Starting phenix.real_space_refine on Wed Mar 4 09:17:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d2l_27142/03_2026/8d2l_27142.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d2l_27142/03_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_27142/03_2026/8d2l_27142.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d2l_27142/03_2026/8d2l_27142.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d2l_27142/03_2026/8d2l_27142.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d2l_27142/03_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-5986/lib/python3.9/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: 2.85, 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: 1.19 Conformation dependent library (CDL) restraints added in 351.2 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: 1.80 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: 3.31 Time building geometry restraints manager: 1.53 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=" C3' DC X 3 " pdb=" O3' DC X 3 " ideal model delta sigma weight residual 1.422 1.506 -0.084 3.00e-02 1.11e+03 7.78e+00 bond pdb=" C1' DC T 21 " pdb=" N1 DC T 21 " ideal model delta sigma weight residual 1.490 1.556 -0.066 3.00e-02 1.11e+03 4.80e+00 bond pdb=" CA GLU A 33 " pdb=" CB GLU A 33 " ideal model delta sigma weight residual 1.530 1.567 -0.037 1.69e-02 3.50e+03 4.68e+00 bond pdb=" CA ASP A 53 " pdb=" CB ASP A 53 " ideal model delta sigma weight residual 1.530 1.565 -0.035 1.69e-02 3.50e+03 4.32e+00 bond pdb=" O5' DA D 31 " pdb=" C5' DA D 31 " ideal model delta sigma weight residual 1.423 1.364 0.059 3.00e-02 1.11e+03 3.80e+00 ... (remaining 12428 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.53: 17522 5.53 - 11.07: 31 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=" 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 angle pdb=" CA GLU A 33 " pdb=" CB GLU A 33 " pdb=" CG GLU A 33 " ideal model delta sigma weight residual 114.10 126.44 -12.34 2.00e+00 2.50e-01 3.81e+01 angle pdb=" N PRO A 892 " pdb=" CD PRO A 892 " pdb=" CG PRO A 892 " ideal model delta sigma weight residual 103.20 95.50 7.70 1.50e+00 4.44e-01 2.64e+01 angle pdb=" C CYS A 613 " pdb=" CA CYS A 613 " pdb=" CB CYS A 613 " ideal model delta sigma weight residual 110.85 118.09 -7.24 1.70e+00 3.46e-01 1.81e+01 ... (remaining 17551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.25: 6948 33.25 - 66.50: 521 66.50 - 99.75: 54 99.75 - 133.00: 3 133.00 - 166.25: 1 Dihedral angle restraints: 7527 sinusoidal: 4331 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 7524 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1725 0.066 - 0.132: 268 0.132 - 0.198: 19 0.198 - 0.264: 4 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: 2.630 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: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.980 Find NCS groups from input model: 0.050 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:9.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 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 : 0.005 0.094 12440 Z= 0.245 Angle : 1.060 35.157 17568 Z= 0.545 Chirality : 0.049 0.330 2020 Planarity : 0.007 0.073 1738 Dihedral : 19.795 166.247 5435 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 covalent geometry : bond 0.00481 (12433) covalent geometry : angle 0.87697 (17556) SS BOND : bond 0.07162 ( 6) SS BOND : angle 22.79990 ( 12) hydrogen bonds : bond 0.07234 ( 573) hydrogen bonds : angle 4.77559 ( 1520) Misc. bond : bond 0.00085 ( 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 : 0.383 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: 1.0219 time to fit residues: 125.6610 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 : 0.358 ------------------------------------------------------------------------------- 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: 6.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 117 optimal weight: 6.9990 overall best weight: 4.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.158069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.119455 restraints weight = 10080.434| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.18 r_work: 0.3115 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.127 12440 Z= 0.335 Angle : 0.947 30.489 17568 Z= 0.475 Chirality : 0.045 0.231 2020 Planarity : 0.006 0.048 1738 Dihedral : 20.967 158.300 3346 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.53 % Allowed : 6.56 % Favored : 91.91 % 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: 0.62 (0.25), residues: 1097 helix: 1.06 (0.22), residues: 545 sheet: -0.09 (0.57), residues: 81 loop : -0.14 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 137 TYR 0.025 0.003 TYR A 986 PHE 0.030 0.003 PHE A 282 TRP 0.019 0.003 TRP A 161 HIS 0.008 0.002 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00690 (12433) covalent geometry : angle 0.74607 (17556) SS BOND : bond 0.08579 ( 6) SS BOND : angle 22.30353 ( 12) hydrogen bonds : bond 0.07211 ( 573) hydrogen bonds : angle 4.35478 ( 1520) Misc. bond : bond 0.00006 ( 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 115 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7200 (pm20) cc_final: 0.6849 (pp20) REVERT: A 230 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7691 (mpt-90) REVERT: A 405 ASP cc_start: 0.5809 (m-30) cc_final: 0.5571 (m-30) REVERT: A 724 ILE cc_start: 0.7769 (mm) cc_final: 0.7497 (mp) outliers start: 14 outliers final: 5 residues processed: 110 average time/residue: 0.9887 time to fit residues: 114.4293 Evaluate side-chains 102 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 643 LYS Chi-restraints excluded: chain A residue 700 GLU 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: 3.9990 chunk 15 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 69 optimal weight: 9.9990 chunk 17 optimal weight: 0.3980 chunk 76 optimal weight: 5.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.160912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.123293 restraints weight = 10244.328| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.18 r_work: 0.3143 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.120 12440 Z= 0.201 Angle : 0.828 30.852 17568 Z= 0.415 Chirality : 0.038 0.223 2020 Planarity : 0.005 0.036 1738 Dihedral : 20.848 159.217 3346 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.20 % Allowed : 7.65 % Favored : 91.15 % 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: 1.05 (0.25), residues: 1097 helix: 1.49 (0.22), residues: 546 sheet: -0.15 (0.57), residues: 81 loop : 0.01 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 112 TYR 0.020 0.002 TYR A 986 PHE 0.020 0.002 PHE A 282 TRP 0.015 0.002 TRP A 161 HIS 0.005 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00377 (12433) covalent geometry : angle 0.59620 (17556) SS BOND : bond 0.08769 ( 6) SS BOND : angle 21.97251 ( 12) hydrogen bonds : bond 0.05963 ( 573) hydrogen bonds : angle 4.08641 ( 1520) Misc. bond : bond 0.00011 ( 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 114 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7178 (pm20) cc_final: 0.6764 (pp20) REVERT: A 230 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.7704 (mpt-90) REVERT: A 724 ILE cc_start: 0.7805 (mm) cc_final: 0.7531 (mp) outliers start: 11 outliers final: 5 residues processed: 109 average time/residue: 0.9383 time to fit residues: 107.9365 Evaluate side-chains 105 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 1048 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 37 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 81 optimal weight: 8.9990 chunk 69 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 17 optimal weight: 0.0070 chunk 100 optimal weight: 4.9990 overall best weight: 4.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.157779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.119855 restraints weight = 10148.112| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.19 r_work: 0.3102 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.134 12440 Z= 0.325 Angle : 0.934 32.974 17568 Z= 0.467 Chirality : 0.045 0.224 2020 Planarity : 0.006 0.043 1738 Dihedral : 20.921 157.334 3346 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.53 % Allowed : 7.98 % Favored : 90.49 % 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: 0.93 (0.25), residues: 1097 helix: 1.38 (0.22), residues: 545 sheet: -0.08 (0.57), residues: 81 loop : -0.05 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 631 TYR 0.024 0.003 TYR A 986 PHE 0.028 0.003 PHE A 282 TRP 0.017 0.003 TRP A 161 HIS 0.008 0.002 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00672 (12433) covalent geometry : angle 0.72632 (17556) SS BOND : bond 0.08400 ( 6) SS BOND : angle 22.46591 ( 12) hydrogen bonds : bond 0.07018 ( 573) hydrogen bonds : angle 4.29445 ( 1520) Misc. bond : bond 0.00017 ( 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 116 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7238 (pm20) cc_final: 0.6843 (pp20) REVERT: A 137 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.6392 (mtt180) REVERT: A 149 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8424 (ttmt) REVERT: A 230 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.7748 (mpt-90) REVERT: A 365 GLU cc_start: 0.8138 (tt0) cc_final: 0.7475 (pt0) REVERT: A 372 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6861 (tt0) REVERT: A 724 ILE cc_start: 0.7767 (mm) cc_final: 0.7482 (mp) outliers start: 14 outliers final: 7 residues processed: 110 average time/residue: 0.9151 time to fit residues: 106.2992 Evaluate side-chains 110 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 643 LYS Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 1048 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 80 optimal weight: 0.0020 chunk 91 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 113 optimal weight: 8.9990 chunk 107 optimal weight: 8.9990 chunk 11 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 overall best weight: 2.