Starting phenix.real_space_refine on Sat Jul 4 13:09:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8i54_35191/07_2026/8i54_35191.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i54_35191/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8i54_35191/07_2026/8i54_35191.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i54_35191/07_2026/8i54_35191.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8i54_35191/07_2026/8i54_35191.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i54_35191/07_2026/8i54_35191.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8i54_35191/07_2026/8i54_35191.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8i54_35191/07_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-dev-6108/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: {'RNA': 33} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p_pur': 9, 'rna3p_pyr': 15} Link IDs: {'rna2p': 9, 'rna3p': 23} 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: 3.71, per 1000 atoms: 0.19 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: 1.96 Conformation dependent library (CDL) restraints added in 542.0 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: 3.46 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: 4.32 Time building geometry restraints manager: 2.68 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: 8980 34.16 - 68.32: 352 68.32 - 102.48: 21 102.48 - 136.64: 3 136.64 - 170.80: 5 Dihedral angle restraints: 9361 sinusoidal: 5442 harmonic: 3919 Sorted by residual: dihedral pdb=" O4' C B 2 " pdb=" C1' C B 2 " pdb=" N1 C B 2 " pdb=" C2 C B 2 " ideal model delta sinusoidal sigma weight residual 200.00 40.94 159.06 1 1.50e+01 4.44e-03 8.25e+01 dihedral pdb=" O4' U B -17 " pdb=" C1' U B -17 " pdb=" N1 U B -17 " pdb=" C2 U B -17 " ideal model delta sinusoidal sigma weight residual 232.00 71.34 160.66 1 1.70e+01 3.46e-03 6.46e+01 dihedral pdb=" CA ASP A 323 " pdb=" C ASP A 323 " pdb=" N LEU A 324 " pdb=" CA LEU A 324 " ideal model delta harmonic sigma weight residual -180.00 -150.92 -29.08 0 5.00e+00 4.00e-02 3.38e+01 ... (remaining 9358 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1563 0.089 - 0.179: 87 0.179 - 0.268: 3 0.268 - 0.358: 2 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=" 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 chirality pdb=" CA LEU A 510 " pdb=" N LEU A 510 " pdb=" C LEU A 510 " pdb=" CB LEU A 510 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.86e+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: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.140 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 22.570 Find NCS groups from input model: 0.070 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.770 ------------------------------------------------------------------------------- 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 : 1.044 37.532 14957 Z= 0.650 Chirality : 0.048 0.447 1656 Planarity : 0.009 0.273 1691 Dihedral : 18.066 170.798 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 0.01301 / 0.90 (10888) covalent geometry : angle 1.04387 / 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 : 0.538 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: 0.2260 time to fit residues: 27.5772 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 : 0.546 ------------------------------------------------------------------------------- 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: 8.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 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 A 336 ASN A1053 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.085866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.071379 restraints weight = 198918.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.074065 restraints weight = 100465.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.075722 restraints weight = 62665.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.076790 restraints weight = 44834.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.077450 restraints weight = 35221.241| |-----------------------------------------------------------------------------| r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 10888 Z= 0.214 Angle : 0.705 11.819 14957 Z= 0.387 Chirality : 0.043 0.478 1656 Planarity : 0.005 0.048 1691 Dihedral : 20.359 168.586 1980 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.27 % Allowed : 13.06 % Favored : 86.67 % Rotamer: Outliers : 1.18 % Allowed : 4.51 % Favored : 94.31 % 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: -0.90 (0.28), residues: 350 sheet: -3.62 (0.46), residues: 84 loop : -2.69 (0.22), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 816 TYR 0.022 0.001 TYR A 80 PHE 0.015 0.001 PHE A 681 TRP 0.016 0.002 TRP A 871 HIS 0.003 0.001 HIS A 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.21 (10888) covalent geometry : angle 0.70523 / 0.39 (14957) hydrogen bonds : bond 0.08364 / 4.76 ( 238) hydrogen bonds : angle 7.04527 / 4.83 ( 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 : 0.536 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 1013 PHE cc_start: 0.8722 (m-80) cc_final: 0.8447 (m-80) REVERT: A 1100 MET cc_start: 0.9019 (mmp) cc_final: 0.8649 (mmm) outliers start: 12 outliers final: 9 residues processed: 74 average time/residue: 0.2327 time to fit residues: 24.5732 Evaluate side-chains 73 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 71 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 chunk 86 optimal weight: 6.9990 chunk 39 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 GLN A 582 ASN ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 820 ASN ** A 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.082906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.068613 restraints weight = 203670.