Starting phenix.real_space_refine on Sun Aug 24 15:51:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i54_35191/08_2025/8i54_35191.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i54_35191/08_2025/8i54_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_2025/8i54_35191.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i54_35191/08_2025/8i54_35191.map" model { file = "/net/cci-nas-00/data/ceres_data/8i54_35191/08_2025/8i54_35191.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i54_35191/08_2025/8i54_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-2.0-5787/lib/python3.9/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: 3.52, per 1000 atoms: 0.18 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: 1.94 Conformation dependent library (CDL) restraints added in 471.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 3.35 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: 4.35 Time building geometry restraints manager: 2.56 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: 9031 34.16 - 68.32: 398 68.32 - 102.48: 30 102.48 - 136.64: 3 136.64 - 170.80: 5 Dihedral angle restraints: 9467 sinusoidal: 5548 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 9464 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1572 0.089 - 0.179: 78 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: 1.140 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: 0.110 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 21.320 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 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= 0.887 Angle : 1.027 37.532 14957 Z= 0.608 Chirality : 0.046 0.447 1656 Planarity : 0.009 0.273 1691 Dihedral : 19.005 170.798 4432 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 aren 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 covalent geometry : bond 0.01293 (10888) covalent geometry : angle 1.02687 (14957) hydrogen bonds : bond 0.20049 ( 238) hydrogen bonds : angle 9.26329 ( 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 : 0.535 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: 0.2474 time to fit residues: 29.3641 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 : 0.574 ------------------------------------------------------------------------------- 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: 9.9990 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... Flipped N/Q/H residues before XYZ refinement: ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 ASN A 336 ASN A 820 ASN A1053 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.084046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.069488 restraints weight = 197477.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.072072 restraints weight = 100029.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.073692 restraints weight = 63038.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.074721 restraints weight = 45329.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.075385 restraints weight = 35787.101| |-----------------------------------------------------------------------------| r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 10888 Z= 0.229 Angle : 0.690 10.986 14957 Z= 0.383 Chirality : 0.042 0.464 1656 Planarity : 0.004 0.047 1691 Dihedral : 21.982 179.453 2086 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.36 % Allowed : 13.60 % Favored : 86.04 % Rotamer: Outliers : 1.08 % Allowed : 4.91 % Favored : 94.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.16 (0.24), residues: 1103 helix: -0.93 (0.27), residues: 343 sheet: -3.61 (0.47), residues: 90 loop : -2.64 (0.22), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 771 TYR 0.014 0.002 TYR A 764 PHE 0.011 0.002 PHE A 607 TRP 0.020 0.002 TRP A 871 HIS 0.004 0.001 HIS A 699 Details of bonding type rmsd covalent geometry : bond 0.00475 (10888) covalent geometry : angle 0.68963 (14957) hydrogen bonds : bond 0.07734 ( 238) hydrogen bonds : angle 6.64478 ( 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 76 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.523 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: 0.6756 (tmm) cc_final: 0.6340 (tmm) REVERT: A 1013 PHE cc_start: 0.8825 (m-80) cc_final: 0.8526 (m-80) REVERT: A 1100 MET cc_start: 0.9123 (mmp) cc_final: 0.8735 (mmm) outliers start: 11 outliers final: 8 residues processed: 71 average time/residue: 0.2617 time to fit residues: 25.6666 Evaluate side-chains 66 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 5.9990 chunk 31 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 93 optimal weight: 0.0870 chunk 71 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 overall best weight: 4.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN A 45 ASN ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 GLN A 582 ASN A 685 ASN ** A 840 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 887 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.082127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.067830 restraints weight = 204099.