Starting phenix.real_space_refine on Fri Aug 22 19:14:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sgt_40467/08_2025/8sgt_40467.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sgt_40467/08_2025/8sgt_40467.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sgt_40467/08_2025/8sgt_40467.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sgt_40467/08_2025/8sgt_40467.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sgt_40467/08_2025/8sgt_40467.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sgt_40467/08_2025/8sgt_40467.map" } resolution = 3.6 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= 0.003 sd= 0.033 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: 5 Type Number sf(0) Gaussians Ca 6 9.91 5 S 30 5.16 5 C 4600 2.51 5 N 1145 2.21 5 O 1338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7119 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 687, 5356 Classifications: {'peptide': 687} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 663} Chain breaks: 6 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 816 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "H" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 941 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' CA': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 2.02, per 1000 atoms: 0.28 Number of scatterers: 7119 At special positions: 0 Unit cell: (120.35, 96.28, 145.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 6 19.99 S 30 16.00 O 1338 8.00 N 1145 7.00 C 4600 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 792 " distance=2.03 Simple disulfide: pdb=" SG CYS L 21 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 380.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1678 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 13 sheets defined 39.1% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 36 through 72 removed outlier: 3.565A pdb=" N ILE A 40 " --> pdb=" O PHE A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 110 removed outlier: 3.638A pdb=" N LEU A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 124 Processing helix chain 'A' and resid 130 through 145 Processing helix chain 'A' and resid 145 through 155 removed outlier: 4.033A pdb=" N VAL A 155 " --> pdb=" O CYS A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 189 removed outlier: 3.787A pdb=" N TYR A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 205 Processing helix chain 'A' and resid 205 through 220 removed outlier: 3.979A pdb=" N ILE A 209 " --> pdb=" O PHE A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 607 removed outlier: 3.567A pdb=" N LEU A 606 " --> pdb=" O LYS A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 665 Processing helix chain 'A' and resid 708 through 717 removed outlier: 3.595A pdb=" N PHE A 713 " --> pdb=" O TRP A 709 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 717 " --> pdb=" O PHE A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 754 removed outlier: 5.178A pdb=" N PHE A 749 " --> pdb=" O PHE A 745 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N TRP A 750 " --> pdb=" O LEU A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 761 through 764 removed outlier: 3.697A pdb=" N ASN A 764 " --> pdb=" O GLU A 761 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 761 through 764' Processing helix chain 'A' and resid 765 through 795 removed outlier: 3.617A pdb=" N VAL A 771 " --> pdb=" O ALA A 767 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE A 794 " --> pdb=" O PHE A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 805 Processing helix chain 'A' and resid 805 through 811 Processing helix chain 'A' and resid 811 through 825 Processing helix chain 'A' and resid 828 through 845 removed outlier: 3.710A pdb=" N VAL A 835 " --> pdb=" O SER A 831 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 843 " --> pdb=" O ASN A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 861 removed outlier: 3.703A pdb=" N ALA A 850 " --> pdb=" O GLY A 846 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN A 861 " --> pdb=" O TYR A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 893 removed outlier: 4.585A pdb=" N LEU A 872 " --> pdb=" O SER A 868 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE A 874 " --> pdb=" O GLY A 870 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER A 875 " --> pdb=" O THR A 871 