Starting phenix.real_space_refine on Fri Jul 3 05:57:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8d2l_27142/07_2026/8d2l_27142.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d2l_27142/07_2026/8d2l_27142.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8d2l_27142/07_2026/8d2l_27142.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d2l_27142/07_2026/8d2l_27142.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8d2l_27142/07_2026/8d2l_27142.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8d2l_27142/07_2026/8d2l_27142.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d2l_27142/07_2026/8d2l_27142.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d2l_27142/07_2026/8d2l_27142.map" } resolution = 2.21 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= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 151 5.49 5 Mg 10 5.21 5 S 20 5.16 5 C 6892 2.51 5 N 2199 2.21 5 O 2955 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12227 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 8720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 8720 Classifications: {'peptide': 1105} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 59, 'TRANS': 1041} Chain breaks: 3 Chain: "B" Number of atoms: 2080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 2080 Unusual residues: {'GTP': 1} Classifications: {'RNA': 96, 'undetermined': 1} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 7, 'rna3p_pur': 44, 'rna3p_pyr': 40} Link IDs: {'rna2p': 12, 'rna3p': 83, None: 1} Not linked: pdbres="GTP B 1 " pdbres=" G B 2 " Chain breaks: 1 Chain: "X" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 267 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "T" Number of atoms: 481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 481 Classifications: {'DNA': 24} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 23} Chain: "D" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 264 Classifications: {'DNA': 13} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 12} Chain: "Y" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Classifications: {'DNA': 3} Link IDs: {'rna3p': 2} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 180 Classifications: {'water': 180} Link IDs: {None: 179} Chain: "B" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 121 Classifications: {'water': 121} Link IDs: {None: 120} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "T" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 2.77, per 1000 atoms: 0.23 Number of scatterers: 12227 At special positions: 0 Unit cell: (95.7, 106.425, 129.525, 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 20 16.00 P 151 15.00 Mg 10 11.99 O 2955 8.00 N 2199 7.00 C 6892 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 575 " - pdb=" SG CYS A 578 " distance=2.08 Simple disulfide: pdb=" SG CYS A 575 " - pdb=" SG CYS A 610 " distance=2.12 Simple disulfide: pdb=" SG CYS A 575 " - pdb=" SG CYS A 613 " distance=1.94 Simple disulfide: pdb=" SG CYS A 578 " - pdb=" SG CYS A 610 " distance=1.94 Simple disulfide: pdb=" SG CYS A 578 " - pdb=" SG CYS A 613 " distance=2.08 Simple disulfide: pdb=" SG CYS A 610 " - pdb=" SG CYS A 613 " distance=2.07 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 473.0 milliseconds 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2074 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 10 sheets defined 50.3% alpha, 10.1% beta 56 base pairs and 96 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 59 through 92 Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 120 through 138 Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'A' and resid 158 through 173 Processing helix chain 'A' and resid 180 through 192 Processing helix chain 'A' and resid 221 through 237 Processing helix chain 'A' and resid 239 through 251 Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 279 through 293 Processing helix chain 'A' and resid 306 through 319 Processing helix chain 'A' and resid 326 through 333 Processing helix chain 'A' and resid 339 through 341 No H-bonds generated for 'chain 'A' and resid 339 through 341' Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 364 through 377 Processing helix chain 'A' and resid 381 through 391 Processing helix chain 'A' and resid 392 through 405 Processing helix chain 'A' and resid 406 through 408 No H-bonds generated for 'chain 'A' and resid 406 