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.071147 restraints weight = 104994.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.072691 restraints weight = 66532.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.073681 restraints weight = 48353.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.074313 restraints weight = 38491.501| |-----------------------------------------------------------------------------| r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 10888 Z= 0.285 Angle : 0.748 12.016 14957 Z= 0.417 Chirality : 0.045 0.487 1656 Planarity : 0.005 0.038 1691 Dihedral : 20.655 176.548 1976 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 24.95 Ramachandran Plot: Outliers : 0.27 % Allowed : 15.23 % Favored : 84.50 % Rotamer: Outliers : 1.28 % Allowed : 6.77 % Favored : 91.95 % 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: -3.64 (0.23), residues: 1103 helix: -1.37 (0.26), residues: 356 sheet: -3.73 (0.51), residues: 90 loop : -2.97 (0.22), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1056 TYR 0.026 0.002 TYR A1146 PHE 0.015 0.002 PHE A 607 TRP 0.023 0.002 TRP A 871 HIS 0.005 0.002 HIS A 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.28 (10888) covalent geometry : angle 0.74835 / 0.42 (14957) hydrogen bonds : bond 0.07938 / 4.62 ( 238) hydrogen bonds : angle 6.97550 / 4.75 ( 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 76 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.380 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 704 MET cc_start: 0.7111 (tmm) cc_final: 0.6657 (tmm) REVERT: A 1100 MET cc_start: 0.9203 (mmp) cc_final: 0.8835 (mmm) outliers start: 13 outliers final: 11 residues processed: 69 average time/residue: 0.2377 time to fit residues: 23.1805 Evaluate side-chains 68 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 885 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: 9.9990 chunk 32 optimal weight: 20.0000 chunk 31 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 96 optimal weight: 0.7980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 145 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 = 0.4241 r_free = 0.4241 target = 0.083840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.069433 restraints weight = 200843.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.072077 restraints weight = 101384.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.073671 restraints weight = 63435.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.074694 restraints weight = 45846.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.075339 restraints weight = 36276.757| |-----------------------------------------------------------------------------| r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.1916 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= 0.162 Angle : 0.641 11.084 14957 Z= 0.355 Chirality : 0.042 0.456 1656 Planarity : 0.004 0.039 1691 Dihedral : 20.596 171.313 1976 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.27 % Allowed : 13.87 % Favored : 85.86 % Rotamer: Outliers : 0.88 % Allowed : 8.44 % Favored : 90.68 % 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: -3.40 (0.24), residues: 1103 helix: -1.04 (0.28), residues: 344 sheet: -3.70 (0.48), residues: 90 loop : -2.86 (0.22), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 771 TYR 0.016 0.002 TYR A 242 PHE 0.011 0.001 PHE A 607 TRP 0.019 0.002 TRP A 871 HIS 0.003 0.001 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.16 (10888) covalent geometry : angle 0.64149 / 0.35 (14957) hydrogen bonds : bond 0.07113 / 4.08 ( 238) hydrogen bonds : angle 6.54408 / 4.44 ( 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 68 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 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: A 337 TRP cc_start: 0.8943 (m100) cc_final: 0.8687 (m100) REVERT: A 704 MET cc_start: 0.6953 (tmm) cc_final: 0.6483 (tmm) REVERT: A 1100 MET cc_start: 0.9139 (mmp) cc_final: 0.8792 (mmm) outliers start: 9 outliers final: 8 residues processed: 62 average time/residue: 0.2226 time to fit residues: 19.5953 Evaluate side-chains 65 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.415 ------------------------------------------------------------------------------- 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: 6.9990 chunk 65 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 2 optimal weight: 0.0070 chunk 69 optimal weight: 0.8980 chunk 31 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.9804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 887 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.084253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.069939 restraints weight = 200468.