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 885 " --> pdb=" O ILE A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 932 removed outlier: 3.577A pdb=" N LEU A 911 " --> pdb=" O THR A 907 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 161 Processing sheet with id=AA2, first strand: chain 'A' and resid 194 through 195 removed outlier: 4.175A pdb=" N PHE A 865 " --> pdb=" O VAL A 195 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 437 through 443 removed outlier: 3.528A pdb=" N CYS A 485 " --> pdb=" O SER A 372 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 382 through 384 removed outlier: 6.871A pdb=" N CYS A 383 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A 492 " --> pdb=" O VAL A 458 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 458 " --> pdb=" O ALA A 492 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU A 454 " --> pdb=" O ILE A 496 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N VAL A 458 " --> pdb=" O GLU A 412 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLU A 412 " --> pdb=" O VAL A 458 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N LEU A 460 " --> pdb=" O ARG A 410 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ARG A 410 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ASN A 462 " --> pdb=" O ASP A 408 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASP A 408 " --> pdb=" O ASN A 462 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 568 through 573 removed outlier: 3.555A pdb=" N VAL A 573 " --> pdb=" O MET A 521 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 511 through 515 removed outlier: 6.200A pdb=" N THR A 512 " --> pdb=" O ILE A 680 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLU A 682 " --> pdb=" O THR A 512 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL A 514 " --> pdb=" O GLU A 682 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 511 through 515 removed outlier: 6.200A pdb=" N THR A 512 " --> pdb=" O ILE A 680 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLU A 682 " --> pdb=" O THR A 512 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL A 514 " --> pdb=" O GLU A 682 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 598 through 600 removed outlier: 6.873A pdb=" N GLN A 623 " --> pdb=" O LYS A 618 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LYS A 618 " --> pdb=" O GLN A 623 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N VAL A 625 " --> pdb=" O THR A 616 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 3 through 4 Processing sheet with id=AB1, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.560A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 11 Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.507A pdb=" N MET H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ALA H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) 376 hydrogen bonds defined for protein. 1044 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.37 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1159 1.31 - 1.44: 2049 1.44 - 1.56: 4028 1.56 - 1.69: 0 1.69 - 1.81: 43 Bond restraints: 7279 Sorted by residual: bond pdb=" C ALA A 931 " pdb=" O ALA A 931 " ideal model delta sigma weight residual 1.236 1.189 0.047 1.26e-02 6.30e+03 1.39e+01 bond pdb=" CA ALA A 931 " pdb=" C ALA A 931 " ideal model delta sigma weight residual 1.523 1.484 0.039 1.35e-02 5.49e+03 8.40e+00 bond pdb=" CA CYS A 933 " pdb=" C CYS A 933 " ideal model delta sigma weight residual 1.527 1.490 0.037 1.30e-02 5.92e+03 7.96e+00 bond pdb=" CA TYR A 932 " pdb=" CB TYR A 932 " ideal model delta sigma weight residual 1.529 1.495 0.034 1.46e-02 4.69e+03 5.51e+00 bond pdb=" C TYR A 932 " pdb=" O TYR A 932 " ideal model delta sigma weight residual 1.236 1.209 0.027 1.28e-02 6.10e+03 4.41e+00 ... (remaining 7274 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 9475 1.64 - 3.27: 331 3.27 - 4.91: 63 4.91 - 6.55: 17 6.55 - 8.19: 5 Bond angle restraints: 9891 Sorted by residual: angle pdb=" CA ARG A 632 " pdb=" CB ARG A 632 " pdb=" CG ARG A 632 " ideal model delta sigma weight residual 114.10 122.29 -8.19 2.00e+00 2.50e-01 1.68e+01 angle pdb=" C THR A 654 " pdb=" N SER A 655 " pdb=" CA SER A 655 " ideal model delta sigma weight residual 121.54 128.96 -7.42 1.91e+00 2.74e-01 1.51e+01 angle pdb=" C GLY L 51 " pdb=" N THR L 52 " pdb=" CA THR L 52 " ideal model delta sigma weight residual 