Starting phenix.real_space_refine on Tue Jan 14 18:48:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sgt_40467/01_2025/8sgt_40467.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sgt_40467/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8sgt_40467/01_2025/8sgt_40467.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sgt_40467/01_2025/8sgt_40467.map" model { file = "/net/cci-nas-00/data/ceres_data/8sgt_40467/01_2025/8sgt_40467.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sgt_40467/01_2025/8sgt_40467.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 5.19, per 1000 atoms: 0.73 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: 1.61 Conformation dependent library (CDL) restraints added in 955.3 milliseconds 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: 0.91 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: 2.25 Time building geometry restraints manager: 1.90 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: 2.250 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: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.340 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.910 ------------------------------------------------------------------------------- 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 7279 Z= 0.323 Angle : 0.750 8.186 9891 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.022 0.003 TRP A 215 HIS 0.012 0.002 HIS A 674 PHE 0.030 0.002 PHE A 505 TYR 0.044 0.002 TYR A 422 ARG 0.013 0.001 ARG L 22 *********************** 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 : 0.825 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: 0.5963 (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: 0.3664 (t80) REVERT: A 175 TRP cc_start: 0.0527 (t-100) cc_final: -0.0844 (m100) REVERT: A 926 PHE cc_start: 0.7555 (m-10) cc_final: 0.7319 (m-10) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.2396 time to fit residues: 43.1149 Evaluate side-chains 58 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 36 optimal weight: 0.2980 chunk 71 optimal weight: 0.5980 chunk 27 optimal weight: 5.9990 chunk 43 optimal weight: 0.0670 chunk 53 optimal weight: 6.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.5520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.141387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.103320 restraints weight = 21828.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.097566 restraints weight = 14696.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.099057 restraints weight = 11272.524| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7279 Z= 0.203 Angle : 0.637 8.476 9891 Z= 0.338 Chirality : 0.044 0.159 1137 Planarity : 0.005 0.049 1240 Dihedral : 4.785 20.911 972 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.57 % Allowed : 7.18 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.27), residues: 900 helix: 1.03 (0.27), residues: 328 sheet: -0.04 (0.34), residues: 237 loop : -0.44 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 182 HIS 0.005 0.001 HIS A 674 PHE 0.022 0.002 PHE A 769 TYR 0.011 0.001 TYR H 60 ARG 0.004 0.000 ARG H 40 *********************** 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 84 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.4878 (mmm) cc_final: 0.4443 (tmm) REVERT: A 175 TRP cc_start: 0.1792 (t-100) cc_final: 0.0269 (m100) REVERT: A 750 TRP cc_start: 0.2088 (OUTLIER) cc_final: 0.0543 (m-90) REVERT: A 926 PHE cc_start: 0.8094 (m-10) cc_final: 0.7792 (m-80) outliers start: 12 outliers final: 8 residues processed: 81 average time/residue: 0.2033 time to fit residues: 22.3895 Evaluate side-chains 71 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 511 VAL 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 L residue 28 VAL 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 78 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 80 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 25 optimal weight: 7.9990 chunk 54 optimal weight: 20.0000 chunk 23 optimal weight: 0.4980 chunk 27 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 72 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 GLN L 80 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.135972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.092644 restraints weight = 21507.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.088415 restraints weight = 15887.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.088944 restraints weight = 12535.510| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 7279 Z= 0.388 Angle : 0.631 7.389 9891 Z= 0.339 Chirality : 0.044 0.168 1137 Planarity : 0.005 0.057 1240 Dihedral : 4.819 24.480 972 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.70 % Allowed : 11.36 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.28), residues: 900 helix: 1.55 (0.27), residues: 326 sheet: -0.39 (0.33), residues: 246 loop : -0.46 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 36 HIS 0.004 0.001 HIS A 674 PHE 0.029 0.002 PHE A 562 TYR 0.021 0.002 TYR H 60 ARG 0.008 0.001 ARG A 668 *********************** 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 62 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.1816 (tpt) cc_final: 0.1232 (mtt) REVERT: A 144 MET cc_start: 0.5260 (mmm) cc_final: 0.5043 (mmm) REVERT: H 34 MET cc_start: 0.8166 (tpp) cc_final: 0.7886 (tpp) outliers start: 13 outliers final: 10 residues processed: 61 average time/residue: 0.1916 time to fit residues: 16.3684 Evaluate side-chains 53 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 76 ILE 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 49 optimal weight: 20.0000 chunk 4 optimal weight: 3.9990 chunk 16 optimal weight: 20.0000 chunk 25 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 1 optimal weight: 20.0000 chunk 69 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 85 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 = 0.4443 r_free = 0.4443 target = 0.136581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.095375 restraints weight = 21634.