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.072543 restraints weight = 103071.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.074101 restraints weight = 65026.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.075096 restraints weight = 47096.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.075741 restraints weight = 37456.343| |-----------------------------------------------------------------------------| r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10888 Z= 0.165 Angle : 0.619 12.165 14957 Z= 0.342 Chirality : 0.041 0.478 1656 Planarity : 0.004 0.037 1691 Dihedral : 20.476 170.766 1976 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.18 % Allowed : 15.23 % Favored : 84.59 % Rotamer: Outliers : 1.18 % Allowed : 9.42 % Favored : 89.40 % 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: -3.28 (0.24), residues: 1103 helix: -0.86 (0.28), residues: 338 sheet: -3.70 (0.47), residues: 90 loop : -2.81 (0.22), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 710 TYR 0.013 0.001 TYR A 764 PHE 0.010 0.001 PHE A 607 TRP 0.020 0.002 TRP A 871 HIS 0.004 0.001 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.16 (10888) covalent geometry : angle 0.61889 / 0.34 (14957) hydrogen bonds : bond 0.06963 / 4.06 ( 238) hydrogen bonds : angle 6.25672 / 4.28 ( 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 74 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.409 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: 0.7456 (OUTLIER) cc_final: 0.6919 (m-30) REVERT: A 337 TRP cc_start: 0.8940 (m100) cc_final: 0.8695 (m100) REVERT: A 704 MET cc_start: 0.7103 (tmm) cc_final: 0.6624 (tmm) REVERT: A 1100 MET cc_start: 0.9049 (mmp) cc_final: 0.8747 (mmm) outliers start: 12 outliers final: 9 residues processed: 67 average time/residue: 0.2229 time to fit residues: 20.6839 Evaluate side-chains 69 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.513 ------------------------------------------------------------------------------- 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 900 ASN 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: 6.9990 chunk 95 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 82 optimal weight: 0.0970 chunk 56 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 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 = 0.4234 r_free = 0.4234 target = 0.083586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.069272 restraints weight = 200861.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.071860 restraints weight = 103969.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.073412 restraints weight = 65751.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.074403 restraints weight = 47703.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.075040 restraints weight = 37991.241| |-----------------------------------------------------------------------------| r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10888 Z= 0.182 Angle : 0.631 10.884 14957 Z= 0.352 Chirality : 0.041 0.465 1656 Planarity : 0.004 0.036 1691 Dihedral : 20.470 171.247 1974 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.18 % Allowed : 14.96 % Favored : 84.86 % Rotamer: Outliers : 1.08 % Allowed : 11.09 % Favored : 87.83 % 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: -3.30 (0.24), residues: 1103 helix: -0.88 (0.28), residues: 339 sheet: -3.70 (0.47), residues: 90 loop : -2.82 (0.22), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 771 TYR 0.029 0.002 TYR A 242 PHE 0.014 0.001 PHE A 114 TRP 0.014 0.002 TRP A 871 HIS 0.004 0.001 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.18 (10888) covalent geometry : angle 0.63070 / 0.35 (14957) hydrogen bonds : bond 0.07091 / 4.12 ( 238) hydrogen bonds : angle 6.28494 / 4.29 ( 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: 11 poor density : 62 time to evaluate : 0.448 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 13 SER cc_start: 0.8336 (OUTLIER) cc_final: 0.7904 (p) REVERT: A 226 ASP cc_start: 0.7433 (OUTLIER) cc_final: 0.6883 (m-30) REVERT: A 337 TRP cc_start: 0.8957 (m100) cc_final: 0.8723 (m100) REVERT: A 1100 MET cc_start: 0.9124 (mmp) cc_final: 0.8770 (mmm) outliers start: 11 outliers final: 8 residues processed: 68 average time/residue: 0.2263 time to fit residues: 21.4567 Evaluate side-chains 69 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 106 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 92 optimal weight: 0.2980 chunk 42 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 6 optimal weight: 0.4980 chunk 81 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 8 optimal weight: 0.4980 chunk 26 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 748 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.085138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.070682 restraints weight = 197590.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.073262 restraints weight = 100343.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.074906 restraints weight = 63270.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.075911 restraints weight = 45202.