121.54 127.86 -6.32 1.91e+00 2.74e-01 1.10e+01 angle pdb=" C ARG A 632 " pdb=" CA ARG A 632 " pdb=" CB ARG A 632 " ideal model delta sigma weight residual 110.35 116.41 -6.06 1.91e+00 2.74e-01 1.01e+01 angle pdb=" N ALA A 931 " pdb=" CA ALA A 931 " pdb=" C ALA A 931 " ideal model delta sigma weight residual 111.82 108.26 3.56 1.16e+00 7.43e-01 9.42e+00 ... (remaining 9886 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 3861 17.93 - 35.86: 287 35.86 - 53.79: 40 53.79 - 71.72: 8 71.72 - 89.65: 11 Dihedral angle restraints: 4207 sinusoidal: 1589 harmonic: 2618 Sorted by residual: dihedral pdb=" CA THR A 528 " pdb=" C THR A 528 " pdb=" N SER A 529 " pdb=" CA SER A 529 " ideal model delta harmonic sigma weight residual 180.00 -158.62 -21.38 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 58.11 34.89 1 1.00e+01 1.00e-02 1.73e+01 dihedral pdb=" CA ARG A 527 " pdb=" C ARG A 527 " pdb=" N THR A 528 " pdb=" CA THR A 528 " ideal model delta harmonic sigma weight residual 180.00 -159.84 -20.16 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 4204 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 931 0.061 - 0.121: 178 0.121 - 0.182: 24 0.182 - 0.242: 1 0.242 - 0.303: 3 Chirality restraints: 1137 Sorted by residual: chirality pdb=" CA CYS A 933 " pdb=" N CYS A 933 " pdb=" C CYS A 933 " pdb=" CB CYS A 933 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA ILE A 935 " pdb=" N ILE A 935 " pdb=" C ILE A 935 " pdb=" CB ILE A 935 " both_signs ideal model delta sigma weight residual False 2.43 2.14 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CB ILE A 615 " pdb=" CA ILE A 615 " pdb=" CG1 ILE A 615 " pdb=" CG2 ILE A 615 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 1134 not shown) Planarity restraints: 1240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 593 " 0.053 5.00e-02 4.00e+02 7.92e-02 1.00e+01 pdb=" N PRO A 594 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO A 594 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 594 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 132 " -0.049 5.00e-02 4.00e+02 7.39e-02 8.74e+00 pdb=" N PRO A 133 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 133 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 133 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 422 " -0.018 2.00e-02 2.50e+03 1.76e-02 6.21e+00 pdb=" CG TYR A 422 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR A 422 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 422 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR A 422 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 422 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 422 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 422 " -0.001 2.00e-02 2.50e+03 ... (remaining 1237 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 104 2.65 - 3.21: 6365 3.21 - 3.78: 10632 3.78 - 4.34: 15000 4.34 - 4.90: 25014 Nonbonded interactions: 57115 Sorted by model distance: nonbonded pdb=" OD2 ASP A 421 " pdb="CA CA A1001 " model vdw 2.090 2.510 nonbonded pdb=" OE1 GLU A 385 " pdb="CA CA A1003 " model vdw 2.219 2.510 nonbonded pdb=" OE2 GLU A 385 " pdb="CA CA A1004 " model vdw 2.236 2.510 nonbonded pdb=" OD1 ASP A 413 " pdb=" OH TYR A 422 " model vdw 2.243 3.040 nonbonded pdb=" O THR A 135 " pdb=" OG SER A 139 " model vdw 2.258 3.040 ... (remaining 57110 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.590 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.930 Find NCS groups from input model: 0.040 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 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 0.068 7282 Z= 0.217 Angle : 0.750 8.186 9897 Z= 0.402 Chirality : 0.050 0.303 1137 Planarity : 0.007 0.079 1240 Dihedral : 13.355 89.651 2520 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.25), residues: 900 helix: -0.86 (0.24), residues: 314 sheet: -0.32 (0.33), residues: 250 loop : -0.72 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 22 TYR 0.044 0.002 TYR A 422 PHE 0.030 0.002 PHE A 505 TRP 0.022 0.003 TRP A 215 HIS 0.012 0.002 HIS A 674 Details of bonding type rmsd covalent geometry : bond 0.00477 ( 7279) covalent geometry : angle 0.75027 ( 9891) SS BOND : bond 0.00189 ( 3) SS BOND : angle 0.74918 ( 6) hydrogen bonds : bond 0.25451 ( 363) hydrogen bonds : angle 8.69297 ( 1044) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.6961 (mtp) cc_final: 0.5964 (mmm) REVERT: A 105 MET cc_start: 0.5214 (mmm) cc_final: 0.4712 (ppp) REVERT: A 169 PHE cc_start: 0.3915 (t80) cc_final: 0.3663 (t80) REVERT: A 175 TRP cc_start: 0.0527 (t-100) cc_final: -0.0843 (m100) REVERT: A 926 PHE cc_start: 0.7555 (m-10) cc_final: 0.7321 (m-10) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.1056 time to fit residues: 19.0277 Evaluate side-chains 59 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 30.0000 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 30.0000 chunk 51 optimal weight: 0.1980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS L 80 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.139095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.096550 restraints weight = 22580.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.092722 restraints weight = 14549.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.094133 restraints weight = 11194.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.094122 restraints weight = 9006.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.094303 restraints weight = 8726.909| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 7282 Z= 0.247 Angle : 0.677 7.797 9897 Z= 0.363 Chirality : 0.045 0.166 1137 Planarity : 0.005 0.051 1240 Dihedral : 5.010 22.828 972 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.70 % Allowed : 8.88 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.27), residues: 900 helix: 1.04 (0.27), residues: 328 sheet: -0.29 (0.34), residues: 242 loop : -0.49 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 22 TYR 0.019 0.002 TYR H 60 PHE 0.025 0.002 PHE A 769 TRP 0.032 0.003 TRP A 182 HIS 0.006 0.002 HIS A 674 Details of bonding type rmsd covalent geometry : bond 0.00551 ( 7279) covalent geometry : angle 0.67667 ( 9891) SS BOND : bond 0.00403 ( 3) SS BOND : angle 0.78054 ( 6) hydrogen bonds : bond 0.05636 ( 363) hydrogen bonds : angle 5.44277 ( 1044) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.4954 (mmm) cc_final: 0.4515 (tmm) REVERT: A 175 TRP cc_start: 0.1819 (t-100) cc_final: 0.0192 (m100) REVERT: A 750 TRP cc_start: 0.2225 (OUTLIER) cc_final: 0.1491 (m100) REVERT: A 926 PHE cc_start: 0.8115 (m-10) cc_final: 0.7769 (m-80) outliers start: 13 outliers final: 8 residues processed: 72 average time/residue: 0.0806 time to fit residues: 8.1071 Evaluate side-chains 55 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 750 TRP Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 78 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 12 optimal weight: 9.9990 chunk 89 optimal weight: 0.5980 chunk 56 optimal weight: 9.9990 chunk 81 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 60 optimal weight: 20.0000 chunk 8 optimal weight: 9.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.135660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.093618 restraints weight = 21149.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.088283 restraints weight = 14586.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.089408 restraints weight = 11666.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.089150 restraints weight = 9708.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.089307 restraints weight = 8689.458| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7282 Z= 0.222 Angle : 0.591 8.197 9897 Z= 0.320 Chirality : 0.044 0.219 1137 Planarity : 0.005 0.048 1240 Dihedral : 4.844 23.026 972 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.00 % Allowed : 10.31 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.27), residues: 900 helix: 1.56 (0.28), residues: 325 sheet: -0.43 (0.33), residues: 244 loop : -0.52 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 668 TYR 0.018 0.002 TYR H 60 PHE 0.027 0.002 PHE A 916 TRP 0.027 0.002 TRP A 182 HIS 0.006 0.001 HIS A 674 Details of bonding type rmsd covalent geometry : bond 0.00486 ( 7279) covalent geometry : angle 0.59064 ( 9891) SS BOND : bond 0.00424 ( 3) SS BOND : angle 0.62325 ( 6) hydrogen bonds : bond 0.04827 ( 363) hydrogen bonds : angle 5.08156 ( 1044) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 48 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.2007 (tpt) cc_final: 0.1475 (mtt) REVERT: A 513 HIS cc_start: 0.7258 (OUTLIER) cc_final: 0.6913 (m-70) REVERT: H 5 GLN cc_start: 0.8090 (tp40) cc_final: 0.7882 (mm110) REVERT: H 34 MET cc_start: 0.8249 (tpp) cc_final: 0.8028 (tpp) outliers start: 23 outliers final: 16 residues processed: 70 average time/residue: 0.0779 time to fit residues: 7.8579 Evaluate side-chains 63 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 46 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 513 HIS Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 78 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 23 optimal weight: 0.6980 chunk 60 optimal weight: 30.0000 chunk 22 optimal weight: 9.9990 chunk 26 optimal weight: 0.0980 chunk 39 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 49 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.137374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.096676 restraints weight = 21533.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.092770 restraints weight = 16593.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.093749 restraints weight = 12950.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.093745 restraints weight = 10101.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.094206 restraints weight = 10055.961| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7282 Z= 0.127 Angle : 0.530 6.704 9897 Z= 0.285 Chirality : 0.042 0.194 1137 Planarity : 0.004 0.041 1240 Dihedral : 4.492 22.353 972 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.31 % Allowed : 12.66 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.28), residues: 900 helix: 1.74 (0.28), residues: 326 sheet: -0.23 (0.33), residues: 248 loop : -0.28 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 410 TYR 0.014 0.001 TYR H 52 PHE 0.026 0.001 PHE A 782 TRP 0.016 0.001 TRP A 182 HIS 0.005 0.001 HIS A 674 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 7279) covalent geometry : angle 0.53035 ( 9891) SS BOND : bond 0.00221 ( 3) SS BOND : angle 0.45626 ( 6) hydrogen bonds : bond 0.04289 ( 363) hydrogen bonds : angle 4.84724 ( 1044) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.2571 (tpt) cc_final: 0.1530 (mtt) REVERT: A 65 MET cc_start: 0.6980 (mtp) cc_final: 0.6062 (tpp) REVERT: A 175 TRP cc_start: 0.1864 (t-100) cc_final: 0.0287 (m100) REVERT: A 183 LEU cc_start: 0.7997 (tt) cc_final: 0.7427 (mt) REVERT: H 5 GLN cc_start: 0.7983 (tp40) cc_final: 0.7764 (mm110) outliers start: 10 outliers final: 7 residues processed: 63 average time/residue: 0.0811 time to fit residues: 7.3280 Evaluate side-chains 56 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 78 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 20.0000 chunk 21 optimal weight: 30.0000 chunk 9 optimal weight: 20.0000 chunk 75 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 54 optimal weight: 20.0000 chunk 70 optimal weight: 0.3980 chunk 25 optimal weight: 10.0000 chunk 15 optimal weight: 0.4980 overall best weight: 3.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.133253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.092126 restraints weight = 21816.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.087034 restraints weight = 15936.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.088101 restraints weight = 12895.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.088090 restraints weight = 9748.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.088152 restraints weight = 10211.657| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 7282 Z= 0.285 Angle : 0.622 5.953 9897 Z= 0.335 Chirality : 0.044 0.155 1137 Planarity : 0.005 0.061 1240 Dihedral : 4.837 23.048 972 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.22 % Allowed : 14.10 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.28), residues: 900 helix: 1.94 (0.28), residues: 318 sheet: -0.51 (0.33), residues: 241 loop : -0.37 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 632 TYR 0.020 0.002 TYR H 60 PHE 0.034 0.003 PHE A 562 TRP 0.022 0.002 TRP A 182 HIS 0.005 0.001 HIS A 630 Details of bonding type rmsd covalent geometry : bond 0.00645 ( 7279) covalent geometry : angle 0.62173 ( 9891) SS BOND : bond 0.00476 ( 3) SS BOND : angle 0.65247 ( 6) hydrogen bonds : bond 0.04393 ( 363) hydrogen bonds : angle 4.96044 ( 1044) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 46 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.2082 (tpt) cc_final: 0.1018 (mtt) REVERT: A 65 MET cc_start: 0.6931 (mtp) cc_final: 0.5927 (tpp) REVERT: A 183 LEU cc_start: 0.8001 (tt) cc_final: 0.7464 (mt) outliers start: 17 outliers final: 13 residues processed: 62 average time/residue: 0.0693 time to fit residues: 6.3240 Evaluate side-chains 54 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 78 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 84 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 30.0000 chunk 72 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 16 optimal weight: 20.0000 chunk 90 optimal weight: 0.7980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 1 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.135724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.097280 restraints weight = 21614.