934A pdb=" N MET A 486 " --> pdb=" O SER A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 501 removed outlier: 3.956A pdb=" N LYS A 500 " --> pdb=" O SER A 497 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL A 501 " --> pdb=" O THR A 498 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 497 through 501' Processing helix chain 'A' and resid 518 through 523 removed outlier: 4.032A pdb=" N LEU A 523 " --> pdb=" O GLU A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 548 removed outlier: 4.011A pdb=" N PHE A 546 " --> pdb=" O ASN A 543 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN A 548 " --> pdb=" O ALA A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 576 Proline residue: A 574 - end of helix Processing helix chain 'A' and resid 579 through 586 Processing helix chain 'A' and resid 589 through 599 Processing helix chain 'A' and resid 608 through 625 Processing helix chain 'A' and resid 644 through 656 Processing helix chain 'A' and resid 665 through 674 removed outlier: 3.774A pdb=" N GLU A 674 " --> pdb=" O ASN A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 707 removed outlier: 3.517A pdb=" N LEU A 701 " --> pdb=" O ASN A 697 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR A 702 " --> pdb=" O LEU A 698 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N PHE A 707 " --> pdb=" O PHE A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 805 removed outlier: 4.540A pdb=" N SER A 801 " --> pdb=" O ASP A 797 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ALA A 802 " --> pdb=" O ALA A 798 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE A 805 " --> pdb=" O SER A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 868 Processing helix chain 'A' and resid 878 through 900 removed outlier: 3.737A pdb=" N ASN A 890 " --> pdb=" O SER A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 936 removed outlier: 3.998A pdb=" N LYS A 926 " --> pdb=" O GLN A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1015 removed outlier: 3.602A pdb=" N GLY A1015 " --> pdb=" O ARG A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1037 removed outlier: 3.720A pdb=" N SER A1036 " --> pdb=" O ASP A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1066 removed outlier: 4.367A pdb=" N LYS A1065 " --> pdb=" O ASN A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1088 removed outlier: 3.854A pdb=" N TYR A1087 " --> pdb=" O LEU A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1102 Processing helix chain 'A' and resid 1106 through 1121 removed outlier: 3.834A pdb=" N LEU A1121 " --> pdb=" O LEU A1117 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1182 removed outlier: 3.564A pdb=" N TRP A1174 " --> pdb=" O ARG A1170 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS A1182 " --> pdb=" O GLN A1178 " (cutoff:3.500A) Processing helix chain 'A' and resid 1193 through 1203 Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 16 Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 20 removed outlier: 4.247A pdb=" N PHE A 777 " --> pdb=" O LEU A 20 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS A 776 " --> pdb=" O ARG A 728 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG A 728 " --> pdb=" O LYS A 776 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 657 through 662 removed outlier: 3.534A pdb=" N LYS A 560 " --> pdb=" O THR A 662 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU A 526 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N TYR A 563 " --> pdb=" O GLY A 524 " (cutoff:3.500A) removed outlier: 11.152A pdb=" N GLY A 524 " --> pdb=" O TYR A 563 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LEU A 527 " --> pdb=" O TYR A 534 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N TYR A 533 " --> pdb=" O ILE A 683 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 824 through 827 removed outlier: 3.561A pdb=" N VAL A 811 " --> pdb=" O ILE A 827 " (cutoff:3.500A) 216 hydrogen bonds defined for protein. 591 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 36 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 3.81 Time building geometry restraints manager: 2.