through 408' Processing helix chain 'A' and resid 421 through 430 Processing helix chain 'A' and resid 441 through 455 Processing helix chain 'A' and resid 458 through 468 Processing helix chain 'A' and resid 486 through 508 Processing helix chain 'A' and resid 524 through 552 Processing helix chain 'A' and resid 558 through 571 Processing helix chain 'A' and resid 594 through 598 Processing helix chain 'A' and resid 611 through 618 Processing helix chain 'A' and resid 621 through 629 Processing helix chain 'A' and resid 633 through 643 Processing helix chain 'A' and resid 653 through 669 Processing helix chain 'A' and resid 681 through 703 Processing helix chain 'A' and resid 712 through 722 Processing helix chain 'A' and resid 725 through 730 Processing helix chain 'A' and resid 742 through 747 removed outlier: 3.767A pdb=" N LEU A 745 " --> pdb=" O THR A 742 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ARG A 747 " --> pdb=" O ARG A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 758 Processing helix chain 'A' and resid 761 through 777 Processing helix chain 'A' and resid 797 through 807 Processing helix chain 'A' and resid 809 through 820 Processing helix chain 'A' and resid 856 through 861 Processing helix chain 'A' and resid 864 through 876 Processing helix chain 'A' and resid 957 through 963 Processing helix chain 'A' and resid 981 through 986 Processing helix chain 'A' and resid 988 through 997 Processing helix chain 'A' and resid 1024 through 1033 removed outlier: 3.647A pdb=" N MET A1028 " --> pdb=" O GLY A1024 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR A1032 " --> pdb=" O MET A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1057 through 1069 removed outlier: 3.721A pdb=" N ALA A1061 " --> pdb=" O SER A1057 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER A1069 " --> pdb=" O ARG A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1086 Processing helix chain 'A' and resid 1094 through 1098 Processing sheet with id=AA1, first strand: chain 'A' and resid 706 through 711 removed outlier: 6.901A pdb=" N TRP A 13 " --> pdb=" O SER A 512 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N VAL A 514 " --> pdb=" O TRP A 13 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU A 15 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N GLU A 516 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N VAL A 17 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE A 24 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL A 43 " --> pdb=" O ILE A 24 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU A 26 " --> pdb=" O ALA A 41 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ALA A 41 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ALA A 28 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ILE A 39 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N SER A 30 " --> pdb=" O LYS A 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 266 removed outlier: 5.719A pdb=" N GLN A 272 " --> pdb=" O ASP A 266 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 302 through 304 Processing sheet with id=AA4, first strand: chain 'A' and resid 588 through 591 Processing sheet with id=AA5, first strand: chain 'A' and resid 846 through 849 Processing sheet with id=AA6, first strand: chain 'A' and resid 854 through 855 Processing sheet with id=AA7, first strand: chain 'A' and resid 899 through 900 Processing sheet with id=AA8, first strand: chain 'A' and resid 921 through 924 Processing sheet with id=AA9, first strand: chain 'A' and resid 948 through 956 removed outlier: 3.653A pdb=" N GLY A1004 " --> pdb=" O VAL A 939 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ARG A 941 " --> pdb=" O GLN A1002 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N GLN A1002 " --> pdb=" O ARG A 941 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1090 through 1093 removed outlier: 6.617A pdb=" N ARG A1048 " --> pdb=" O PHE A1043 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N PHE A1043 " --> pdb=" O ARG A1048 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASN A1050 " --> pdb=" O THR A1041 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU A1011 " --> pdb=" O ILE A1106 " (cutoff:3.500A) 432 hydrogen bonds defined for protein. 