Starting phenix.real_space_refine on Wed May 21 06:39:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i54_35191/05_2025/8i54_35191.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i54_35191/05_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_35191/05_2025/8i54_35191.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i54_35191/05_2025/8i54_35191.map" model { file = "/net/cci-nas-00/data/ceres_data/8i54_35191/05_2025/8i54_35191.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i54_35191/05_2025/8i54_35191.cif" } resolution = 3.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 9.16, per 1000 atoms: 0.47 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: 4.87 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 8.69 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: 6.88 Time building geometry restraints manager: 5.85 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.290 Extract box with map and model: 0.650 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 47.320 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.070 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.630 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.16 (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 TRP 0.011 0.002 TRP A 871 HIS 0.005 0.002 HIS A 699 PHE 0.030 0.002 PHE A 578 TYR 0.043 0.002 TYR A 80 ARG 0.009 0.001 ARG A 710 Details of bonding type rmsd hydrogen bonds : bond 0.20049 ( 238) hydrogen bonds : angle 9.26329 ( 627) covalent geometry : bond 0.01293 (10888) covalent geometry : angle 1.02687 (14957) *********************** 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 : 1.636 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: 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: 0.5179 time to fit residues: 62.2347 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 : 1.495 ------------------------------------------------------------------------------- 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 97 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 67 optimal weight: 8.9990 chunk 105 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 GLN A 286 ASN ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4241 r_free = 0.4241 target = 0.083937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.069348 restraints weight = 197236.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.071946 restraints weight = 100370.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.073562 restraints weight = 63260.505| |-----------------------------------------------------------------------------| r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 10888 Z= 0.240 Angle : 0.689 10.953 14957 Z= 0.384 Chirality : 0.042 0.469 1656 Planarity : 0.005 0.044 1691 Dihedral : 21.992 179.307 2086 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.36 % Allowed : 13.60 % Favored : 86.04 % Rotamer: Outliers : 1.18 % Allowed : 4.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.24), residues: 1103 helix: -0.94 (0.28), residues: 342 sheet: -3.62 (0.47), residues: 90 loop : -2.67 (0.22), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 871 HIS 0.005 0.001 HIS A 699 PHE 0.012 0.002 PHE A 607 TYR 0.015 0.002 TYR A 764 ARG 0.004 0.001 ARG A 771 Details of bonding type rmsd hydrogen bonds : bond 0.07547 ( 238) hydrogen bonds : angle 6.72572 ( 627) covalent geometry : bond 0.00495 (10888) covalent geometry : angle 0.68919 (14957) *********************** 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 77 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 1.465 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 329 MET cc_start: 0.6851 (mtm) cc_final: 0.6441 (mpp) REVERT: A 704 MET cc_start: 0.6855 (tmm) cc_final: 0.6584 (tmm) REVERT: A 1100 MET cc_start: 0.9165 (mmp) cc_final: 0.8779 (mmm) outliers start: 12 outliers final: 10 residues processed: 71 average time/residue: 0.5291 time to fit residues: 52.4060 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 : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 493 LYS Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 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 53 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 114 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 chunk 89 optimal weight: 6.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 840 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 887 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.081864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.067573 restraints weight = 202878.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.070019 restraints weight = 105882.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.071559 restraints weight = 67654.608| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 10888 Z= 0.263 Angle : 0.720 11.153 14957 Z= 0.403 Chirality : 0.043 0.476 1656 Planarity : 0.005 0.045 1691 Dihedral : 22.190 170.358 2082 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 25.10 Ramachandran Plot: Outliers : 0.27 % Allowed : 15.50 % Favored : 84.22 % Rotamer: Outliers : 1.47 % Allowed : 7.