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.17: 9093 1.17 - 1.52: 7169 1.52 - 1.87: 3725 1.87 - 2.22: 0 2.22 - 2.57: 1 Bond restraints: 19988 Sorted by residual: bond pdb=" C SER A 289 " pdb=" N TYR A 319 " ideal model delta sigma weight residual 1.332 2.566 -1.233 1.40e-02 5.10e+03 7.76e+03 bond pdb=" ND2 ASN A 29 " pdb="HD21 ASN A 29 " ideal model delta sigma weight residual 0.860 0.979 -0.119 2.00e-02 2.50e+03 3.55e+01 bond pdb=" ND2 ASN A 512 " pdb="HD22 ASN A 512 " ideal model delta sigma weight residual 0.860 0.979 -0.119 2.00e-02 2.50e+03 3.55e+01 bond pdb=" ND2 ASN A 512 " pdb="HD21 ASN A 512 " ideal model delta sigma weight residual 0.860 0.979 -0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" ND2 ASN A 29 " pdb="HD22 ASN A 29 " ideal model delta sigma weight residual 0.860 0.973 -0.113 2.00e-02 2.50e+03 3.19e+01 ... (remaining 19983 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.55: 35672 7.55 - 15.11: 13 15.11 - 22.66: 0 22.66 - 30.21: 1 30.21 - 37.77: 4 Bond angle restraints: 35690 Sorted by residual: angle pdb=" O SER A 289 " pdb=" C SER A 289 " pdb=" N TYR A 319 " ideal model delta sigma weight residual 122.59 87.05 35.54 1.33e+00 5.65e-01 7.14e+02 angle pdb=" CA SER A 289 " pdb=" C SER A 289 " pdb=" N TYR A 319 " ideal model delta sigma weight residual 116.84 79.31 37.53 1.71e+00 3.42e-01 4.82e+02 angle pdb=" C MET A 258 " pdb=" CA MET A 258 " pdb=" HA MET A 258 " ideal model delta sigma weight residual 110.00 72.23 37.77 3.00e+00 1.11e-01 1.58e+02 angle pdb=" N MET A 258 " pdb=" CA MET A 258 " pdb=" HA MET A 258 " ideal model delta sigma weight residual 110.00 74.22 35.78 3.00e+00 1.11e-01 1.42e+02 angle pdb=" CB MET A 258 " pdb=" CA MET A 258 " pdb=" HA MET A 258 " ideal model delta sigma weight residual 109.00 81.82 27.18 3.00e+00 1.11e-01 8.21e+01 ... (remaining 35685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.16: 8939 34.16 - 68.32: 397 68.32 - 102.48: 22 102.48 - 136.64: 0 136.64 - 170.80: 3 Dihedral angle restraints: 9361 sinusoidal: 5442 harmonic: 3919 Sorted by residual: dihedral pdb=" C4' U B -18 " pdb=" C3' U B -18 " pdb=" C2' U B -18 " pdb=" C1' U B -18 " ideal model delta sinusoidal sigma weight residual 36.34 -38.25 74.60 1 3.10e+00 1.04e-01 7.34e+02 dihedral pdb=" C4' A B -10 " pdb=" C3' A B -10 " pdb=" C2' A B -10 " pdb=" C1' A B -10 " ideal model delta sinusoidal sigma weight residual 36.34 -36.39 72.74 1 3.10e+00 1.04e-01 7.03e+02 dihedral pdb=" C4' A B -9 " pdb=" C3' A B -9 " pdb=" C2' A B -9 " pdb=" C1' A B -9 " ideal model delta sinusoidal sigma weight residual 36.35 -36.30 72.64 1 3.10e+00 1.04e-01 7.01e+02 ... (remaining 9358 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1516 0.089 - 0.179: 89 0.179 - 0.268: 39 0.268 - 0.358: 11 0.358 - 0.447: 1 Chirality restraints: 1656 Sorted by residual: chirality pdb=" CA MET A 258 " pdb=" N MET A 258 " pdb=" C MET A 258 " pdb=" CB MET A 258 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 4.99e+00 chirality pdb=" C2' U B -17 " pdb=" C3' U B -17 " pdb=" O2' U B -17 " pdb=" C1' U B -17 " both_signs ideal model delta sigma weight residual False -2.79 -2.48 -0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CA ASN A 29 " pdb=" N ASN A 29 " pdb=" C ASN A 29 " pdb=" CB ASN A 29 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 1653 not shown) Planarity restraints: 2775 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 29 " -0.310 2.00e-02 2.50e+03 4.04e-01 2.45e+03 pdb=" CG ASN A 29 " 0.008 2.00e-02 2.50e+03 pdb=" OD1 ASN A 29 " 0.303 2.00e-02 2.50e+03 pdb=" ND2 ASN A 29 " -0.004 2.00e-02 2.50e+03 pdb="HD21 ASN A 29 " 0.631 2.00e-02 2.50e+03 pdb="HD22 ASN A 29 " -0.626 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 512 " -0.245 2.00e-02 2.50e+03 2.51e-01 9.44e+02 pdb=" CG ASN A 512 " 0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN A 512 " 0.229 2.00e-02 2.50e+03 pdb=" ND2 ASN A 512 " 0.004 2.00e-02 2.50e+03 pdb="HD21 ASN A 512 " 0.358 2.00e-02 2.50e+03 pdb="HD22 ASN A 512 " -0.369 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 289 " -0.190 2.00e-02 2.50e+03 2.73e-01 7.47e+02 pdb=" C SER A 289 " 0.442 2.00e-02 2.50e+03 pdb=" O SER A 289 " -0.259 2.00e-02 2.50e+03 pdb=" N TYR A 319 " 0.008 2.00e-02 2.50e+03 ... (remaining 2772 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.27: 2766 2.27 - 2.85: 42416 2.85 - 3.43: 47792 3.43 - 4.02: 63235 4.02 - 4.60: 95215 Nonbonded interactions: 251424 Sorted by model distance: nonbonded pdb=" H PHE A 968 " pdb=" OP1 DG C -4 " model vdw 1.684 2.450 nonbonded pdb=" H MET A 258 " pdb=" HA MET A 258 " model vdw 1.706 1.816 nonbonded pdb=" O PHE A1013 " pdb=" H PHE A1016 " model vdw 1.723 2.450 nonbonded pdb=" O ASP A 121 " pdb=" H LEU A 125 " model vdw 1.725 2.450 nonbonded pdb=" OE1 GLU A 627 " pdb=" H GLU A 627 " model vdw 1.729 2.450 ... (remaining 251419 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.080 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 19.540 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 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 : 0.013 1.233 10888 Z= 0.903 Angle : 1.077 37.532 14957 Z= 0.653 Chirality : 0.062 0.447 1656 Planarity : 0.009 0.273 1691 Dihedral : 18.389 170.798 4326 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.36 % Allowed : 12.81 % Favored : 86.83 % Rotamer: Outliers : 0.98 % Allowed : 0.69 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.16 (0.24), residues: 1101 helix: -1.22 (0.27), residues: 