1254 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 141 hydrogen bonds 266 hydrogen bond angles 0 basepair planarities 56 basepair parallelities 96 stacking parallelities Total time for adding SS restraints: 2.80 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2464 1.33 - 1.46: 4671 1.46 - 1.60: 5094 1.60 - 1.73: 176 1.73 - 1.87: 28 Bond restraints: 12433 Sorted by residual: bond pdb=" C1' DC T 21 " pdb=" N1 DC T 21 " ideal model delta sigma weight residual 1.468 1.556 -0.088 1.40e-02 5.10e+03 3.93e+01 bond pdb=" C3' DC X 3 " pdb=" O3' DC X 3 " ideal model delta sigma weight residual 1.435 1.506 -0.071 1.30e-02 5.92e+03 2.95e+01 bond pdb=" C5' DT X 4 " pdb=" C4' DT X 4 " ideal model delta sigma weight residual 1.512 1.548 -0.036 7.00e-03 2.04e+04 2.60e+01 bond pdb=" C1' DT T 22 " pdb=" N1 DT T 22 " ideal model delta sigma weight residual 1.468 1.534 -0.066 1.40e-02 5.10e+03 2.25e+01 bond pdb=" C3' DT D 30 " pdb=" O3' DT D 30 " ideal model delta sigma weight residual 1.435 1.376 0.059 1.30e-02 5.92e+03 2.08e+01 ... (remaining 12428 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.53: 17520 5.53 - 11.07: 33 11.07 - 16.60: 2 16.60 - 22.13: 0 22.13 - 27.67: 1 Bond angle restraints: 17556 Sorted by residual: angle pdb=" CA CYS A 613 " pdb=" CB CYS A 613 " pdb=" SG CYS A 613 " ideal model delta sigma weight residual 114.40 142.07 -27.67 2.30e+00 1.89e-01 1.45e+02 angle pdb=" O4' DC T 21 " pdb=" C1' DC T 21 " pdb=" N1 DC T 21 " ideal model delta sigma weight residual 108.00 113.55 -5.55 7.00e-01 2.04e+00 6.29e+01 angle pdb=" O4' DC X 3 " pdb=" C1' DC X 3 " pdb=" N1 DC X 3 " ideal model delta sigma weight residual 108.00 113.45 -5.45 7.00e-01 2.04e+00 6.07e+01 angle pdb=" O4' DG T 17 " pdb=" C1' DG T 17 " pdb=" N9 DG T 17 " ideal model delta sigma weight residual 108.00 113.27 -5.27 7.00e-01 2.04e+00 5.67e+01 angle pdb=" N CYS A 613 " pdb=" CA CYS A 613 " pdb=" CB CYS A 613 " ideal model delta sigma weight residual 110.16 100.24 9.92 1.48e+00 4.57e-01 4.49e+01 ... (remaining 17551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.25: 6903 33.25 - 66.50: 482 66.50 - 99.75: 54 99.75 - 133.00: 3 133.00 - 166.25: 1 Dihedral angle restraints: 7443 sinusoidal: 4247 harmonic: 3196 Sorted by residual: dihedral pdb=" CB CYS A 578 " pdb=" SG CYS A 578 " pdb=" SG CYS A 610 " pdb=" CB CYS A 610 " ideal model delta sinusoidal sigma weight residual -86.00 -172.88 86.88 1 1.00e+01 1.00e-02 9.08e+01 dihedral pdb=" CA ASP A 590 " pdb=" C ASP A 590 " pdb=" N HIS A 591 " pdb=" CA HIS A 591 " ideal model delta harmonic sigma weight residual 180.00 147.74 32.26 0 5.00e+00 4.00e-02 4.16e+01 dihedral pdb=" CB CYS A 575 " pdb=" SG CYS A 575 " pdb=" SG CYS A 613 " pdb=" CB CYS A 613 " ideal model delta sinusoidal sigma weight residual -86.00 -141.31 55.31 1 1.00e+01 1.00e-02 4.14e+01 ... (remaining 7440 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1697 0.066 - 0.132: 293 0.132 - 0.198: 23 0.198 - 0.264: 3 0.264 - 0.330: 4 Chirality restraints: 2020 Sorted by residual: chirality pdb=" CG LEU A 84 " pdb=" CB LEU A 84 " pdb=" CD1 LEU A 84 " pdb=" CD2 LEU A 84 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CB ILE A 24 " pdb=" CA ILE A 24 " pdb=" CG1 ILE A 24 " pdb=" CG2 ILE A 24 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C1' G B 30 " pdb=" O4' G B 30 " pdb=" C2' G B 30 " pdb=" N9 G B 30 " both_signs ideal model delta sigma weight residual False 2.46 2.18 0.28 2.00e-01 2.50e+01 1.89e+00 ... (remaining 2017 not shown) Planarity restraints: 1738 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 363 " 0.026 2.00e-02 2.50e+03 3.28e-02 1.88e+01 pdb=" CG PHE A 363 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 PHE A 363 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 PHE A 363 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 363 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE A 363 " 0.018 2.00e-02 2.50e+03 pdb=" CZ PHE A 363 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A1020 " 0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C THR A1020 " -0.059 2.00e-02 2.50e+03 pdb=" O THR A1020 " 0.022 2.00e-02 2.50e+03 pdb=" N THR A1021 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 613 " 0.016 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C CYS A 613 " -0.057 2.00e-02 2.50e+03 pdb=" O CYS A 613 " 0.022 2.00e-02 2.50e+03 pdb=" N ASN A 614 " 0.019 2.00e-02 2.50e+03 ... (remaining 1735 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 327 2.60 - 3.18: 9650 3.18 - 3.75: 24183 3.75 - 4.33: 31757 4.33 - 4.90: 46822 Nonbonded interactions: 112739 Sorted by model distance: nonbonded pdb=" OE2 GLU A 516 " pdb="MG MG A1202 " model vdw 2.031 2.170 nonbonded pdb=" OD1 ASP A 590 " pdb="MG MG A1201 " model vdw 2.045 2.170 nonbonded pdb=" OP2 DT D 28 " pdb="MG MG A1202 " model vdw 2.058 2.170 nonbonded pdb=" O3' DA X 13 " pdb="MG MG A1201 " model vdw 2.066 2.170 nonbonded pdb=" OP1 U B 78 " pdb="MG MG B 205 " model vdw 2.067 2.170 ... (remaining 112734 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.110 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 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:6.