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.076478 restraints weight = 35799.520| |-----------------------------------------------------------------------------| r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 10888 Z= 0.125 Angle : 0.593 10.720 14957 Z= 0.326 Chirality : 0.040 0.464 1656 Planarity : 0.003 0.036 1691 Dihedral : 20.365 172.172 1974 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.18 % Allowed : 13.96 % Favored : 85.86 % Rotamer: Outliers : 1.08 % Allowed : 11.48 % Favored : 87.44 % 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: -3.19 (0.24), residues: 1103 helix: -0.78 (0.29), residues: 345 sheet: -3.70 (0.46), residues: 90 loop : -2.76 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1011 TYR 0.014 0.001 TYR A 242 PHE 0.009 0.001 PHE A 607 TRP 0.017 0.002 TRP A1174 HIS 0.003 0.001 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.13 (10888) covalent geometry : angle 0.59285 / 0.33 (14957) hydrogen bonds : bond 0.06866 / 3.91 ( 238) hydrogen bonds : angle 6.01484 / 4.11 ( 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 72 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.422 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: A 13 SER cc_start: 0.8180 (OUTLIER) cc_final: 0.7798 (p) REVERT: A 337 TRP cc_start: 0.8889 (m100) cc_final: 0.8675 (m100) REVERT: A 1100 MET cc_start: 0.9023 (mmp) cc_final: 0.8724 (mmm) outliers start: 11 outliers final: 8 residues processed: 66 average time/residue: 0.2451 time to fit residues: 22.3746 Evaluate side-chains 67 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 26 THR 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 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: 4.9990 chunk 25 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 26 optimal weight: 0.1980 chunk 107 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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 = 0.4254 r_free = 0.4254 target = 0.084354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.069895 restraints weight = 198599.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.072473 restraints weight = 101523.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.074067 restraints weight = 63823.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.075067 restraints weight = 45959.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.075701 restraints weight = 36481.198| |-----------------------------------------------------------------------------| r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10888 Z= 0.160 Angle : 0.605 10.844 14957 Z= 0.335 Chirality : 0.040 0.467 1656 Planarity : 0.003 0.037 1691 Dihedral : 20.337 175.661 1974 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.18 % Allowed : 14.78 % Favored : 85.04 % Rotamer: Outliers : 1.18 % Allowed : 11.78 % Favored : 87.05 % 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: -0.74 (0.29), residues: 340 sheet: -3.70 (0.46), residues: 90 loop : -2.75 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1011 TYR 0.017 0.001 TYR A 242 PHE 0.010 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 0.00319 / 0.16 (10888) covalent geometry : angle 0.60510 / 0.33 (14957) hydrogen bonds : bond 0.06977 / 3.98 ( 238) hydrogen bonds : angle 6.04342 / 4.13 ( 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: 12 poor density : 60 time to evaluate : 0.353 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: A 13 SER cc_start: 0.8250 (OUTLIER) cc_final: 0.7861 (p) REVERT: A 226 ASP cc_start: 0.7452 (OUTLIER) cc_final: 0.6920 (m-30) REVERT: A 337 TRP cc_start: 0.8937 (m100) cc_final: 0.8737 (m100) REVERT: A 1100 MET cc_start: 0.9069 (mmp) cc_final: 0.8727 (mmm) outliers start: 12 outliers final: 10 residues processed: 65 average time/residue: 0.2603 time to fit residues: 23.3516 Evaluate side-chains 71 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER 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 900 ASN 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: 4.9990 chunk 73 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 80 optimal weight: 0.1980 chunk 39 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 278 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.084730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.070228 restraints weight = 198003.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.072821 restraints weight = 101219.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.074419 restraints weight = 63608.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.075430 restraints weight = 45777.