345 sheet: -3.34 (0.49), residues: 79 loop : -2.54 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 710 TYR 0.043 0.002 TYR A 80 PHE 0.030 0.002 PHE A 578 TRP 0.011 0.002 TRP A 871 HIS 0.005 0.002 HIS A 699 Details of bonding type rmsd/Z covalent geometry : bond 0.01303 / 0.90 (10888) covalent geometry : angle 1.07656 / 0.65 (14957) hydrogen bonds : bond 0.20049 / 11.54 ( 238) hydrogen bonds : angle 9.26329 / 6.40 ( 627) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 96 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Evaluate side-chains 85 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 623 ILE cc_start: 0.9150 (mt) cc_final: 0.8709 (tp) REVERT: A 1013 PHE cc_start: 0.8434 (m-80) cc_final: 0.8101 (m-80) REVERT: A 1098 LYS cc_start: 0.8169 (tttt) cc_final: 0.7714 (tptm) REVERT: A 1100 MET cc_start: 0.8844 (mmp) cc_final: 0.8448 (mmm) outliers start: 10 outliers final: 5 residues processed: 85 average time/residue: 0.2075 time to fit residues: 25.0057 Evaluate side-chains 71 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 493 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 GLN A 145 ASN A 286 ASN A1053 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.085785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.071400 restraints weight = 198774.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.074099 restraints weight = 101053.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.075774 restraints weight = 63151.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.076832 restraints weight = 45101.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.077504 restraints weight = 35321.789| |-----------------------------------------------------------------------------| r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 10888 Z= 0.249 Angle : 1.011 17.625 14957 Z= 0.469 Chirality : 0.076 1.018 1656 Planarity : 0.005 0.050 1691 Dihedral : 19.687 165.630 1980 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.27 % Allowed : 13.06 % Favored : 86.67 % Rotamer: Outliers : 1.18 % Allowed : 4.71 % Favored : 94.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.16 (0.24), residues: 1103 helix: -0.92 (0.28), residues: 350 sheet: -3.55 (0.48), residues: 80 loop : -2.70 (0.22), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 816 TYR 0.020 0.001 TYR A 80 PHE 0.016 0.001 PHE A 681 TRP 0.017 0.002 TRP A 871 HIS 0.003 0.001 HIS A 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.25 (10888) covalent geometry : angle 1.01082 / 0.47 (14957) hydrogen bonds : bond 0.08156 / 4.58 ( 238) hydrogen bonds : angle 7.00592 / 4.79 ( 627) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 96 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Evaluate side-chains 78 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 704 MET cc_start: 0.6884 (tmm) cc_final: 0.6494 (tmm) REVERT: A 1013 PHE cc_start: 0.8829 (m-80) cc_final: 0.8576 (m-80) REVERT: A 1100 MET cc_start: 0.9106 (mmp) cc_final: 0.8716 (mmm) outliers start: 12 outliers final: 10 residues processed: 74 average time/residue: 0.2230 time to fit residues: 23.6225 Evaluate side-chains 74 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 493 LYS Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 1053 ASN Chi-restraints excluded: chain A residue 1114 TYR Chi-restraints excluded: chain A residue 1116 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 90 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 14 optimal weight: 8.9990 chunk 93 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 86 optimal weight: 6.9990 chunk 39 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 GLN ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 ASN A 820 ASN A 887 GLN ** A 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.082709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.068510 restraints weight = 203169.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.071006 restraints weight = 105187.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.072570 restraints weight = 67152.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.073571 restraints weight = 48690.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.074138 restraints weight = 38664.364| |-----------------------------------------------------------------------------| r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 10888 Z= 0.278 Angle : 0.872 17.599 14957 Z= 0.435 Chirality : 0.058 0.522 1656 Planarity : 0.005 0.038 1691 Dihedral : 20.066 166.765 1978 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 25.05 Ramachandran Plot: Outliers : 0.18 % Allowed : 14.96 % Favored : 84.86 % Rotamer: Outliers : 1.18 % Allowed : 7.07 % Favored : 91.