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 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 : 0.006 0.094 12440 Z= 0.369 Angle : 1.081 35.157 17568 Z= 0.631 Chirality : 0.050 0.330 2020 Planarity : 0.007 0.073 1738 Dihedral : 19.407 166.247 5351 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.23), residues: 1097 helix: 0.34 (0.21), residues: 546 sheet: -0.27 (0.60), residues: 76 loop : -0.46 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1048 TYR 0.018 0.003 TYR A 986 PHE 0.071 0.003 PHE A 363 TRP 0.023 0.002 TRP A 721 HIS 0.004 0.001 HIS A 574 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.36 (12433) covalent geometry : angle 0.90250 / 0.56 (17556) SS BOND : bond 0.07162 / 4.58 ( 6) SS BOND : angle 22.79990 / 14.94 ( 12) hydrogen bonds : bond 0.07234 / 5.14 ( 573) hydrogen bonds : angle 4.77559 / 3.45 ( 1520) Misc. bond : bond 0.00085 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.414 Fit side-chains REVERT: A 21 GLU cc_start: 0.7780 (tp30) cc_final: 0.7527 (mm-30) REVERT: A 33 GLU cc_start: 0.6796 (pm20) cc_final: 0.6472 (pm20) REVERT: A 724 ILE cc_start: 0.7914 (mm) cc_final: 0.7690 (mp) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.9455 time to fit residues: 116.7499 Evaluate side-chains 102 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 117 optimal weight: 6.9990 overall best weight: 3.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.159985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.121438 restraints weight = 10085.501| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.19 r_work: 0.3146 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.114 12440 Z= 0.256 Angle : 0.896 28.967 17568 Z= 0.457 Chirality : 0.044 0.237 2020 Planarity : 0.006 0.048 1738 Dihedral : 20.377 160.674 3262 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.31 % Allowed : 6.01 % Favored : 92.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.25), residues: 1097 helix: 1.17 (0.22), residues: 546 sheet: -0.13 (0.58), residues: 81 loop : -0.10 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 137 TYR 0.022 0.002 TYR A 986 PHE 0.026 0.002 PHE A 282 TRP 0.018 0.002 TRP A 161 HIS 0.006 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.24 (12433) covalent geometry : angle 0.68457 / 0.37 (17556) SS BOND : bond 0.08450 / 5.49 ( 6) SS BOND : angle 22.13973 / 13.99 ( 12) hydrogen bonds : bond 0.06869 / 4.83 ( 573) hydrogen bonds : angle 4.25617 / 3.09 ( 1520) Misc. bond : bond 0.00009 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7185 (pm20) cc_final: 0.6885 (pp20) REVERT: A 724 ILE cc_start: 0.7836 (mm) cc_final: 0.7579 (mp) outliers start: 12 outliers final: 3 residues processed: 109 average time/residue: 0.9749 time to fit residues: 111.9064 Evaluate side-chains 101 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 98 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 1048 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 111 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 63 optimal weight: 0.4980 chunk 53 optimal weight: 0.0170 chunk 69 optimal weight: 10.0000 chunk 17 optimal weight: 0.6980 chunk 76 optimal weight: 8.9990 overall best weight: 1.0020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.163485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.126589 restraints weight = 10295.450| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.15 r_work: 0.3198 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.125 12440 Z= 0.167 Angle : 0.808 30.126 17568 Z= 0.412 Chirality : 0.039 0.227 2020 Planarity : 0.004 0.037 1738 Dihedral : 20.307 160.106 3262 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.87 % Allowed : 7.32 % Favored : 91.