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.090970 restraints weight = 14875.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.091779 restraints weight = 11719.424| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7279 Z= 0.259 Angle : 0.545 5.696 9891 Z= 0.295 Chirality : 0.042 0.155 1137 Planarity : 0.004 0.040 1240 Dihedral : 4.600 23.054 972 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.96 % Allowed : 11.88 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.28), residues: 900 helix: 1.73 (0.28), residues: 328 sheet: -0.33 (0.33), residues: 243 loop : -0.38 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 182 HIS 0.005 0.001 HIS A 674 PHE 0.031 0.002 PHE A 916 TYR 0.013 0.001 TYR H 60 ARG 0.004 0.000 ARG A 668 *********************** 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 66 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.2532 (tpt) cc_final: 0.1467 (mtt) REVERT: A 65 MET cc_start: 0.6928 (mtp) cc_final: 0.5943 (tpp) REVERT: A 175 TRP cc_start: 0.2093 (t-100) cc_final: 0.0481 (m100) REVERT: A 183 LEU cc_start: 0.8106 (tt) cc_final: 0.7465 (mt) REVERT: A 513 HIS cc_start: 0.7190 (OUTLIER) cc_final: 0.6867 (m-70) REVERT: H 34 MET cc_start: 0.8223 (tpp) cc_final: 0.7972 (tpp) outliers start: 15 outliers final: 10 residues processed: 66 average time/residue: 0.1838 time to fit residues: 17.4362 Evaluate side-chains 57 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 513 HIS Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 845 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 63 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 17 optimal weight: 40.0000 chunk 10 optimal weight: 30.0000 chunk 55 optimal weight: 20.0000 chunk 31 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 21 optimal weight: 30.0000 chunk 67 optimal weight: 10.0000 chunk 64 optimal weight: 30.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.130495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.088646 restraints weight = 21473.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.084097 restraints weight = 15660.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.085087 restraints weight = 12405.349| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.4956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.082 7279 Z= 0.666 Angle : 0.770 7.728 9891 Z= 0.413 Chirality : 0.049 0.202 1137 Planarity : 0.006 0.085 1240 Dihedral : 5.432 23.022 972 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.22 % Favored : 95.56 % Rotamer: Outliers : 3.26 % Allowed : 13.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.28), residues: 900 helix: 1.82 (0.28), residues: 319 sheet: -0.93 (0.32), residues: 245 loop : -0.75 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 182 HIS 0.009 0.002 HIS A 630 PHE 0.045 0.003 PHE A 562 TYR 0.028 0.002 TYR H 60 ARG 0.006 0.001 ARG A 668 *********************** 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 65 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 40 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.2035 (tpt) cc_final: 0.0863 (mtt) REVERT: A 65 MET cc_start: 0.7027 (mtp) cc_final: 0.6293 (tpp) REVERT: A 183 LEU cc_start: 0.7931 (tt) cc_final: 0.7401 (mt) REVERT: A 495 THR cc_start: 0.8970 (OUTLIER) cc_final: 0.8651 (p) REVERT: A 754 PHE cc_start: 0.2053 (m-10) cc_final: 0.1809 (m-10) REVERT: H 34 MET cc_start: 0.8312 (tpp) cc_final: 0.7989 (tpp) outliers start: 25 outliers final: 19 residues processed: 60 average time/residue: 0.1509 time to fit residues: 14.0223 Evaluate side-chains 55 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 35 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 PHE Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 587 PHE 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 671 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 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 Chi-restraints excluded: chain H residue 119 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 54 optimal weight: 30.0000 chunk 63 optimal weight: 20.0000 chunk 36 optimal weight: 0.0370 chunk 85 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 6 optimal weight: 30.0000 chunk 67 optimal weight: 10.0000 chunk 78 optimal weight: 0.6980 overall best weight: 0.6458 ------------------------------------------------------------------------------- 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 = 0.4427 r_free = 0.4427 target = 0.135374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.095213 restraints weight = 21507.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.090993 restraints weight = 15460.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.091947 restraints weight = 12148.733| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7279 Z= 0.171 Angle : 0.541 8.247 9891 Z= 0.290 Chirality : 0.043 0.168 1137 Planarity : 0.004 0.040 1240 Dihedral : 4.647 22.679 972 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.70 % Allowed : 15.