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.070297 restraints weight = 105887.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.071858 restraints weight = 67575.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.072856 restraints weight = 48939.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.073403 restraints weight = 39078.922| |-----------------------------------------------------------------------------| r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 10888 Z= 0.260 Angle : 0.708 11.134 14957 Z= 0.397 Chirality : 0.043 0.470 1656 Planarity : 0.004 0.044 1691 Dihedral : 22.120 170.073 2080 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 25.30 Ramachandran Plot: Outliers : 0.27 % Allowed : 14.78 % Favored : 84.95 % Rotamer: Outliers : 1.28 % Allowed : 7.75 % Favored : 90.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.50 (0.24), residues: 1103 helix: -1.26 (0.27), residues: 344 sheet: -3.73 (0.51), residues: 90 loop : -2.84 (0.22), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 771 TYR 0.019 0.002 TYR A 764 PHE 0.016 0.002 PHE A 607 TRP 0.021 0.002 TRP A 871 HIS 0.005 0.001 HIS A 626 Details of bonding type rmsd covalent geometry : bond 0.00537 (10888) covalent geometry : angle 0.70797 (14957) hydrogen bonds : bond 0.07384 ( 238) hydrogen bonds : angle 6.64638 ( 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 72 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.554 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 226 ASP cc_start: 0.7633 (OUTLIER) cc_final: 0.7242 (m-30) REVERT: A 704 MET cc_start: 0.7165 (tmm) cc_final: 0.6700 (tmm) REVERT: A 1100 MET cc_start: 0.9098 (mmp) cc_final: 0.8762 (mmm) outliers start: 13 outliers final: 8 residues processed: 67 average time/residue: 0.2751 time to fit residues: 25.1085 Evaluate side-chains 65 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 493 LYS Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 857 LEU 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: 0.0470 chunk 14 optimal weight: 8.9990 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 chunk 28 optimal weight: 20.0000 chunk 67 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 overall best weight: 2.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4244 r_free = 0.4244 target = 0.083707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.069314 restraints weight = 199205.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.071868 restraints weight = 101265.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.073464 restraints weight = 63628.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.074456 restraints weight = 45622.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.075088 restraints weight = 36437.870| |-----------------------------------------------------------------------------| r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10888 Z= 0.172 Angle : 0.614 10.580 14957 Z= 0.342 Chirality : 0.040 0.451 1656 Planarity : 0.004 0.038 1691 Dihedral : 21.867 175.395 2080 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 18.73 Ramachandran Plot: Outliers : 0.18 % Allowed : 14.51 % Favored : 85.31 % Rotamer: Outliers : 1.18 % Allowed : 9.72 % 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 aren not related in a simple way. whole: -3.34 (0.24), residues: 1103 helix: -1.02 (0.28), residues: 344 sheet: -3.66 (0.49), residues: 90 loop : -2.80 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 710 TYR 0.019 0.002 TYR A 242 PHE 0.011 0.001 PHE A 607 TRP 0.024 0.002 TRP A 871 HIS 0.004 0.001 HIS A 626 Details of bonding type rmsd covalent geometry : bond 0.00355 (10888) covalent geometry : angle 0.61392 (14957) hydrogen bonds : bond 0.06864 ( 238) hydrogen bonds : angle 6.17008 ( 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 73 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.524 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: 0.8398 (OUTLIER) cc_final: 0.8028 (p) REVERT: A 1100 MET cc_start: 0.9096 (mmp) cc_final: 0.8763 (mmm) outliers start: 12 outliers final: 10 residues processed: 67 average time/residue: 0.2893 time to fit residues: 26.2343 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 : 0.543 ------------------------------------------------------------------------------- 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 104 VAL Chi-restraints excluded: chain A residue 220 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 7 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 26 optimal weight: 0.3980 chunk 87 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.082538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.068130 restraints weight = 200140.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.070656 restraints weight = 102420.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.072210 restraints weight = 64559.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.073213 restraints weight = 46487.