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.25), residues: 1097 helix: 1.57 (0.22), residues: 546 sheet: -0.29 (0.59), residues: 76 loop : 0.01 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 137 TYR 0.016 0.001 TYR A 986 PHE 0.017 0.001 PHE A 282 TRP 0.014 0.001 TRP A 161 HIS 0.003 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.14 (12433) covalent geometry : angle 0.57062 / 0.31 (17556) SS BOND : bond 0.08509 / 5.59 ( 6) SS BOND : angle 21.90532 / 13.58 ( 12) hydrogen bonds : bond 0.05824 / 4.16 ( 573) hydrogen bonds : angle 4.01271 / 2.94 ( 1520) Misc. bond : bond 0.00023 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.283 Fit side-chains REVERT: A 33 GLU cc_start: 0.7103 (pm20) cc_final: 0.6759 (pp20) REVERT: A 230 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7657 (mpt-90) REVERT: A 631 ARG cc_start: 0.7148 (ttm-80) cc_final: 0.6936 (ptm160) REVERT: A 724 ILE cc_start: 0.7821 (mm) cc_final: 0.7551 (mp) REVERT: A 864 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7662 (mp0) outliers start: 8 outliers final: 1 residues processed: 109 average time/residue: 1.0069 time to fit residues: 115.4253 Evaluate side-chains 98 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 96 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 470 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 37 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 106 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.158907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.120620 restraints weight = 10128.042| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.24 r_work: 0.3107 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.124 12440 Z= 0.292 Angle : 0.914 32.689 17568 Z= 0.464 Chirality : 0.046 0.261 2020 Planarity : 0.006 0.056 1738 Dihedral : 20.348 158.550 3262 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.09 % Allowed : 8.85 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.25), residues: 1097 helix: 1.51 (0.22), residues: 546 sheet: -0.12 (0.57), residues: 81 loop : -0.01 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1107 TYR 0.022 0.003 TYR A 986 PHE 0.027 0.003 PHE A 282 TRP 0.016 0.002 TRP A 161 HIS 0.007 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00577 / 0.28 (12433) covalent geometry : angle 0.70282 / 0.37 (17556) SS BOND : bond 0.08507 / 5.37 ( 6) SS BOND : angle 22.39170 / 14.14 ( 12) hydrogen bonds : bond 0.06857 / 4.77 ( 573) hydrogen bonds : angle 4.20616 / 3.06 ( 1520) Misc. bond : bond 0.00012 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.393 Fit side-chains REVERT: A 137 ARG cc_start: 0.9040 (OUTLIER) cc_final: 0.6333 (mtt180) REVERT: A 149 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8400 (ttmt) REVERT: A 230 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7723 (mpt-90) REVERT: A 724 ILE cc_start: 0.7770 (mm) cc_final: 0.7495 (mp) REVERT: A 1048 ARG cc_start: 0.7966 (mtt90) cc_final: 0.7588 (mtt90) outliers start: 10 outliers final: 5 residues processed: 106 average time/residue: 0.9409 time to fit residues: 105.3929 Evaluate side-chains 104 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 137 ARG Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 813 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 80 optimal weight: 0.0670 chunk 91 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 113 optimal weight: 8.9990 chunk 107 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 overall best weight: 3.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.159042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.121067 restraints weight = 10197.678| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.21 r_work: 0.3115 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 12440 Z= 0.263 Angle : 0.892 31.953 17568 Z= 0.453 Chirality : 0.044 0.243 2020 Planarity : 0.005 0.050 1738 Dihedral : 20.355 158.166 3262 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.20 % Allowed : 9.40 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.25), residues: 1097 helix: 1.53 (0.22), residues: 546 sheet: -0.10 (0.57), residues: 81 loop : 0.00 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 631 TYR 0.022 0.002 TYR A 986 PHE 0.025 0.002 PHE A 282 TRP 0.016 0.002 TRP A 161 HIS 0.007 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.25 (12433) covalent geometry : angle 0.67712 / 0.36 (17556) SS BOND : bond 0.08546 / 5.48 ( 6) SS BOND : angle 22.23069 / 13.84 ( 12) hydrogen bonds : bond 0.06624 / 4.62 ( 573) hydrogen bonds : angle 4.19130 / 3.06 ( 1520) Misc. bond : bond 0.00009 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.375 Fit side-chains REVERT: A 149 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8392 (ttmt) REVERT: A 230 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7733 (mpt-90) REVERT: A 365 GLU cc_start: 0.8133 (tt0) cc_final: 0.7474 (pt0) REVERT: A 372 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6827 (tt0) REVERT: A 724 ILE cc_start: 0.7841 (mm) cc_final: 0.7558 (mp) REVERT: A 1048 ARG cc_start: 0.7962 (mtt90) cc_final: 0.7608 (mtt90) outliers start: 11 outliers final: 5 residues processed: 105 average time/residue: 0.8264 time to fit residues: 91.8837 Evaluate side-chains 104 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 813 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 82 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 87 optimal weight: 0.7980 chunk 18 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 119 optimal weight: 30.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.158434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.120526 restraints weight = 10156.183| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.22 r_work: 0.3106 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.124 12440 Z= 0.281 Angle : 0.919 32.454 17568 Z= 0.466 Chirality : 0.045 0.253 2020 Planarity : 0.006 0.046 1738 Dihedral : 20.367 157.781 3262 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.20 % Allowed : 9.51 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.25), residues: 1097 helix: 1.50 (0.22), residues: 545 sheet: -0.08 (0.57), residues: 81 loop : -0.03 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 631 TYR 0.023 0.002 TYR A 986 PHE 0.026 0.002 PHE A 282 TRP 0.016 0.002 TRP A 161 HIS 0.007 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.27 (12433) covalent geometry : angle 0.70359 / 0.37 (17556) SS BOND : bond 0.07912 / 4.93 ( 6) SS BOND : angle 22.62224 / 14.25 ( 12) hydrogen bonds : bond 0.06834 / 4.75 ( 573) hydrogen bonds : angle 4.23948 / 3.09 ( 1520) Misc. bond : bond 0.00019 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.389 Fit side-chains REVERT: A 137 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.6386 (mtt180) REVERT: A 149 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8392 (ttmt) REVERT: A 230 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7747 (mpt-90) REVERT: A 365 GLU cc_start: 0.8142 (tt0) cc_final: 0.7474 (pt0) REVERT: A 372 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6895 (tt0) REVERT: A 724 ILE cc_start: 0.7824 (mm) cc_final: 0.7538 (mp) outliers start: 11 outliers final: 6 residues processed: 105 average time/residue: 0.8670 time to fit residues: 96.6880 Evaluate side-chains 104 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 137 ARG Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 813 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 81 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 94 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 60 optimal weight: 0.6980 chunk 32 optimal weight: 8.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.159664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.122225 restraints weight = 10158.762| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.17 r_work: 0.3122 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.116 12440 Z= 0.233 Angle : 0.873 31.816 17568 Z= 0.443 Chirality : 0.042 0.231 2020 Planarity : 0.005 0.091 1738 Dihedral : 20.339 158.255 3262 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.20 % Allowed : 10.16 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.25), residues: 1097 helix: 1.62 (0.22), residues: 546 sheet: -0.09 (0.58), residues: 81 loop : 0.03 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1048 TYR 0.021 0.002 TYR A 986 PHE 0.023 0.002 PHE A 282 TRP 0.016 0.002 TRP A 161 HIS 0.006 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.21 (12433) covalent geometry : angle 0.64970 / 0.35 (17556) SS BOND : bond 0.08333 / 5.32 ( 6) SS BOND : angle 22.33429 / 13.93 ( 12) hydrogen bonds : bond 0.06404 / 4.48 ( 573) hydrogen bonds : angle 4.14088 / 3.03 ( 1520) Misc. bond : bond 0.00008 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.403 Fit side-chains REVERT: A 137 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.6404 (mtt180) REVERT: A 149 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8380 (ttmt) REVERT: A 230 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7743 (mpt-90) REVERT: A 365 GLU cc_start: 0.8141 (tt0) cc_final: 0.7502 (pt0) REVERT: A 372 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6866 (tt0) REVERT: A 724 ILE cc_start: 0.7859 (mm) cc_final: 0.7580 (mp) REVERT: A 1048 ARG cc_start: 0.7978 (mtt90) cc_final: 0.7774 (mtt90) outliers start: 11 outliers final: 6 residues processed: 106 average time/residue: 0.8495 time to fit residues: 95.6306 Evaluate side-chains 107 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 137 ARG Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 813 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.160100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.122213 restraints weight = 10136.865| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.15 r_work: 0.3141 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 12440 Z= 0.220 Angle : 0.859 31.633 17568 Z= 0.436 Chirality : 0.042 0.232 2020 Planarity : 0.005 0.082 1738 Dihedral : 20.321 158.499 3262 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.20 % Allowed : 10.27 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.25), residues: 1097 helix: 1.68 (0.22), residues: 546 sheet: -0.08 (0.58), residues: 81 loop : 0.06 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1048 TYR 0.021 0.002 TYR A 986 PHE 0.022 0.002 PHE A 282 TRP 0.015 0.002 TRP A 161 HIS 0.006 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.20 (12433) covalent geometry : angle 0.63375 / 0.34 (17556) SS BOND : bond 0.08423 / 5.42 ( 6) SS BOND : angle 22.21770 / 13.81 ( 12) hydrogen bonds : bond 0.06270 / 4.39 ( 573) hydrogen bonds : angle 4.10323 / 3.01 ( 1520) Misc. bond : bond 0.00003 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.298 Fit side-chains REVERT: A 137 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.6416 (mtt180) REVERT: A 149 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8363 (ttmt) REVERT: A 230 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7718 (mpt-90) REVERT: A 365 GLU cc_start: 0.8094 (tt0) cc_final: 0.7452 (pt0) REVERT: A 724 ILE cc_start: 0.7868 (mm) cc_final: 0.7579 (mp) REVERT: A 1048 ARG cc_start: 0.7983 (mtt90) cc_final: 0.7578 (mtt90) outliers start: 11 outliers final: 5 residues processed: 105 average time/residue: 0.8859 time to fit residues: 98.7071 Evaluate side-chains 104 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 137 ARG Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 813 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 6 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 chunk 63 optimal weight: 0.0040 chunk 104 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 28 optimal weight: 0.0980 overall best weight: 0.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.163982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.126365 restraints weight = 10210.295| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.11 r_work: 0.3217 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.120 12440 Z= 0.162 Angle : 0.803 30.410 17568 Z= 0.408 Chirality : 0.038 0.228 2020 Planarity : 0.004 0.071 1738 Dihedral : 20.275 159.569 3262 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.66 % Allowed : 10.71 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.25), residues: 1097 helix: 1.87 (0.22), residues: 546 sheet: -0.17 (0.60), residues: 76 loop : 0.13 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1048 TYR 0.016 0.001 TYR A 986 PHE 0.014 0.001 PHE A 282 TRP 0.015 0.001 TRP A 161 HIS 0.004 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.13 (12433) covalent geometry : angle 0.56064 / 0.30 (17556) SS BOND : bond 0.08506 / 5.49 ( 6) SS BOND : angle 21.99710 / 13.64 ( 12) hydrogen bonds : bond 0.05552 / 3.96 ( 573) hydrogen bonds : angle 3.91764 / 2.88 ( 1520) Misc. bond : bond 0.00021 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 102 time to evaluate : 0.397 Fit side-chains REVERT: A 137 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.6500 (mtt180) REVERT: A 230 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7702 (mpt-90) REVERT: A 365 GLU cc_start: 0.8018 (tt0) cc_final: 0.7389 (pt0) REVERT: A 724 ILE cc_start: 0.7836 (mm) cc_final: 0.7541 (mp) REVERT: A 728 ARG cc_start: 0.6698 (tmm-80) cc_final: 