Starting phenix.real_space_refine on Mon Apr 28 07:11:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sgt_40467/04_2025/8sgt_40467.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sgt_40467/04_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_40467/04_2025/8sgt_40467.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sgt_40467/04_2025/8sgt_40467.map" model { file = "/net/cci-nas-00/data/ceres_data/8sgt_40467/04_2025/8sgt_40467.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sgt_40467/04_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 4.77, per 1000 atoms: 0.67 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: 1.56 Conformation dependent library (CDL) restraints added in 944.5 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: 0.89 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: 2.29 Time building geometry restraints manager: 1.88 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: 2.470 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.840 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.580 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.25451 ( 363) hydrogen bonds : angle 8.69297 ( 1044) SS BOND : bond 0.00189 ( 3) SS BOND : angle 0.74918 ( 6) covalent geometry : bond 0.00477 ( 7279) covalent geometry : angle 0.75027 ( 9891) *********************** 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 : 0.810 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: 0.2221 time to fit residues: 40.0531 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 : 0.788 ------------------------------------------------------------------------------- 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 = 0.103319 restraints weight = 21828.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.097560 restraints weight = 14694.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.099097 restraints weight = 11259.777| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 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 7282 Z= 0.143 Angle : 0.637 8.476 9897 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 Details of bonding type rmsd hydrogen bonds : bond 0.05314 ( 363) hydrogen bonds : angle 5.33214 ( 1044) SS BOND : bond 0.00292 ( 3) SS BOND : angle 0.62664 ( 6) covalent geometry : bond 0.00303 ( 7279) covalent geometry : angle 0.63660 ( 9891) *********************** 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 : 0.770 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: 0.1793 (t-100) cc_final: 0.0270 (m100) REVERT: A 750 TRP cc_start: 0.2089 (OUTLIER) cc_final: 0.0543 (m-90) REVERT: A 926 PHE cc_start: 0.8095 (m-10) cc_final: 0.7793 (m-80) outliers start: 12 outliers final: 8 residues processed: 81 average time/residue: 0.2031 time to fit residues: 22.4766 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 : 0.886 ------------------------------------------------------------------------------- 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: 1.9990 chunk 71 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 54 optimal weight: 20.0000 chunk 23 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 72 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 80 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.139269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.098810 restraints weight = 22527.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.094281 restraints weight = 13922.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.095459 restraints weight = 10947.189| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7282 Z= 0.191 Angle : 0.580 7.829 9897 Z= 0.311 Chirality : 0.043 0.165 1137 Planarity : 0.005 0.044 1240 Dihedral : 4.611 23.911 972 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.44 % Allowed : 10.57 % Favored : 87.99 % 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: 0.48 (0.28), residues: 900 helix: 1.57 (0.27), residues: 326 sheet: -0.27 (0.33), residues: 252 loop : -0.35 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 36 HIS 0.004 0.001 HIS A 674 PHE 0.027 0.002 PHE A 754 TYR 0.016 0.001 TYR H 60 ARG 0.005 0.000 ARG A 668 Details of bonding type rmsd hydrogen bonds : bond 0.04853 ( 363) hydrogen bonds : angle 4.96243 ( 1044) SS BOND : bond 0.00363 ( 3) SS BOND : angle 0.73559 ( 6) covalent geometry : bond 0.00422 ( 7279) covalent geometry : angle 0.57980 ( 9891) *********************** 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 65 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.1989 (tpt) cc_final: 0.1415 (mtt) REVERT: H 34 MET cc_start: 0.8096 (tpp) cc_final: 0.7851 (tpp) outliers start: 11 outliers final: 6 residues processed: 64 average time/residue: 0.1925 time to fit residues: 17.3087 Evaluate side-chains 54 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.846 ------------------------------------------------------------------------------- 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 28 VAL Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain H residue 30 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: 1.9990 chunk 16 optimal weight: 20.0000 chunk 25 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 1 optimal weight: 0.0270 chunk 69 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 72 optimal weight: 0.5980 chunk 45 optimal weight: 4.9990 overall best weight: 0.8440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 GLN H 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.140468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.100828 restraints weight = 22533.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.097369 restraints weight = 14943.