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.090556 restraints weight = 15186.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.092021 restraints weight = 11276.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.091700 restraints weight = 8318.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.091836 restraints weight = 9344.533| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.4732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7282 Z= 0.128 Angle : 0.512 5.284 9897 Z= 0.277 Chirality : 0.042 0.169 1137 Planarity : 0.004 0.039 1240 Dihedral : 4.492 22.518 972 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.96 % Allowed : 14.62 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.28), residues: 900 helix: 2.09 (0.28), residues: 319 sheet: -0.28 (0.33), residues: 242 loop : -0.28 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 410 TYR 0.010 0.001 TYR A 46 PHE 0.021 0.001 PHE A 884 TRP 0.017 0.001 TRP A 182 HIS 0.004 0.001 HIS A 674 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 7279) covalent geometry : angle 0.51188 ( 9891) SS BOND : bond 0.00208 ( 3) SS BOND : angle 0.42905 ( 6) hydrogen bonds : bond 0.03901 ( 363) hydrogen bonds : angle 4.67453 ( 1044) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.2046 (tpt) cc_final: 0.1533 (mtt) REVERT: A 53 MET cc_start: 0.3086 (ttp) cc_final: 0.2788 (ptt) REVERT: A 65 MET cc_start: 0.7131 (mtp) cc_final: 0.6138 (tpp) REVERT: A 183 LEU cc_start: 0.7982 (tt) cc_final: 0.7557 (mm) REVERT: A 495 THR cc_start: 0.8782 (OUTLIER) cc_final: 0.8556 (p) REVERT: H 5 GLN cc_start: 0.8042 (tp40) cc_final: 0.7773 (mm110) outliers start: 15 outliers final: 11 residues processed: 62 average time/residue: 0.0712 time to fit residues: 6.5397 Evaluate side-chains 57 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 57 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 21 optimal weight: 50.0000 chunk 39 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 56 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 35 optimal weight: 0.0770 chunk 30 optimal weight: 0.6980 chunk 1 optimal weight: 9.9990 overall best weight: 1.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.135368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.097642 restraints weight = 21238.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.093208 restraints weight = 16151.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.092841 restraints weight = 12259.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.092843 restraints weight = 10572.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.092915 restraints weight = 9655.879| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7282 Z= 0.138 Angle : 0.508 5.034 9897 Z= 0.275 Chirality : 0.042 0.169 1137 Planarity : 0.004 0.037 1240 Dihedral : 4.365 22.713 972 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.96 % Allowed : 15.27 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.29), residues: 900 helix: 2.15 (0.29), residues: 319 sheet: -0.35 (0.33), residues: 243 loop : -0.16 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 410 TYR 0.010 0.001 TYR A 46 PHE 0.020 0.001 PHE A 769 TRP 0.016 0.001 TRP A 182 HIS 0.003 0.001 HIS A 674 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 7279) covalent geometry : angle 0.50753 ( 9891) SS BOND : bond 0.00242 ( 3) SS BOND : angle 0.46791 ( 6) hydrogen bonds : bond 0.03766 ( 363) hydrogen bonds : angle 4.60055 ( 1044) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.1944 (tpt) cc_final: 0.1481 (mtt) REVERT: A 53 MET cc_start: 0.3019 (ttp) cc_final: 0.2755 (ptt) REVERT: A 65 MET cc_start: 0.7109 (mtp) cc_final: 0.6133 (tpp) REVERT: A 183 LEU cc_start: 0.7766 (tt) cc_final: 0.7436 (mm) REVERT: A 495 THR cc_start: 0.8789 (OUTLIER) cc_final: 0.8569 (p) REVERT: H 5 GLN cc_start: 0.8060 (tp40) cc_final: 0.7800 (mm110) outliers start: 15 outliers final: 12 residues processed: 60 average time/residue: 0.0774 time to fit residues: 6.9228 Evaluate side-chains 57 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 57 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 23 optimal weight: 10.0000 chunk 21 optimal weight: 0.1980 chunk 81 optimal weight: 0.6980 chunk 48 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 55 optimal weight: 6.9990 chunk 0 optimal weight: 40.0000 chunk 44 optimal weight: 10.0000 chunk 18 optimal weight: 30.0000 chunk 69 optimal weight: 4.