0.6423 (tmt-80) REVERT: A 864 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7571 (mp0) REVERT: A 1048 ARG cc_start: 0.7888 (mtt90) cc_final: 0.7612 (mtt90) REVERT: A 1118 ARG cc_start: 0.7632 (mmm-85) cc_final: 0.7251 (mmt-90) outliers start: 6 outliers final: 2 residues processed: 107 average time/residue: 0.9389 time to fit residues: 106.4901 Evaluate side-chains 98 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 94 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ARG Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 773 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 96 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 56 optimal weight: 0.2980 chunk 97 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 48 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 601 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.162897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.125112 restraints weight = 10216.090| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.14 r_work: 0.3190 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.121 12440 Z= 0.173 Angle : 0.808 30.693 17568 Z= 0.410 Chirality : 0.039 0.223 2020 Planarity : 0.004 0.064 1738 Dihedral : 20.244 159.423 3262 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 0.55 % Allowed : 11.58 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.25), residues: 1097 helix: 1.92 (0.22), residues: 546 sheet: -0.08 (0.58), residues: 81 loop : 0.16 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1048 TYR 0.017 0.001 TYR A 986 PHE 0.017 0.001 PHE A 282 TRP 0.015 0.001 TRP A 161 HIS 0.004 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 (12433) covalent geometry : angle 0.56788 / 0.31 (17556) SS BOND : bond 0.08570 / 5.55 ( 6) SS BOND : angle 21.99480 / 13.63 ( 12) hydrogen bonds : bond 0.05630 / 3.99 ( 573) hydrogen bonds : angle 3.90228 / 2.87 ( 1520) Misc. bond : bond 0.00010 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 0.354 Fit side-chains REVERT: A 137 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.6483 (mtt180) REVERT: A 230 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7700 (mpt-90) REVERT: A 365 GLU cc_start: 0.8034 (tt0) cc_final: 0.7396 (pt0) REVERT: A 724 ILE cc_start: 0.7867 (mm) cc_final: 0.7582 (mp) REVERT: A 728 ARG cc_start: 0.6734 (tmm-80) cc_final: 0.6463 (tmt-80) REVERT: A 864 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7570 (mp0) REVERT: A 1048 ARG cc_start: 0.7814 (mtt90) cc_final: 0.7431 (mtt90) REVERT: A 1118 ARG cc_start: 0.7637 (mmm-85) cc_final: 0.7236 (mmt-90) outliers start: 5 outliers final: 2 residues processed: 101 average time/residue: 0.9513 time to fit residues: 101.7173 Evaluate side-chains 102 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 98 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ARG Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 773 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 85 optimal weight: 0.0050 chunk 105 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 74 optimal weight: 8.9990 chunk 68 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 overall best weight: 3.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.158991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.120736 restraints weight = 10073.533| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.23 r_work: 0.3115 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.131 12440 Z= 0.272 Angle : 0.910 32.064 17568 Z= 0.461 Chirality : 0.044 0.266 2020 Planarity : 0.006 0.056 1738 Dihedral : 20.306 158.385 3262 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 0.66 % Allowed : 11.48 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.25), residues: 1097 helix: 1.72 (0.22), residues: 547 sheet: -0.05 (0.58), residues: 81 loop : 0.05 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1048 TYR 0.022 0.003 TYR A 986 PHE 0.027 0.002 PHE A 282 TRP 0.015 0.002 TRP A 161 HIS 0.006 0.001 HIS A 574 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.26 (12433) covalent geometry : angle 0.68791 / 0.36 (17556) SS BOND : bond 0.07952 / 4.89 ( 6) SS BOND : angle 22.78746 / 14.53 ( 12) hydrogen bonds : bond 0.06638 / 4.60 ( 573) hydrogen bonds : angle 4.14449 / 3.03 ( 1520) Misc. bond : bond 0.00018 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5314.62 seconds wall clock time: 91 minutes 6.80 seconds (5466.80 seconds total)