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.073845 restraints weight = 36968.893| |-----------------------------------------------------------------------------| r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10888 Z= 0.197 Angle : 0.632 10.880 14957 Z= 0.356 Chirality : 0.040 0.462 1656 Planarity : 0.004 0.038 1691 Dihedral : 21.881 174.983 2080 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 22.26 Ramachandran Plot: Outliers : 0.18 % Allowed : 16.59 % Favored : 83.23 % Rotamer: Outliers : 1.57 % Allowed : 11.48 % 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 aren not related in a simple way. whole: -3.46 (0.24), residues: 1103 helix: -1.09 (0.28), residues: 339 sheet: -3.72 (0.48), residues: 90 loop : -2.88 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 771 TYR 0.018 0.002 TYR A 242 PHE 0.014 0.001 PHE A 607 TRP 0.013 0.002 TRP A 871 HIS 0.003 0.001 HIS A 626 Details of bonding type rmsd covalent geometry : bond 0.00415 (10888) covalent geometry : angle 0.63224 (14957) hydrogen bonds : bond 0.06416 ( 238) hydrogen bonds : angle 6.17972 ( 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 76 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 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: symmetry clash REVERT: A 13 SER cc_start: 0.8417 (OUTLIER) cc_final: 0.8076 (p) REVERT: A 226 ASP cc_start: 0.7522 (OUTLIER) cc_final: 0.6904 (m-30) REVERT: A 329 MET cc_start: 0.6064 (mtm) cc_final: 0.5788 (mpp) REVERT: A 704 MET cc_start: 0.7195 (tmm) cc_final: 0.6755 (tmm) REVERT: A 851 THR cc_start: 0.4237 (OUTLIER) cc_final: 0.3985 (p) REVERT: A 1100 MET cc_start: 0.9048 (mmp) cc_final: 0.8717 (mmm) outliers start: 16 outliers final: 12 residues processed: 69 average time/residue: 0.2798 time to fit residues: 26.2242 Evaluate side-chains 71 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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 104 VAL Chi-restraints excluded: chain A residue 220 LEU 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 851 THR Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain A residue 1070 ASP 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: 4.9990 chunk 50 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 2 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 ASN A 670 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.084636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.070276 restraints weight = 196745.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.072853 restraints weight = 100370.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.074441 restraints weight = 62885.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.075434 restraints weight = 45143.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.076099 restraints weight = 35783.552| |-----------------------------------------------------------------------------| r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.2943 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= 0.127 Angle : 0.561 9.980 14957 Z= 0.312 Chirality : 0.039 0.447 1656 Planarity : 0.003 0.038 1691 Dihedral : 21.575 169.008 2080 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 14.05 % Favored : 85.86 % Rotamer: Outliers : 1.18 % Allowed : 12.07 % 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 aren not related in a simple way. whole: -3.20 (0.24), residues: 1103 helix: -0.77 (0.29), residues: 332 sheet: -3.53 (0.49), residues: 90 loop : -2.78 (0.22), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 710 TYR 0.016 0.001 TYR A 262 PHE 0.009 0.001 PHE A 182 TRP 0.013 0.002 TRP A 871 HIS 0.003 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00272 (10888) covalent geometry : angle 0.56081 (14957) hydrogen bonds : bond 0.05878 ( 238) hydrogen bonds : angle 5.78416 ( 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 74 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.553 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 13 SER cc_start: 0.7988 (OUTLIER) cc_final: 0.7606 (p) REVERT: A 1100 MET cc_start: 0.9064 (mmp) cc_final: 0.8697 (mmm) outliers start: 12 outliers final: 9 residues processed: 69 average time/residue: 0.2970 time to fit residues: 27.9542 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 : 0.607 ------------------------------------------------------------------------------- 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 104 VAL Chi-restraints excluded: chain A residue 220 LEU 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 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: 0.9990 chunk 46 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.083534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.069171 restraints weight = 199392.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.071717 restraints weight = 101546.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.073299 restraints weight = 63899.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.074282 restraints weight = 45931.