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.133832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.095275 restraints weight = 21636.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.088851 restraints weight = 15789.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.090153 restraints weight = 11674.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.089840 restraints weight = 9706.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.089920 restraints weight = 8810.760| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7282 Z= 0.198 Angle : 0.531 5.580 9897 Z= 0.289 Chirality : 0.042 0.153 1137 Planarity : 0.004 0.040 1240 Dihedral : 4.528 22.732 972 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.48 % Allowed : 14.49 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.29), residues: 900 helix: 2.22 (0.29), residues: 319 sheet: -0.46 (0.33), residues: 242 loop : -0.27 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 668 TYR 0.012 0.001 TYR H 60 PHE 0.019 0.002 PHE A 562 TRP 0.017 0.002 TRP H 36 HIS 0.004 0.001 HIS A 630 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 7279) covalent geometry : angle 0.53146 ( 9891) SS BOND : bond 0.00362 ( 3) SS BOND : angle 0.57745 ( 6) hydrogen bonds : bond 0.03804 ( 363) hydrogen bonds : angle 4.64349 ( 1044) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 45 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.1839 (tpt) cc_final: 0.0819 (mtt) REVERT: A 53 MET cc_start: 0.3077 (ttp) cc_final: 0.2573 (ttp) REVERT: A 65 MET cc_start: 0.7057 (mtp) cc_final: 0.6111 (tpp) REVERT: A 183 LEU cc_start: 0.7841 (tt) cc_final: 0.7505 (mm) REVERT: A 495 THR cc_start: 0.8872 (OUTLIER) cc_final: 0.8630 (p) outliers start: 19 outliers final: 17 residues processed: 63 average time/residue: 0.0715 time to fit residues: 6.7179 Evaluate side-chains 61 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 43 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 674 HIS Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 78 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 90 optimal weight: 0.3980 chunk 38 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 57 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 76 optimal weight: 0.7980 chunk 11 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.135772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.098778 restraints weight = 21517.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.093313 restraints weight = 16583.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.092660 restraints weight = 13037.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.092852 restraints weight = 11579.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.092945 restraints weight = 9962.468| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.5162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7282 Z= 0.113 Angle : 0.511 7.684 9897 Z= 0.274 Chirality : 0.042 0.165 1137 Planarity : 0.004 0.036 1240 Dihedral : 4.313 22.172 972 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.70 % Allowed : 15.80 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.29), residues: 900 helix: 2.25 (0.29), residues: 320 sheet: -0.27 (0.33), residues: 244 loop : -0.17 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 410 TYR 0.011 0.001 TYR A 539 PHE 0.019 0.001 PHE A 769 TRP 0.017 0.001 TRP A 182 HIS 0.004 0.001 HIS A 674 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 7279) covalent geometry : angle 0.51076 ( 9891) SS BOND : bond 0.00182 ( 3) SS BOND : angle 0.36981 ( 6) hydrogen bonds : bond 0.03633 ( 363) hydrogen bonds : angle 4.48043 ( 1044) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.1776 (tpt) cc_final: 0.1324 (mtt) REVERT: A 53 MET