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.58 (0.23), residues: 1103 helix: -1.29 (0.26), residues: 350 sheet: -3.69 (0.51), residues: 90 loop : -2.94 (0.22), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1056 TYR 0.019 0.002 TYR A1146 PHE 0.014 0.002 PHE A 607 TRP 0.022 0.002 TRP A 871 HIS 0.005 0.002 HIS A 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.28 (10888) covalent geometry : angle 0.87219 / 0.44 (14957) hydrogen bonds : bond 0.07960 / 4.55 ( 238) hydrogen bonds : angle 7.04981 / 4.80 ( 627) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 96 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Evaluate side-chains 75 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 704 MET cc_start: 0.7119 (tmm) cc_final: 0.6676 (tmm) REVERT: A 1100 MET cc_start: 0.9105 (mmp) cc_final: 0.8759 (mmm) outliers start: 12 outliers final: 10 residues processed: 69 average time/residue: 0.2125 time to fit residues: 21.1633 Evaluate side-chains 67 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 493 LYS Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 1078 ASP Chi-restraints excluded: chain A residue 1114 TYR Chi-restraints excluded: chain A residue 1116 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.083639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.069324 restraints weight = 201291.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.071875 restraints weight = 103775.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.073445 restraints weight = 65811.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.074460 restraints weight = 47676.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.075160 restraints weight = 37772.450| |-----------------------------------------------------------------------------| r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 10888 Z= 0.206 Angle : 0.782 18.315 14957 Z= 0.391 Chirality : 0.054 0.501 1656 Planarity : 0.004 0.038 1691 Dihedral : 20.092 171.427 1976 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 20.05 Ramachandran Plot: Outliers : 0.27 % Allowed : 14.23 % Favored : 85.49 % Rotamer: Outliers : 0.88 % Allowed : 8.83 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.51 (0.24), residues: 1103 helix: -1.14 (0.27), residues: 344 sheet: -3.72 (0.50), residues: 90 loop : -2.93 (0.22), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1061 TYR 0.016 0.002 TYR A 764 PHE 0.013 0.001 PHE A 607 TRP 0.014 0.002 TRP A 871 HIS 0.004 0.001 HIS A 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.21 (10888) covalent geometry : angle 0.78210 / 0.39 (14957) hydrogen bonds : bond 0.07695 / 4.37 ( 238) hydrogen bonds : angle 6.75027 / 4.58 ( 627) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 96 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Evaluate side-chains 69 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 704 MET cc_start: 0.7044 (tmm) cc_final: 0.6577 (tmm) REVERT: A 1100 MET cc_start: 0.9103 (mmp) cc_final: 0.8793 (mmm) outliers start: 9 outliers final: 8 residues processed: 63 average time/residue: 0.2090 time to fit residues: 18.4033 Evaluate side-chains 67 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 493 LYS Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 1114 TYR Chi-restraints excluded: chain A residue 1116 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 7 optimal weight: 0.1980 chunk 65 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 106 optimal weight: 0.2980 chunk 104 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 26 optimal weight: 0.8980 chunk 87 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.084569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.070254 restraints weight = 199347.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.072827 restraints weight = 102388.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.074420 restraints weight = 64778.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.075421 restraints weight = 46758.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.076112 restraints weight = 37116.232| |-----------------------------------------------------------------------------| r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 10888 Z= 0.157 Angle : 0.731 19.488 14957 Z= 0.359 Chirality : 0.052 0.589 1656 Planarity : 0.004 0.047 1691 Dihedral : 19.963 169.841 1976 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.18 % Allowed : 14.60 % Favored : 85.22 % Rotamer: Outliers : 1.08 % Allowed : 9.81 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.32 (0.24), residues: 1103 helix: -0.87 (0.28), residues: 338 sheet: -3.72 (0.47), residues: 90 loop : -2.85 (0.22), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 710 TYR 0.012 0.001 TYR A 764 PHE 0.009 0.001 PHE A 607 TRP 0.016 0.001 TRP A 871 HIS 0.004 0.001 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.16 (10888) covalent geometry : angle 0.73093 / 0.36 (14957) hydrogen bonds : bond 0.07435 / 4.23 ( 238) hydrogen bonds : angle 6.43191 / 4.39 ( 627) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 96 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Evaluate side-chains 73 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 ASP cc_start: 0.7475 (OUTLIER) cc_final: 0.6896 (m-30) REVERT: A 704 MET cc_start: 0.7078 (tmm) cc_final: 0.6595 (tmm) REVERT: A 1013 PHE cc_start: 0.8661 (m-80) cc_final: 0.8461 (m-80) REVERT: A 1100 MET cc_start: 0.9057 (mmp) cc_final: 0.8752 (mmm) outliers start: 11 outliers final: 9 residues processed: 67 average time/residue: 0.2161 time to fit residues: 20.2671 Evaluate side-chains 72 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 242 TYR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 493 LYS Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 1114 TYR Chi-restraints excluded: chain A residue 1116 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 83 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 95 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.084115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.069828 restraints weight = 199734.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.072400 restraints weight = 102709.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.073988 restraints weight = 64873.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.074972 restraints weight = 46610.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.075601 restraints weight = 37124.788| |-----------------------------------------------------------------------------| r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 10888 Z= 0.173 Angle : 0.730 19.750 14957 Z= 0.360 Chirality : 0.052 0.560 1656 Planarity : 0.004 0.040 1691 Dihedral : 19.892 172.198 1974 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 18.58 Ramachandran Plot: Outliers : 0.18 % Allowed : 14.32 % Favored : 85.49 % Rotamer: Outliers : 0.98 % Allowed : 11.09 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.29 (0.24), residues: 1103 helix: -0.87 (0.28), residues: 339 sheet: -3.72 (0.48), residues: 90 loop : -2.81 (0.22), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 710 TYR 0.014 0.001 TYR A 764 PHE 0.011 0.001 PHE A 607 TRP 0.011 0.001 TRP A 871 HIS 0.004 0.001 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.17 (10888) covalent geometry : angle 0.72986 / 0.36 (14957) hydrogen bonds : bond 0.07563 / 4.34 ( 238) hydrogen bonds : angle 6.34296 / 4.33 ( 627) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 96 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Evaluate side-chains 73 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 ASP cc_start: 0.7583 (OUTLIER) cc_final: 0.6985 (m-30) REVERT: A 1100 MET cc_start: 0.9178 (mmp) cc_final: 0.8809 (mmm) outliers start: 10 outliers final: 9 residues processed: 68 average time/residue: 0.2170 time to fit residues: 20.2729 Evaluate side-chains 70 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 493 LYS Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 1114 TYR Chi-restraints excluded: chain A residue 1116 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 106 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 66 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 582 ASN A 748 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.084922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.070483 restraints weight = 198379.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.073087 restraints weight = 100724.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.074705 restraints weight = 63044.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.075732 restraints weight = 44969.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.076291 restraints weight = 35628.203| |-----------------------------------------------------------------------------| r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 10888 Z= 0.142 Angle : 0.709 19.378 14957 Z= 0.348 Chirality : 0.051 0.548 1656 Planarity : 0.003 0.038 1691 Dihedral : 19.841 171.281 1974 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.18 % Allowed : 14.51 % Favored : 85.31 % Rotamer: Outliers : 1.08 % Allowed : 11.68 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.18 (0.24), residues: 1103 helix: -0.78 (0.29), residues: 338 sheet: -3.60 (0.49), residues: 80 loop : -2.77 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 710 TYR 0.012 0.001 TYR A 262 PHE 0.009 0.001 PHE A 607 TRP 0.012 0.001 TRP A 871 HIS 0.003 0.001 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 (10888) covalent geometry : angle 0.70933 / 0.35 (14957) hydrogen bonds : bond 0.07456 / 4.24 ( 238) hydrogen bonds : angle 6.17304 / 4.22 ( 627) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 