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.074899 restraints weight = 36392.901| |-----------------------------------------------------------------------------| r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10888 Z= 0.156 Angle : 0.573 9.550 14957 Z= 0.322 Chirality : 0.039 0.442 1656 Planarity : 0.004 0.037 1691 Dihedral : 21.529 174.218 2080 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 15.14 % Favored : 84.77 % Rotamer: Outliers : 1.37 % Allowed : 12.66 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.27 (0.24), residues: 1103 helix: -0.89 (0.28), residues: 341 sheet: -3.63 (0.48), residues: 90 loop : -2.79 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 710 TYR 0.015 0.001 TYR A 262 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 covalent geometry : bond 0.00329 (10888) covalent geometry : angle 0.57265 (14957) hydrogen bonds : bond 0.05848 ( 238) hydrogen bonds : angle 5.77859 ( 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 75 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.539 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 13 SER cc_start: 0.8224 (OUTLIER) cc_final: 0.7846 (p) REVERT: A 704 MET cc_start: 0.7138 (tmm) cc_final: 0.6628 (tmm) REVERT: A 851 THR cc_start: 0.4418 (OUTLIER) cc_final: 0.4164 (p) REVERT: A 1013 PHE cc_start: 0.8601 (m-80) cc_final: 0.8377 (m-80) REVERT: A 1100 MET cc_start: 0.9104 (mmp) cc_final: 0.8744 (mmm) outliers start: 14 outliers final: 12 residues processed: 68 average time/residue: 0.3065 time to fit residues: 28.3364 Evaluate side-chains 74 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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 104 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 481 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 851 THR Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 999 PHE 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: 0.9980 chunk 0 optimal weight: 4.9990 chunk 27 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.081596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.067279 restraints weight = 200786.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.069755 restraints weight = 102781.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.071276 restraints weight = 65011.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.072246 restraints weight = 47067.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.072870 restraints weight = 37533.747| |-----------------------------------------------------------------------------| r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10888 Z= 0.217 Angle : 0.640 11.612 14957 Z= 0.361 Chirality : 0.041 0.510 1656 Planarity : 0.004 0.037 1691 Dihedral : 21.754 179.950 2080 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 23.58 Ramachandran Plot: Outliers : 0.18 % Allowed : 17.68 % Favored : 82.14 % Rotamer: Outliers : 1.57 % Allowed : 13.35 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.55 (0.24), residues: 1103 helix: -1.16 (0.27), residues: 339 sheet: -3.72 (0.47), residues: 90 loop : -2.96 (0.22), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 771 TYR 0.018 0.002 TYR A 764 PHE 0.014 0.002 PHE A 182 TRP 0.011 0.002 TRP A 871 HIS 0.004 0.001 HIS A 626 Details of bonding type rmsd covalent geometry : bond 0.00453 (10888) covalent geometry : angle 0.63958 (14957) hydrogen bonds : bond 0.06085 ( 238) hydrogen bonds : angle 6.06001 ( 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 76 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 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: symmetry clash REVERT: A 13 SER cc_start: 0.8273 (OUTLIER) cc_final: 0.7877 (p) REVERT: A 329 MET cc_start: 0.6099 (mtm) cc_final: 0.5843 (mpp) REVERT: A 704 MET cc_start: 0.7246 (tmm) cc_final: 0.6748 (tmm) REVERT: A 851 THR cc_start: 0.4675 (OUTLIER) cc_final: 0.4245 (p) REVERT: A 1013 PHE cc_start: 0.8535 (m-80) cc_final: 0.8278 (m-80) REVERT: A 1100 MET cc_start: 0.9067 (mmp) cc_final: 0.8747 (mmm) outliers start: 16 outliers final: 13 residues processed: 69 average time/residue: 0.2979 time to fit residues: 28.0319 Evaluate side-chains 72 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.656 ------------------------------------------------------------------------------- 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 104 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 481 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 851 THR Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 999 PHE 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: 2.9990 chunk 73 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** A 250 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 = 0.4268 r_free = 0.4268 target = 0.084751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.070385 restraints weight = 197149.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.072970 restraints weight = 100389.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.074569 restraints weight = 62823.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.075576 restraints weight = 44838.