cc_start: 0.3091 (ttp) cc_final: 0.2768 (ptt) REVERT: A 65 MET cc_start: 0.7094 (mtp) cc_final: 0.6260 (tpt) REVERT: A 183 LEU cc_start: 0.7863 (tt) cc_final: 0.7531 (mm) REVERT: H 5 GLN cc_start: 0.8005 (tp40) cc_final: 0.7764 (mm110) outliers start: 13 outliers final: 13 residues processed: 57 average time/residue: 0.0784 time to fit residues: 6.6827 Evaluate side-chains 57 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 78 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 20.0000 chunk 66 optimal weight: 30.0000 chunk 85 optimal weight: 0.0670 chunk 16 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 chunk 83 optimal weight: 0.9990 chunk 63 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 overall best weight: 4.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.131041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.087964 restraints weight = 21745.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.083441 restraints weight = 14393.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.084944 restraints weight = 11549.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.084231 restraints weight = 9339.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.084513 restraints weight = 9179.389| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.5626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 7282 Z= 0.353 Angle : 0.671 6.833 9897 Z= 0.363 Chirality : 0.045 0.159 1137 Planarity : 0.005 0.074 1240 Dihedral : 5.043 23.179 972 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.33 % Favored : 95.56 % Rotamer: Outliers : 2.48 % Allowed : 15.40 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.28), residues: 900 helix: 2.21 (0.29), residues: 317 sheet: -0.70 (0.33), residues: 225 loop : -0.58 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 632 TYR 0.018 0.002 TYR L 33 PHE 0.031 0.003 PHE A 562 TRP 0.022 0.002 TRP H 36 HIS 0.008 0.002 HIS A 630 Details of bonding type rmsd covalent geometry : bond 0.00795 ( 7279) covalent geometry : angle 0.67067 ( 9891) SS BOND : bond 0.00666 ( 3) SS BOND : angle 0.82227 ( 6) hydrogen bonds : bond 0.04244 ( 363) hydrogen bonds : angle 4.90462 ( 1044) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 40 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.7101 (mtp) cc_final: 0.6234 (mmt) REVERT: A 183 LEU cc_start: 0.7982 (tt) cc_final: 0.7709 (mm) REVERT: H 5 GLN cc_start: 0.8036 (tp40) cc_final: 0.7824 (mm110) outliers start: 19 outliers final: 19 residues processed: 57 average time/residue: 0.0675 time to fit residues: 5.9594 Evaluate side-chains 57 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 38 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 674 HIS Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 116 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 17 optimal weight: 8.9990 chunk 10 optimal weight: 30.0000 chunk 70 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.134793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.093612 restraints weight = 21275.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.088659 restraints weight = 13347.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.089583 restraints weight = 10588.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.089659 restraints weight = 8636.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.089599 restraints weight = 8806.103| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.5544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7282 Z= 0.121 Angle : 0.530 6.827 9897 Z= 0.284 Chirality : 0.042 0.166 1137 Planarity : 0.004 0.037 1240 Dihedral : 4.521 21.945 972 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.96 % Allowed : 16.06 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.29), residues: 900 helix: 2.33 (0.29), residues: 318 sheet: -0.39 (0.34), residues: 225 loop : -0.48 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 98 TYR 0.009 0.001 TYR A 923 PHE 0.019 0.001 PHE A 769 TRP 0.043 0.002 TRP A 851 HIS 0.005 0.001 HIS A 674 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 7279) covalent geometry : angle 0.53047 ( 9891) SS BOND : bond 0.00176 ( 3) SS BOND : angle 0.41687 ( 6) hydrogen bonds : bond 0.03661 ( 363) hydrogen bonds : angle 4.59548 ( 1044) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1661.38 seconds wall clock time: 29 minutes 21.36 seconds (1761.36 seconds total)