96 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Evaluate side-chains 74 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 ASP cc_start: 0.7372 (OUTLIER) cc_final: 0.6851 (m-30) REVERT: A 1013 PHE cc_start: 0.8365 (m-80) cc_final: 0.8054 (m-80) REVERT: A 1100 MET cc_start: 0.8964 (mmp) cc_final: 0.8636 (mmm) outliers start: 11 outliers final: 8 residues processed: 69 average time/residue: 0.2386 time to fit residues: 23.0006 Evaluate side-chains 69 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 493 LYS Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 1114 TYR Chi-restraints excluded: chain A residue 1116 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 102 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 23 optimal weight: 8.9990 chunk 82 optimal weight: 0.3980 chunk 24 optimal weight: 0.8980 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 278 GLN A 582 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.084447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.070001 restraints weight = 198500.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.072596 restraints weight = 101334.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.074206 restraints weight = 63555.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.075233 restraints weight = 45344.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.075879 restraints weight = 35848.047| |-----------------------------------------------------------------------------| r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 10888 Z= 0.165 Angle : 0.720 19.050 14957 Z= 0.354 Chirality : 0.051 0.529 1656 Planarity : 0.004 0.037 1691 Dihedral : 19.810 171.691 1974 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.18 % Allowed : 14.60 % Favored : 85.22 % Rotamer: Outliers : 0.98 % Allowed : 12.07 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.22 (0.24), residues: 1103 helix: -0.90 (0.28), residues: 346 sheet: -3.57 (0.50), residues: 80 loop : -2.78 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 710 TYR 0.013 0.001 TYR A 764 PHE 0.011 0.001 PHE A 607 TRP 0.011 0.001 TRP A 871 HIS 0.003 0.001 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.16 (10888) covalent geometry : angle 0.71998 / 0.35 (14957) hydrogen bonds : bond 0.07627 / 4.35 ( 238) hydrogen bonds : angle 6.15734 / 4.21 ( 627) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 96 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Evaluate side-chains 72 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 ASP cc_start: 0.7333 (OUTLIER) cc_final: 0.6753 (m-30) REVERT: A 1013 PHE cc_start: 0.8467 (m-80) cc_final: 0.8206 (m-80) REVERT: A 1100 MET cc_start: 0.8975 (mmp) cc_final: 0.8659 (mmm) outliers start: 10 outliers final: 9 residues processed: 66 average time/residue: 0.2485 time to fit residues: 22.6263 Evaluate side-chains 71 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 493 LYS Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 1114 TYR Chi-restraints excluded: chain A residue 1116 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 39 optimal weight: 9.9990 chunk 64 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.084765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.070338 restraints weight = 197928.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.072923 restraints weight = 100566.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.074526 restraints weight = 63117.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.075541 restraints weight = 45227.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.076161 restraints weight = 35798.232| |-----------------------------------------------------------------------------| r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10888 Z= 0.148 Angle : 0.709 18.753 14957 Z= 0.348 Chirality : 0.051 0.514 1656 Planarity : 0.004 0.037 1691 Dihedral : 19.790 171.258 1974 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.18 % Allowed : 14.51 % Favored : 85.31 % Rotamer: Outliers : 0.98 % Allowed : 12.27 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.17 (0.24), residues: 1103 helix: -0.81 (0.28), residues: 340 sheet: -3.53 (0.50), residues: 80 loop : -2.75 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 710 TYR 0.013 0.001 TYR A 764 PHE 0.011 0.001 PHE A 578 TRP 0.013 0.002 TRP A1174 HIS 0.003 0.001 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.15 (10888) covalent geometry : angle 0.70915 / 0.35 (14957) hydrogen bonds : bond 0.07553 / 4.29 ( 238) hydrogen bonds : angle 6.05037 / 4.13 ( 627) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 96 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Evaluate side-chains 73 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 ASP cc_start: 0.7431 (OUTLIER) cc_final: 0.6836 (m-30) REVERT: A 