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.076214 restraints weight = 35507.318| |-----------------------------------------------------------------------------| r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10888 Z= 0.114 Angle : 0.555 9.462 14957 Z= 0.306 Chirality : 0.038 0.447 1656 Planarity : 0.003 0.037 1691 Dihedral : 21.463 176.849 2080 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 13.87 % Favored : 86.04 % Rotamer: Outliers : 1.18 % Allowed : 14.13 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.19 (0.24), residues: 1103 helix: -0.81 (0.28), residues: 335 sheet: -3.47 (0.50), residues: 90 loop : -2.75 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1011 TYR 0.015 0.001 TYR A 262 PHE 0.011 0.001 PHE A 703 TRP 0.018 0.002 TRP A1174 HIS 0.003 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00246 (10888) covalent geometry : angle 0.55461 (14957) hydrogen bonds : bond 0.05352 ( 238) hydrogen bonds : angle 5.62719 ( 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 74 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.552 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 1100 MET cc_start: 0.8991 (mmp) cc_final: 0.8602 (mmm) outliers start: 12 outliers final: 12 residues processed: 68 average time/residue: 0.2959 time to fit residues: 27.4060 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 : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 481 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 999 PHE Chi-restraints excluded: chain A residue 1006 VAL 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: 0.3980 chunk 82 optimal weight: 10.0000 chunk 87 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.083849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.069508 restraints weight = 197396.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.072049 restraints weight = 100795.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.073600 restraints weight = 63418.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.074582 restraints weight = 45743.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.075196 restraints weight = 36339.905| |-----------------------------------------------------------------------------| r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10888 Z= 0.137 Angle : 0.558 9.534 14957 Z= 0.311 Chirality : 0.038 0.452 1656 Planarity : 0.003 0.036 1691 Dihedral : 21.458 177.808 2080 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 16.23 % Favored : 83.68 % Rotamer: Outliers : 1.08 % Allowed : 14.03 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.21 (0.24), residues: 1103 helix: -0.85 (0.28), residues: 343 sheet: -3.47 (0.49), residues: 90 loop : -2.77 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 710 TYR 0.014 0.001 TYR A 242 PHE 0.011 0.001 PHE A 607 TRP 0.013 0.002 TRP A1174 HIS 0.003 0.001 HIS A 626 Details of bonding type rmsd covalent geometry : bond 0.00291 (10888) covalent geometry : angle 0.55758 (14957) hydrogen bonds : bond 0.05339 ( 238) hydrogen bonds : angle 5.65388 ( 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 : 0.570 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: 0.7114 (tmm) cc_final: 0.6609 (tmm) REVERT: A 1100 MET cc_start: 0.9026 (mmp) cc_final: 0.8659 (mmm) outliers start: 11 outliers final: 10 residues processed: 66 average time/residue: 0.3235 time to fit residues: 28.5892 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 : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1006 VAL 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: 2.9990 chunk 5 optimal weight: 6.9990 chunk 32 optimal weight: 20.0000 chunk 98 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 720 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.082752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.068467 restraints weight = 199105.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.070949 restraints weight = 101768.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.072488 restraints weight = 64428.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.073467 restraints weight = 46473.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.074080 restraints weight = 37013.865| |-----------------------------------------------------------------------------| r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10888 Z= 0.171 Angle : 0.590 9.600 14957 Z= 0.331 Chirality : 0.039 0.454 1656 Planarity : 0.004 0.101 1691 Dihedral : 21.549 179.881 2076 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 20.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 16.68 % Favored : 83.23 % Rotamer: Outliers : 1.18 % Allowed : 14.33 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.35 (0.24), residues: 1103 helix: -1.01 (0.28), residues: 347 sheet: -3.48 (0.50), residues: 90 loop : -2.86 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 101 TYR 0.015 0.002 TYR A 242 PHE 0.015 0.001 PHE A 578 TRP 0.011 0.002 TRP A1174 HIS 0.003 0.001 HIS A 626 Details of bonding type rmsd covalent geometry : bond 0.00359 (10888) covalent geometry : angle 0.59004 (14957) hydrogen bonds : bond 0.05568 ( 238) hydrogen bonds : angle 5.76678 ( 627) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3855.72 seconds wall clock time: 66 minutes 48.01 seconds (4008.01 seconds total)