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.24), residues: 1103 helix: -1.33 (0.27), residues: 344 sheet: -3.76 (0.51), residues: 90 loop : -2.90 (0.22), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 871 HIS 0.006 0.002 HIS A 626 PHE 0.016 0.002 PHE A 607 TYR 0.020 0.002 TYR A 764 ARG 0.006 0.001 ARG A 771 Details of bonding type rmsd hydrogen bonds : bond 0.07454 ( 238) hydrogen bonds : angle 6.67452 ( 627) covalent geometry : bond 0.00541 (10888) covalent geometry : angle 0.71968 (14957) *********************** 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 74 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 1.499 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: 0.7660 (OUTLIER) cc_final: 0.7245 (m-30) REVERT: A 704 MET cc_start: 0.7218 (tmm) cc_final: 0.6771 (tmm) REVERT: A 1100 MET cc_start: 0.9117 (mmp) cc_final: 0.8786 (mmm) REVERT: A 1192 MET cc_start: 0.7055 (mmm) cc_final: 0.6845 (mmt) outliers start: 15 outliers final: 10 residues processed: 68 average time/residue: 0.5682 time to fit residues: 52.9612 Evaluate side-chains 67 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 1.361 ------------------------------------------------------------------------------- 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 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 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 64 optimal weight: 0.9980 chunk 24 optimal weight: 10.0000 chunk 110 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 GLN A 582 ASN A 748 ASN ** A1053 ASN ** 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 = 0.4219 r_free = 0.4219 target = 0.082541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.068155 restraints weight = 200527.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.070642 restraints weight = 102166.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.072195 restraints weight = 64552.449| |-----------------------------------------------------------------------------| r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10888 Z= 0.205 Angle : 0.649 10.667 14957 Z= 0.362 Chirality : 0.041 0.463 1656 Planarity : 0.004 0.040 1691 Dihedral : 21.998 178.951 2082 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 22.94 Ramachandran Plot: Outliers : 0.27 % Allowed : 15.87 % Favored : 83.86 % Rotamer: Outliers : 1.47 % Allowed : 10.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.24), residues: 1103 helix: -1.26 (0.27), residues: 346 sheet: -3.74 (0.49), residues: 90 loop : -2.93 (0.22), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 871 HIS 0.005 0.001 HIS A 626 PHE 0.014 0.001 PHE A 182 TYR 0.018 0.002 TYR A 764 ARG 0.005 0.001 ARG A 771 Details of bonding type rmsd hydrogen bonds : bond 0.06880 ( 238) hydrogen bonds : angle 6.35934 ( 627) covalent geometry : bond 0.00423 (10888) covalent geometry : angle 0.64947 (14957) *********************** 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 77 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 1.393 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 13 SER cc_start: 0.8494 (OUTLIER) cc_final: 0.8125 (p) REVERT: A 1100 MET cc_start: 0.9165 (mmp) cc_final: 0.8842 (mmm) outliers start: 15 outliers final: 11 residues processed: 70 average time/residue: 0.5662 time to fit residues: 54.4114 Evaluate side-chains 68 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 1.426 ------------------------------------------------------------------------------- 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 900 ASN 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 70 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 111 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.083782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.069348 restraints weight = 199214.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.071925 restraints weight = 101448.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.073501 restraints weight = 63812.863| |-----------------------------------------------------------------------------| r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10888 Z= 0.150 Angle : 0.592 10.154 14957 Z= 0.330 Chirality : 0.039 0.446 1656 Planarity : 0.004 0.038 1691 Dihedral : 21.767 174.778 2080 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.18 % Allowed : 15.59 % Favored : 84.22 % Rotamer: Outliers : 1.37 % Allowed : 12.17 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.24), residues: 1103 helix: -0.97 (0.28), residues: 339 sheet: -3.64 (0.49), residues: 90 loop : -2.80 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 871 HIS 0.003 0.001 HIS A 626 PHE 0.011 0.001 PHE A 607 TYR 0.023 0.001 TYR A 242 ARG 0.003 0.000 ARG A 710 Details of bonding type rmsd hydrogen bonds : bond 0.06258 ( 238) hydrogen bonds : angle 5.97916 ( 627) covalent geometry : bond 0.00317 (10888) covalent geometry : angle 0.59198 (14957) *********************** 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 75 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 1.373 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: 0.8178 (OUTLIER) cc_final: 0.7791 (p) REVERT: A 1100 MET cc_start: 0.9237 (mmp) cc_final: 0.8857 (mmm) outliers start: 14 outliers final: 10 residues processed: 67 average time/residue: 0.5719 time to fit residues: 52.3691 Evaluate side-chains 70 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 1.479 ------------------------------------------------------------------------------- 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 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 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 50 optimal weight: 7.9990 chunk 101 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.082267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.067860 restraints weight = 199844.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.070365 restraints weight = 102449.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.071909 restraints weight = 64665.939| |-----------------------------------------------------------------------------| r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 10888 Z= 0.196 Angle : 0.620 9.822 14957 Z= 0.349 Chirality : 0.040 0.448 1656 Planarity : 0.004 0.037 1691 Dihedral : 21.728 171.507 2080 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 22.