538 MET cc_start: 0.4517 (mmt) cc_final: 0.4293 (mmt) REVERT: A 1013 PHE cc_start: 0.8623 (m-80) cc_final: 0.8309 (m-80) REVERT: A 1100 MET cc_start: 0.9088 (mmp) cc_final: 0.8742 (mmm) outliers start: 10 outliers final: 9 residues processed: 67 average time/residue: 0.2620 time to fit residues: 24.3904 Evaluate side-chains 72 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 493 LYS Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 1114 TYR Chi-restraints excluded: chain A residue 1116 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 80 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 82 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 67 optimal weight: 8.9990 chunk 29 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 ASN ** A 336 ASN ** 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 = 0.4249 r_free = 0.4249 target = 0.083952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.069488 restraints weight = 198157.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.072051 restraints weight = 101694.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.073632 restraints weight = 63918.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.074642 restraints weight = 45938.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.075261 restraints weight = 36430.944| |-----------------------------------------------------------------------------| r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10888 Z= 0.176 Angle : 0.729 18.305 14957 Z= 0.361 Chirality : 0.052 0.595 1656 Planarity : 0.004 0.038 1691 Dihedral : 19.811 172.333 1974 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.18 % Allowed : 15.23 % Favored : 84.59 % Rotamer: Outliers : 0.98 % Allowed : 12.27 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.24 (0.24), residues: 1103 helix: -0.88 (0.28), residues: 340 sheet: -3.60 (0.50), residues: 80 loop : -2.80 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 710 TYR 0.015 0.001 TYR A 764 PHE 0.012 0.001 PHE A 607 TRP 0.016 0.002 TRP A1174 HIS 0.004 0.001 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.18 (10888) covalent geometry : angle 0.72913 / 0.36 (14957) hydrogen bonds : bond 0.07579 / 4.35 ( 238) hydrogen bonds : angle 6.09202 / 4.16 ( 627) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 96 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Evaluate side-chains 71 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 ASP cc_start: 0.7400 (OUTLIER) cc_final: 0.6824 (m-30) REVERT: A 704 MET cc_start: 0.7174 (tmm) cc_final: 0.6752 (tmm) REVERT: A 1013 PHE cc_start: 0.8349 (m-80) cc_final: 0.8088 (m-80) REVERT: A 1100 MET cc_start: 0.9005 (mmp) cc_final: 0.8689 (mmm) outliers start: 10 outliers final: 9 residues processed: 66 average time/residue: 0.2081 time to fit residues: 19.1601 Evaluate side-chains 70 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 493 LYS Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 1114 TYR Chi-restraints excluded: chain A residue 1116 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 41 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 98 optimal weight: 0.6980 chunk 70 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 108 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.083925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.069460 restraints weight = 198263.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.072089 restraints weight = 101391.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.073647 restraints weight = 63299.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.074615 restraints weight = 45641.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.075251 restraints weight = 36387.509| |-----------------------------------------------------------------------------| r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10888 Z= 0.163 Angle : 0.714 17.868 14957 Z= 0.355 Chirality : 0.052 0.615 1656 Planarity : 0.004 0.069 1691 Dihedral : 19.820 171.912 1974 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 19.31 Ramachandran Plot: Outliers : 0.18 % Allowed : 15.14 % Favored : 84.68 % Rotamer: Outliers : 1.08 % Allowed : 12.46 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.23 (0.24), residues: 1103 helix: -0.91 (0.28), residues: 342 sheet: -3.56 (0.50), residues: 80 loop : -2.78 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 710 TYR 0.014 0.001 TYR A 764 PHE 0.014 0.001 PHE A 578 TRP 0.015 0.002 TRP A1174 HIS 0.004 0.001 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 (10888) covalent geometry : angle 0.71387 / 0.35 (14957) hydrogen bonds : bond 0.07232 / 4.16 ( 238) hydrogen bonds : angle 6.00889 / 4.10 ( 627) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3161.13 seconds wall clock time: 54 minutes 48.78 seconds (3288.78 seconds total)