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.28), residues: 900 helix: 2.15 (0.28), residues: 311 sheet: -0.74 (0.33), residues: 236 loop : -0.37 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 182 HIS 0.003 0.001 HIS A 459 PHE 0.020 0.002 PHE A 916 TYR 0.010 0.001 TYR A 46 ARG 0.003 0.000 ARG A 410 *********************** 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 57 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.2205 (tpt) cc_final: 0.1074 (mtt) REVERT: A 64 PHE cc_start: 0.8137 (t80) cc_final: 0.7821 (t80) REVERT: A 65 MET cc_start: 0.7234 (mtp) cc_final: 0.6488 (tpp) REVERT: A 183 LEU cc_start: 0.7995 (tt) cc_final: 0.7589 (mm) outliers start: 13 outliers final: 10 residues processed: 57 average time/residue: 0.1737 time to fit residues: 14.4715 Evaluate side-chains 51 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 845 LEU 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 116 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 78 optimal weight: 0.0070 chunk 46 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 13 optimal weight: 30.0000 overall best weight: 2.7404 ------------------------------------------------------------------------------- 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 = 0.4387 r_free = 0.4387 target = 0.132567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.094599 restraints weight = 21383.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.088704 restraints weight = 16316.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.089871 restraints weight = 12447.110| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 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 : 0.006 0.055 7279 Z= 0.375 Angle : 0.593 5.911 9891 Z= 0.319 Chirality : 0.043 0.151 1137 Planarity : 0.004 0.053 1240 Dihedral : 4.785 22.652 972 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.74 % Allowed : 15.67 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.28), residues: 900 helix: 2.18 (0.28), residues: 312 sheet: -0.90 (0.33), residues: 230 loop : -0.43 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 36 HIS 0.006 0.001 HIS A 630 PHE 0.029 0.002 PHE A 884 TYR 0.014 0.001 TYR H 60 ARG 0.004 0.001 ARG A 668 *********************** 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 64 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 43 time to evaluate : 0.808 Fit side-chains revert: symmetry clash REVERT: A 50 MET cc_start: 0.2044 (tpt) cc_final: 0.0874 (mtt) REVERT: A 64 PHE cc_start: 0.7968 (t80) cc_final: 0.7499 (t80) REVERT: A 65 MET cc_start: 0.7154 (mtp) cc_final: 0.6497 (tpp) REVERT: A 183 LEU cc_start: 0.7851 (tt) cc_final: 0.7514 (mm) REVERT: A 543 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7799 (pm20) outliers start: 21 outliers final: 17 residues processed: 60 average time/residue: 0.1647 time to fit residues: 14.6365 Evaluate side-chains 59 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 41 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 674 HIS Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 769 PHE Chi-restraints excluded: chain A residue 773 ILE 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 59 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 48 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 51 optimal weight: 0.1980 chunk 9 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 39 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 69 optimal weight: 0.2980 chunk 8 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 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 = 0.4423 r_free = 0.4423 target = 0.135057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.095573 restraints weight = 21262.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.090546 restraints weight = 14325.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.091513 restraints weight = 11433.716| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.5155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7279 Z= 0.168 Angle : 0.521 5.836 9891 Z= 0.279 Chirality : 0.041 0.154 1137 Planarity : 0.004 0.039 1240 Dihedral : 4.508 22.280 972 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.70 % Allowed : 16.45 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.29), residues: 900 helix: 2.33 (0.28), residues: 311 sheet: -0.66 (0.34), residues: 228 loop : -0.33 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 182 HIS 0.003 0.001 HIS A 674 PHE 0.028 0.001 PHE A 884 TYR 0.009 0.001 TYR A 46 ARG 0.009 0.000 ARG A 547 *********************** 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 59 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.2048 (tpt) cc_final: 0.0944 (mtt) REVERT: A 64 PHE cc_start: 0.8176 (t80) cc_final: 0.7876 (t80) REVERT: A 65 MET cc_start: 0.7075 (mtp) cc_final: 0.6446 (tpp) REVERT: A 144 MET cc_start: 0.4165 (mmm) cc_final: 0.2512 (ttp) REVERT: A 183 LEU cc_start: 0.7935 (tt) cc_final: 0.7548 (mm) REVERT: H 113 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8445 (pm20) outliers start: 13 outliers final: 12 residues processed: 56 average time/residue: 0.1835 time to fit residues: 15.1094 Evaluate side-chains 55 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 674 HIS Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 769 PHE Chi-restraints excluded: chain A residue 773 ILE 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 113 GLN Chi-restraints excluded: chain H residue 116 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 47 optimal weight: 8.9990 chunk 69 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 40 optimal weight: 0.0770 chunk 15 optimal weight: 0.0040 chunk 29 optimal weight: 8.9990 chunk 64 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 61 optimal weight: 20.0000 overall best weight: 1.6156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 630 HIS ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.133820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.094405 restraints weight = 21515.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.088018 restraints weight = 14497.