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 16.59 % Favored : 83.32 % Rotamer: Outliers : 1.57 % Allowed : 12.56 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.24), residues: 1103 helix: -1.25 (0.27), residues: 347 sheet: -3.66 (0.51), residues: 86 loop : -2.90 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 871 HIS 0.004 0.001 HIS A 626 PHE 0.013 0.001 PHE A 607 TYR 0.019 0.002 TYR A 242 ARG 0.004 0.000 ARG A 771 Details of bonding type rmsd hydrogen bonds : bond 0.06200 ( 238) hydrogen bonds : angle 6.07149 ( 627) covalent geometry : bond 0.00414 (10888) covalent geometry : angle 0.61983 (14957) *********************** 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 75 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 1.593 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: 0.8389 (OUTLIER) cc_final: 0.8023 (p) REVERT: A 704 MET cc_start: 0.7323 (tmm) cc_final: 0.6823 (tmm) REVERT: A 1100 MET cc_start: 0.9189 (mmp) cc_final: 0.8835 (mmm) outliers start: 16 outliers final: 14 residues processed: 68 average time/residue: 0.5730 time to fit residues: 53.9186 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 : 1.503 ------------------------------------------------------------------------------- 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 145 ASN Chi-restraints excluded: chain A residue 329 MET 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 900 ASN Chi-restraints excluded: chain A residue 999 PHE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 79 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 0.0030 chunk 82 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 37 optimal weight: 9.9990 chunk 72 optimal weight: 0.5980 chunk 29 optimal weight: 7.9990 overall best weight: 0.8392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.085266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.070860 restraints weight = 196110.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.073497 restraints weight = 100016.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.075093 restraints weight = 62620.411| |-----------------------------------------------------------------------------| r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.3156 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= 0.111 Angle : 0.544 9.218 14957 Z= 0.302 Chirality : 0.038 0.436 1656 Planarity : 0.003 0.037 1691 Dihedral : 21.462 171.325 2080 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 13.69 % Favored : 86.22 % Rotamer: Outliers : 1.08 % Allowed : 13.54 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.24), residues: 1103 helix: -0.76 (0.28), residues: 336 sheet: -3.53 (0.49), residues: 90 loop : -2.71 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 871 HIS 0.003 0.001 HIS A 57 PHE 0.009 0.001 PHE A 703 TYR 0.015 0.001 TYR A 262 ARG 0.004 0.000 ARG A 710 Details of bonding type rmsd hydrogen bonds : bond 0.05550 ( 238) hydrogen bonds : angle 5.61035 ( 627) covalent geometry : bond 0.00241 (10888) covalent geometry : angle 0.54411 (14957) *********************** 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 76 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 1.415 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 1100 MET cc_start: 0.8982 (mmp) cc_final: 0.8606 (mmm) outliers start: 11 outliers final: 10 residues processed: 69 average time/residue: 0.5523 time to fit residues: 52.2032 Evaluate side-chains 73 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 1.381 ------------------------------------------------------------------------------- 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 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 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 63 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 99 optimal weight: 0.0570 chunk 65 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 100 optimal weight: 0.6980 overall best weight: 1.7502 ------------------------------------------------------------------------------- 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 = 0.4249 r_free = 0.4249 target = 0.083894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.069563 restraints weight = 198267.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.072095 restraints weight = 100946.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.073645 restraints weight = 63409.115| |-----------------------------------------------------------------------------| r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10888 Z= 0.143 Angle : 0.555 9.173 14957 Z= 0.312 Chirality : 0.038 0.441 1656 Planarity : 0.003 0.035 1691 Dihedral : 21.432 171.535 2080 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 15.59 % Favored : 84.32 % Rotamer: Outliers : 1.28 % Allowed : 13.74 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.24), residues: 1103 helix: -0.83 (0.28), residues: 344 sheet: -3.48 (0.50), residues: 86 loop : -2.72 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 871 HIS 0.003 0.001 HIS A 626 PHE 0.011 0.001 PHE A 607 TYR 0.015 0.001 TYR A 242 ARG 0.004 0.000 ARG A 710 Details of bonding type rmsd hydrogen bonds : bond 0.05566 ( 238) hydrogen bonds : angle 5.64833 ( 627) covalent geometry : bond 0.00303 (10888) covalent geometry : angle 0.55504 (14957) *********************** 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 75 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 1.398 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: 0.8206 (OUTLIER) cc_final: 0.7775 (p) REVERT: A 704 MET cc_start: 0.7255 (tmm) cc_final: 0.6736 (tmm) REVERT: A 1100 MET cc_start: 0.9123 (mmp) cc_final: 0.8734 (mmm) outliers start: 13 outliers final: 11 residues processed: 69 average time/residue: 0.5740 time to fit residues: 54.3375 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 : 1.422 ------------------------------------------------------------------------------- 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 329 MET 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 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 14 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 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 278 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.081477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.067146 restraints weight = 200162.