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.159266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.121821 restraints weight = 10217.161| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.19 r_work: 0.3123 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 12440 Z= 0.242 Angle : 0.862 31.802 17568 Z= 0.432 Chirality : 0.040 0.221 2020 Planarity : 0.005 0.034 1738 Dihedral : 20.857 158.324 3346 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.53 % Allowed : 8.52 % Favored : 89.95 % 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: 1.55 (0.22), residues: 546 sheet: -0.11 (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 A 631 TYR 0.021 0.002 TYR A 986 PHE 0.024 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 covalent geometry : bond 0.00480 (12433) covalent geometry : angle 0.63811 (17556) SS BOND : bond 0.08505 ( 6) SS BOND : angle 22.18817 ( 12) hydrogen bonds : bond 0.06316 ( 573) hydrogen bonds : angle 4.14623 ( 1520) Misc. bond : bond 0.00007 ( 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 114 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7253 (pm20) cc_final: 0.6812 (pp20) REVERT: A 137 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.6454 (mtt180) REVERT: A 149 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8377 (ttmt) REVERT: A 230 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7730 (mpt-90) REVERT: A 365 GLU cc_start: 0.8114 (tt0) cc_final: 0.7450 (pt0) REVERT: A 372 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6830 (tt0) REVERT: A 724 ILE cc_start: 0.7854 (mm) cc_final: 0.7566 (mp) outliers start: 14 outliers final: 8 residues processed: 109 average time/residue: 0.9013 time to fit residues: 103.7846 Evaluate side-chains 109 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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 643 LYS 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 Chi-restraints excluded: chain A residue 1048 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 82 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 42 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 = 0.3796 r_free = 0.3796 target = 0.156358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.118397 restraints weight = 10183.250| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.22 r_work: 0.3087 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.153 12440 Z= 0.417 Angle : 1.017 33.617 17568 Z= 0.509 Chirality : 0.050 0.245 2020 Planarity : 0.007 0.053 1738 Dihedral : 20.969 155.820 3346 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.97 % Allowed : 8.31 % Favored : 89.73 % 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: 1.18 (0.22), residues: 545 sheet: -0.10 (0.57), residues: 81 loop : -0.13 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1107 TYR 0.026 0.003 TYR A 986 PHE 0.031 0.003 PHE A 282 TRP 0.018 0.003 TRP A 161 HIS 0.008 0.002 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00879 (12433) covalent geometry : angle 0.82359 (17556) SS BOND : bond 0.08146 ( 6) SS BOND : angle 22.81279 ( 12) hydrogen bonds : bond 0.07679 ( 573) hydrogen bonds : angle 4.47374 ( 1520) Misc. bond : bond 0.00067 ( 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 118 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7281 (pm20) cc_final: 0.6815 (pp20) REVERT: A 137 ARG cc_start: 0.9110 (OUTLIER) cc_final: 0.6450 (mtt180) REVERT: A 149 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8449 (ttmt) REVERT: A 230 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.7744 (mpt-90) REVERT: A 365 GLU cc_start: 0.8112 (tt0) cc_final: 0.7443 (pt0) REVERT: A 372 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6963 (tt0) REVERT: A 679 GLN cc_start: 0.5099 (tt0) cc_final: 0.4792 (tt0) REVERT: A 724 ILE cc_start: 0.7804 (mm) cc_final: 0.7509 (mp) outliers start: 18 outliers final: 10 residues processed: 112 average time/residue: 0.9156 time to fit residues: 108.3846 Evaluate side-chains 111 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP 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 643 LYS 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 Chi-restraints excluded: chain A residue 1048 ARG Chi-restraints excluded: chain A residue 1074 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 81 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.158991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.121845 restraints weight = 10176.880| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.17 r_work: 0.3119 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 12440 Z= 0.244 Angle : 0.872 32.076 17568 Z= 0.437 Chirality : 0.041 0.221 2020 Planarity : 0.005 0.036 1738 Dihedral : 20.873 157.965 3346 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.64 % Allowed : 9.51 % Favored : 88.85 % 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: 1.03 (0.25), residues: 1097 helix: 1.48 (0.22), residues: 546 sheet: -0.07 (0.58), residues: 81 loop : -0.03 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 137 TYR 0.022 0.002 TYR A 986 PHE 0.023 0.002 PHE A 282 TRP 0.017 0.002 TRP A 161 HIS 0.006 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00486 (12433) covalent geometry : angle 0.64696 (17556) SS BOND : bond 0.08278 ( 6) SS BOND : angle 22.38922 ( 12) hydrogen bonds : bond 0.06298 ( 573) hydrogen bonds : angle 4.18486 ( 1520) Misc. bond : bond 0.00009 ( 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 119 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7242 (pm20) cc_final: 0.6888 (pp20) REVERT: A 137 ARG cc_start: 0.9039 (OUTLIER) cc_final: 0.6415 (mtt180) REVERT: A 149 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8354 (ttmt) REVERT: A 230 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7735 (mpt-90) REVERT: A 365 GLU cc_start: 0.8105 (tt0) cc_final: 0.7453 (pt0) REVERT: A 372 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6894 (tt0) REVERT: A 679 GLN cc_start: 0.5172 (tt0) cc_final: 0.4804 (tt0) REVERT: A 724 ILE cc_start: 0.7834 (mm) cc_final: 0.7544 (mp) outliers start: 15 outliers final: 9 residues processed: 114 average time/residue: 0.9107 time to fit residues: 109.8004 Evaluate side-chains 110 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 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 643 LYS 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 Chi-restraints excluded: chain A residue 1048 ARG Chi-restraints excluded: chain A residue 1074 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 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 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.158810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.121584 restraints weight = 10138.506| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.16 r_work: 0.3115 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 12440 Z= 0.255 Angle : 0.877 32.206 17568 Z= 0.439 Chirality : 0.041 0.221 2020 Planarity : 0.005 0.036 1738 Dihedral : 20.857 158.083 3346 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.64 % Allowed : 9.51 % Favored : 88.85 % 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: 1.05 (0.25), residues: 1097 helix: 1.50 (0.22), residues: 546 sheet: -0.09 (0.58), residues: 81 loop : -0.01 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 137 TYR 0.022 0.002 TYR A 986 PHE 0.025 0.002 PHE A 282 TRP 0.017 0.002 TRP A 161 HIS 0.006 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00513 (12433) covalent geometry : angle 0.65458 (17556) SS BOND : bond 0.08374 ( 6) SS BOND : angle 22.31436 ( 12) hydrogen bonds : bond 0.06462 ( 573) hydrogen bonds : angle 4.19521 ( 1520) Misc. bond : bond 0.00014 ( 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 115 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7297 (pm20) cc_final: 0.6930 (pp20) REVERT: A 137 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.6433 (mtt180) REVERT: A 149 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8358 (ttmt) REVERT: A 230 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7744 (mpt-90) REVERT: A 365 GLU cc_start: 0.8119 (tt0) cc_final: 0.7455 (pt0) REVERT: A 372 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6908 (tt0) REVERT: A 724 ILE cc_start: 0.7837 (mm) cc_final: 0.7547 (mp) outliers start: 15 outliers final: 10 residues processed: 110 average time/residue: 0.9239 time to fit residues: 107.4353 Evaluate side-chains 108 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LYS 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 643 LYS 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 Chi-restraints excluded: chain A residue 1048 ARG Chi-restraints excluded: chain A residue 1074 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 6 optimal weight: 0.6980 chunk 120 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 13 optimal weight: 0.5980 chunk 77 optimal weight: 10.0000 chunk 74 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 28 optimal weight: 0.0770 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.163317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.127197 restraints weight = 10205.958| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.11 r_work: 0.3196 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.122 12440 Z= 0.162 Angle : 0.795 30.804 17568 Z= 0.398 Chirality : 0.037 0.226 2020 Planarity : 0.004 0.035 1738 Dihedral : 20.739 159.664 3346 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.20 % Allowed : 9.95 % Favored : 88.85 % 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: 1.36 (0.25), residues: 1097 helix: 1.82 (0.22), residues: 546 sheet: -0.16 (0.60), residues: 76 loop : 0.09 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 631 TYR 0.017 0.001 TYR A 986 PHE 0.016 0.001 PHE A 282 TRP 0.016 0.001 TRP A 161 HIS 0.004 0.001 HIS A 574 Details of bonding type rmsd covalent geometry : bond 0.00277 (12433) covalent geometry : angle 0.54944 (17556) SS BOND : bond 0.08617 ( 6) SS BOND : angle 22.01480 ( 12) hydrogen bonds : bond 0.05380 ( 573) hydrogen bonds : angle 3.93353 ( 1520) Misc. bond : bond 0.00013 ( 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 110 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7913 (tp30) cc_final: 0.7697 (mm-30) REVERT: A 33 GLU cc_start: 0.7210 (pm20) cc_final: 0.6864 (pp20) REVERT: A 137 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.6489 (mtt180) REVERT: A 149 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8304 (mttp) REVERT: A 365 GLU cc_start: 0.8040 (tt0) cc_final: 0.7412 (pt0) REVERT: A 724 ILE cc_start: 0.7848 (mm) cc_final: 0.7549 (mp) REVERT: A 864 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7656 (mp0) outliers start: 11 outliers final: 6 residues processed: 108 average time/residue: 0.9461 time to fit residues: 108.3272 Evaluate side-chains 105 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 470 ASP Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 1048 ARG Chi-restraints excluded: chain A residue 1074 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 96 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 56 optimal weight: 0.0570 chunk 97 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 overall best weight: 2.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 ASN A 601 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.159617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.121736 restraints weight = 10148.472| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.21 r_work: 0.3132 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1462 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= 0.234 Angle : 0.852 31.854 17568 Z= 0.426 Chirality : 0.040 0.214 2020 Planarity : 0.005 0.036 1738 Dihedral : 20.796 158.593 3346 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.98 % Allowed : 10.71 % Favored : 88.31 % 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: 1.28 (0.25), residues: 1097 helix: 1.73 (0.22), residues: 546 sheet: -0.09 (0.58), residues: 81 loop : 0.07 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 631 TYR 0.022 0.002 TYR A 986 PHE 0.023 0.002 PHE A 282 TRP 0.020 0.002 TRP A 387 HIS 0.006 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00462 (12433) covalent geometry : angle 0.62414 (17556) SS BOND : bond 0.08448 ( 6) SS BOND : angle 22.19708 ( 12) hydrogen bonds : bond 0.06168 ( 573) hydrogen bonds : angle 4.07573 ( 1520) Misc. bond : bond 0.00014 ( 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 106 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7264 (pm20) cc_final: 0.6976 (pp20) REVERT: A 137 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.6453 (mtt180) REVERT: A 149 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8346 (ttmt) REVERT: A 230 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.7735 (mpt-90) REVERT: A 365 GLU cc_start: 0.8112 (tt0) cc_final: 0.7462 (pt0) REVERT: A 724 ILE cc_start: 0.7833 (mm) cc_final: 0.7536 (mp) outliers start: 9 outliers final: 6 residues processed: 105 average time/residue: 0.8159 time to fit residues: 90.9351 Evaluate side-chains 107 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.294 ------------------------------------------------------------------------------- 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 773 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 1048 ARG Chi-restraints excluded: chain A residue 1074 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 85 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 3 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 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 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.158785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.120922 restraints weight = 10095.278| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.16 r_work: 0.3118 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.119 12440 Z= 0.264 Angle : 0.879 32.226 17568 Z= 0.440 Chirality : 0.041 0.221 2020 Planarity : 0.005 0.036 1738 Dihedral : 20.852 158.115 3346 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.20 % Allowed : 10.49 % Favored : 88.31 % 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: 1.15 (0.25), residues: 1097 helix: 1.59 (0.22), residues: 547 sheet: -0.10 (0.58), residues: 81 loop : 0.04 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 830 TYR 0.022 0.002 TYR A 986 PHE 0.025 0.002 PHE A 282 TRP 0.025 0.002 TRP A 387 HIS 0.006 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00532 (12433) covalent geometry : angle 0.65906 (17556) SS BOND : bond 0.08478 ( 6) SS BOND : angle 22.25428 ( 12) hydrogen bonds : bond 0.06450 ( 573) hydrogen bonds : angle 4.18332 ( 1520) Misc. bond : bond 0.00021 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5363.18 seconds wall clock time: 91 minutes 45.84 seconds (5505.84 seconds total)