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.089256 restraints weight = 11257.278| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.5327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7279 Z= 0.249 Angle : 0.539 7.898 9891 Z= 0.289 Chirality : 0.042 0.198 1137 Planarity : 0.004 0.039 1240 Dihedral : 4.487 22.006 972 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.35 % Allowed : 15.93 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.29), residues: 900 helix: 2.35 (0.28), residues: 311 sheet: -0.67 (0.33), residues: 229 loop : -0.31 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 182 HIS 0.004 0.001 HIS A 674 PHE 0.029 0.002 PHE A 884 TYR 0.010 0.001 TYR A 46 ARG 0.003 0.000 ARG A 547 *********************** 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 62 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 44 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.2070 (tpt) cc_final: 0.0960 (mtt) REVERT: A 64 PHE cc_start: 0.8157 (t80) cc_final: 0.7841 (t80) REVERT: A 65 MET cc_start: 0.7049 (mtp) cc_final: 0.6428 (tpp) REVERT: A 144 MET cc_start: 0.4401 (mmm) cc_final: 0.2734 (ttp) REVERT: A 183 LEU cc_start: 0.7945 (tt) cc_final: 0.7605 (mm) REVERT: A 431 PHE cc_start: 0.8309 (OUTLIER) cc_final: 0.8058 (t80) REVERT: H 113 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8511 (pm20) outliers start: 18 outliers final: 14 residues processed: 59 average time/residue: 0.1707 time to fit residues: 14.9218 Evaluate side-chains 58 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 42 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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 597 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 674 HIS Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 769 PHE Chi-restraints excluded: chain A residue 773 ILE 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 H residue 30 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 113 GLN 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 15 optimal weight: 7.9990 chunk 21 optimal weight: 0.8980 chunk 34 optimal weight: 7.9990 chunk 13 optimal weight: 30.0000 chunk 47 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 66 optimal weight: 20.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.4409 r_free = 0.4409 target = 0.133992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.095825 restraints weight = 21784.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.088948 restraints weight = 15503.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.090102 restraints weight = 12170.568| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.5479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7279 Z= 0.234 Angle : 0.525 5.743 9891 Z= 0.283 Chirality : 0.042 0.153 1137 Planarity : 0.004 0.038 1240 Dihedral : 4.465 21.857 972 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.22 % Allowed : 15.93 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.29), residues: 900 helix: 2.38 (0.28), residues: 310 sheet: -0.65 (0.34), residues: 229 loop : -0.29 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 182 HIS 0.008 0.001 HIS A 630 PHE 0.028 0.002 PHE A 884 TYR 0.009 0.001 TYR A 46 ARG 0.002 0.000 ARG A 410 ********************** 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 63 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 46 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.2138 (tpt) cc_final: 0.1585 (mtt) REVERT: A 53 MET cc_start: 0.3166 (ttp) cc_final: 0.2767 (ptt) REVERT: A 64 PHE cc_start: 0.8090 (t80) cc_final: 0.7754 (t80) REVERT: A 65 MET cc_start: 0.7086 (mtp) cc_final: 0.6445 (tpp) REVERT: A 144 MET cc_start: 0.4472 (mmm) cc_final: 0.2789 (ttm) REVERT: A 183 LEU cc_start: 0.7896 (tt) cc_final: 0.7584 (mm) REVERT: A 711 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7567 (tp30) REVERT: H 113 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.8494 (pm20) outliers start: 17 outliers final: 16 residues processed: 60 average time/residue: 0.1725 time to fit residues: 15.1015 Evaluate side-chains 61 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 0.844 ------------------------------------------------------------------------------- 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 597 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 674 HIS Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 769 PHE Chi-restraints excluded: chain A residue 773 ILE 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 H residue 30 THR Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 113 GLN 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 46 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 70 optimal weight: 10.0000 chunk 10 optimal weight: 30.0000 chunk 83 optimal weight: 0.5980 chunk 9 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 31 optimal weight: 9.9990 chunk 88 optimal weight: 0.6980 chunk 61 optimal weight: 10.0000 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 = 0.4412 r_free = 0.4412 target = 0.134374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.096800 restraints weight = 21504.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.091030 restraints weight = 14990.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.092195 restraints weight = 11230.464| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.5569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7279 Z= 0.204 Angle : 0.534 9.621 9891 Z= 0.286 Chirality : 0.042 0.191 1137 Planarity : 0.004 0.037 1240 Dihedral : 4.376 21.881 972 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.22 % Allowed : 16.58 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.29), residues: 900 helix: 2.49 (0.28), residues: 311 sheet: -0.56 (0.34), residues: 225 loop : -0.31 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 182 HIS 0.008 0.001 HIS A 630 PHE 0.027 0.001 PHE A 884 TYR 0.009 0.001 TYR A 46 ARG 0.003 0.000 ARG A 547 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2668.90 seconds wall clock time: 49 minutes 57.75 seconds (2997.75 seconds total)