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.069606 restraints weight = 102921.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.071127 restraints weight = 65295.552| |-----------------------------------------------------------------------------| r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.3725 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 : 0.637 9.354 14957 Z= 0.359 Chirality : 0.040 0.452 1656 Planarity : 0.004 0.049 1691 Dihedral : 21.747 179.303 2080 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 24.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 17.95 % Favored : 81.96 % Rotamer: Outliers : 1.57 % Allowed : 13.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.24), residues: 1103 helix: -1.16 (0.27), residues: 341 sheet: -3.59 (0.51), residues: 86 loop : -2.91 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 871 HIS 0.005 0.001 HIS A 626 PHE 0.015 0.002 PHE A 607 TYR 0.018 0.002 TYR A 764 ARG 0.006 0.001 ARG A 710 Details of bonding type rmsd hydrogen bonds : bond 0.06082 ( 238) hydrogen bonds : angle 5.96564 ( 627) covalent geometry : bond 0.00453 (10888) covalent geometry : angle 0.63656 (14957) *********************** 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 75 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 1.431 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: 0.8345 (OUTLIER) cc_final: 0.7961 (p) REVERT: A 704 MET cc_start: 0.7408 (tmm) cc_final: 0.7126 (tmm) REVERT: A 1100 MET cc_start: 0.9083 (mmp) cc_final: 0.8777 (mmm) outliers start: 16 outliers final: 13 residues processed: 69 average time/residue: 0.5992 time to fit residues: 55.6501 Evaluate side-chains 70 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 1.397 ------------------------------------------------------------------------------- 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 329 MET 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 857 LEU Chi-restraints excluded: chain A residue 885 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 90 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 113 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 = 0.4211 r_free = 0.4211 target = 0.082044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.067673 restraints weight = 199579.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.070157 restraints weight = 102689.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.071701 restraints weight = 65144.985| |-----------------------------------------------------------------------------| r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.3816 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= 0.180 Angle : 0.608 10.281 14957 Z= 0.341 Chirality : 0.039 0.470 1656 Planarity : 0.004 0.091 1691 Dihedral : 21.685 179.969 2080 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 21.81 Ramachandran Plot: Outliers : 0.18 % Allowed : 16.59 % Favored : 83.23 % Rotamer: Outliers : 1.28 % Allowed : 14.13 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.24), residues: 1103 helix: -1.24 (0.27), residues: 348 sheet: -3.63 (0.49), residues: 86 loop : -2.92 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 871 HIS 0.003 0.001 HIS A 626 PHE 0.013 0.001 PHE A 578 TYR 0.016 0.002 TYR A 262 ARG 0.005 0.000 ARG A 710 Details of bonding type rmsd hydrogen bonds : bond 0.05707 ( 238) hydrogen bonds : angle 5.90788 ( 627) covalent geometry : bond 0.00375 (10888) covalent geometry : angle 0.60778 (14957) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 96 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Evaluate side-chains 71 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 1.420 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: 0.8332 (OUTLIER) cc_final: 0.7951 (p) REVERT: A 704 MET cc_start: 0.7299 (tmm) cc_final: 0.7011 (tmm) REVERT: A 1011 ARG cc_start: 0.9157 (mmm160) cc_final: 0.8849 (mmm-85) REVERT: A 1100 MET cc_start: 0.9055 (mmp) cc_final: 0.8728 (mmm) outliers start: 13 outliers final: 12 residues processed: 64 average time/residue: 0.5776 time to fit residues: 50.3664 Evaluate side-chains 69 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 1.390 ------------------------------------------------------------------------------- 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 329 MET 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 900 ASN 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 18 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.082628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.068231 restraints weight = 198781.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.070743 restraints weight = 102131.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.072276 restraints weight = 64618.972| |-----------------------------------------------------------------------------| r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10888 Z= 0.154 Angle : 0.582 9.861 14957 Z= 0.326 Chirality : 0.039 0.466 1656 Planarity : 0.004 0.084 1691 Dihedral : 21.588 179.268 2080 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 20.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 16.77 % Favored : 83.14 % Rotamer: Outliers : 1.28 % Allowed : 14.72 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.24), residues: 1103 helix: -1.12 (0.27), residues: 347 sheet: -3.57 (0.50), residues: 86 loop : -2.90 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 871 HIS 0.002 0.001 HIS A 601 PHE 0.012 0.001 PHE A 607 TYR 0.016 0.002 TYR A 262 ARG 0.007 0.000 ARG A 101 Details of bonding type rmsd hydrogen bonds : bond 0.05522 ( 238) hydrogen bonds : angle 5.77710 ( 627) covalent geometry : bond 0.00323 (10888) covalent geometry : angle 0.58187 (14957) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5998.08 seconds wall clock time: 104 minutes 34.44 seconds (6274.44 seconds total)