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.076057 restraints weight = 36272.505| |-----------------------------------------------------------------------------| r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10888 Z= 0.138 Angle : 0.585 10.881 14957 Z= 0.326 Chirality : 0.040 0.469 1656 Planarity : 0.003 0.037 1691 Dihedral : 20.317 179.198 1974 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.18 % Allowed : 14.14 % Favored : 85.68 % Rotamer: Outliers : 1.08 % Allowed : 12.27 % Favored : 86.65 % 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: -3.15 (0.24), residues: 1103 helix: -0.76 (0.29), residues: 341 sheet: -3.64 (0.47), residues: 90 loop : -2.73 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 710 TYR 0.014 0.001 TYR A 242 PHE 0.015 0.001 PHE A 578 TRP 0.015 0.002 TRP A 871 HIS 0.004 0.001 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.14 (10888) covalent geometry : angle 0.58542 / 0.33 (14957) hydrogen bonds : bond 0.06667 / 3.76 ( 238) hydrogen bonds : angle 5.90108 / 4.02 ( 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: 11 poor density : 62 time to evaluate : 0.459 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: A 13 SER cc_start: 0.8227 (OUTLIER) cc_final: 0.7842 (p) REVERT: A 226 ASP cc_start: 0.7377 (OUTLIER) cc_final: 0.6910 (m-30) REVERT: A 538 MET cc_start: 0.4660 (mmt) cc_final: 0.4429 (mmt) REVERT: A 1100 MET cc_start: 0.8917 (mmp) cc_final: 0.8602 (mmm) outliers start: 11 outliers final: 9 residues processed: 66 average time/residue: 0.2760 time to fit residues: 24.9002 Evaluate side-chains 71 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER 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 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 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: 0.5980 chunk 21 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 67 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 = 0.4261 r_free = 0.4261 target = 0.084580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.070096 restraints weight = 197219.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.072670 restraints weight = 101103.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.074247 restraints weight = 63640.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.075260 restraints weight = 45918.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.075819 restraints weight = 36380.603| |-----------------------------------------------------------------------------| r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10888 Z= 0.141 Angle : 0.583 10.432 14957 Z= 0.324 Chirality : 0.040 0.465 1656 Planarity : 0.004 0.064 1691 Dihedral : 20.281 176.813 1974 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.18 % Allowed : 14.60 % Favored : 85.22 % Rotamer: Outliers : 1.08 % Allowed : 12.07 % Favored : 86.85 % 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: -3.15 (0.24), residues: 1103 helix: -0.74 (0.29), residues: 340 sheet: -3.63 (0.47), residues: 90 loop : -2.74 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 710 TYR 0.026 0.001 TYR A 242 PHE 0.010 0.001 PHE A 607 TRP 0.013 0.001 TRP A 871 HIS 0.003 0.001 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 (10888) covalent geometry : angle 0.58254 / 0.32 (14957) hydrogen bonds : bond 0.06523 / 3.68 ( 238) hydrogen bonds : angle 5.85182 / 4.00 ( 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 72 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.521 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: A 13 SER cc_start: 0.8172 (OUTLIER) cc_final: 0.7780 (p) REVERT: A 226 ASP cc_start: 0.7411 (OUTLIER) cc_final: 0.6867 (m-30) REVERT: A 1100 MET cc_start: 0.9049 (mmp) cc_final: 0.8712 (mmm) outliers start: 11 outliers final: 9 residues processed: 65 average time/residue: 0.2311 time to fit residues: 21.4205 Evaluate side-chains 72 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER 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 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 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: 0.9980 chunk 5 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 98 optimal weight: 0.4980 chunk 70 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 108 optimal weight: 0.4980 chunk 48 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 250 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 = 0.4288 r_free = 0.4288 target = 0.085886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.071379 restraints weight = 195832.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.073999 restraints weight = 100074.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.075607 restraints weight = 62864.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.076625 restraints weight = 45149.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.077295 restraints weight = 35718.370| |-----------------------------------------------------------------------------| r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10888 Z= 0.110 Angle : 0.555 10.066 14957 Z= 0.308 Chirality : 0.039 0.449 1656 Planarity : 0.003 0.037 1691 Dihedral : 20.194 172.542 1974 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.18 % Allowed : 13.24 % Favored : 86.58 % Rotamer: Outliers : 0.88 % Allowed : 12.37 % 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: -2.99 (0.25), residues: 1103 helix: -0.65 (0.29), residues: 340 sheet: -3.46 (0.49), residues: 80 loop : -2.65 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 710 TYR 0.017 0.001 TYR A 242 PHE 0.016 0.001 PHE A 578 TRP 0.015 0.002 TRP A 871 HIS 0.002 0.001 HIS A 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 (10888) covalent geometry : angle 0.55452 / 0.31 (14957) hydrogen bonds : bond 0.06217 / 3.46 ( 238) hydrogen bonds : angle 5.67108 / 3.88 ( 627) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3483.95 seconds wall clock time: 60 minutes 24.11 seconds (3624.11 seconds total)