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.097382 restraints weight = 12351.252| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7282 Z= 0.125 Angle : 0.519 6.018 9897 Z= 0.280 Chirality : 0.042 0.151 1137 Planarity : 0.004 0.040 1240 Dihedral : 4.348 22.760 972 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.57 % Allowed : 11.49 % 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: 0.63 (0.28), residues: 900 helix: 1.70 (0.28), residues: 328 sheet: -0.23 (0.33), residues: 251 loop : -0.25 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 182 HIS 0.004 0.001 HIS A 674 PHE 0.058 0.002 PHE A 782 TYR 0.010 0.001 TYR A 46 ARG 0.002 0.000 ARG A 668 Details of bonding type rmsd hydrogen bonds : bond 0.04308 ( 363) hydrogen bonds : angle 4.76512 ( 1044) SS BOND : bond 0.00235 ( 3) SS BOND : angle 0.48818 ( 6) covalent geometry : bond 0.00268 ( 7279) covalent geometry : angle 0.51876 ( 9891) *********************** 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 70 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.2440 (tpt) cc_final: 0.1402 (mtt) REVERT: A 65 MET cc_start: 0.6911 (mtp) cc_final: 0.5878 (tpp) REVERT: A 175 TRP cc_start: 0.1928 (t-100) cc_final: 0.0364 (m100) REVERT: A 183 LEU cc_start: 0.8101 (tt) cc_final: 0.7491 (mt) outliers start: 12 outliers final: 7 residues processed: 69 average time/residue: 0.2733 time to fit residues: 28.1402 Evaluate side-chains 58 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 1.569 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 27 optimal weight: 9.9990 chunk 17 optimal weight: 40.0000 chunk 10 optimal weight: 20.0000 chunk 55 optimal weight: 20.0000 chunk 31 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 21 optimal weight: 40.0000 chunk 67 optimal weight: 10.0000 chunk 64 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN H 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.130960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.089036 restraints weight = 21520.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.084463 restraints weight = 15582.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.085488 restraints weight = 12344.423| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.4702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.097 7282 Z= 0.500 Angle : 0.816 7.913 9897 Z= 0.438 Chirality : 0.050 0.217 1137 Planarity : 0.007 0.090 1240 Dihedral : 5.393 22.884 972 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.22 % Favored : 95.67 % Rotamer: Outliers : 2.74 % Allowed : 12.79 % Favored : 84.46 % 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: 0.15 (0.28), residues: 900 helix: 1.81 (0.28), residues: 319 sheet: -0.85 (0.32), residues: 247 loop : -0.74 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP H 111 HIS 0.009 0.002 HIS A 630 PHE 0.060 0.004 PHE A 562 TYR 0.033 0.003 TYR H 60 ARG 0.011 0.001 ARG A 595 Details of bonding type rmsd hydrogen bonds : bond 0.05087 ( 363) hydrogen bonds : angle 5.27420 ( 1044) SS BOND : bond 0.00783 ( 3) SS BOND : angle 1.03206 ( 6) covalent geometry : bond 0.01134 ( 7279) covalent geometry : angle 0.81586 ( 9891) *********************** 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 61 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 40 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.2166 (tpt) cc_final: 0.0984 (mtt) REVERT: A 65 MET cc_start: 0.6992 (mtp) cc_final: 0.6166 (tpt) REVERT: A 183 LEU cc_start: 0.7936 (tt) cc_final: 0.7449 (mt) REVERT: H 34 MET cc_start: 0.8391 (tpp) cc_final: 0.8082 (tpp) outliers start: 21 outliers final: 16 residues processed: 56 average time/residue: 0.1807 time to fit residues: 15.7793 Evaluate side-chains 53 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 37 time to evaluate : 0.788 ------------------------------------------------------------------------------- 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 505 PHE 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 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: 0.9990 chunk 72 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 36 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4426 r_free = 0.4426 target = 0.135383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.098645 restraints weight = 21615.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.092677 restraints weight = 17133.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.092858 restraints weight = 16174.687| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.4675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7282 Z= 0.134 Angle : 0.543 8.404 9897 Z= 0.291 Chirality : 0.042 0.184 1137 Planarity : 0.004 0.041 1240 Dihedral : 4.691 22.784 972 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.57 % Allowed : 15.14 % Favored : 83.29 % 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: 0.51 (0.28), residues: 900 helix: 2.05 (0.28), residues: 319 sheet: -0.62 (0.33), residues: 236 loop : -0.51 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 182 HIS 0.004 0.001 HIS A 674 PHE 0.027 0.002 PHE A 782 TYR 0.009 0.001 TYR A 46 ARG 0.004 0.000 ARG A 410 Details of bonding type rmsd hydrogen bonds : bond 0.04057 ( 363) hydrogen bonds : angle 4.86556 ( 1044) SS BOND : bond 0.00203 ( 3) SS BOND : angle 0.43447 ( 6) covalent geometry : bond 0.00292 ( 7279) covalent geometry : angle 0.54311 ( 9891) *********************** 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: 12 poor density : 45 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.2102 (tpt) cc_final: 0.0910 (mtt) REVERT: A 65 MET cc_start: 0.7092 (mtp) cc_final: 0.6289 (tpp) REVERT: A 183 LEU cc_start: 0.7804 (tt) cc_final: 0.7451 (mm) outliers start: 12 outliers final: 9 residues processed: 56 average time/residue: 0.2067 time to fit residues: 17.4953 Evaluate side-chains 52 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 610 LEU 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 78 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 5 optimal weight: 0.5980 chunk 3 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 13 optimal weight: 30.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 = 0.4397 r_free = 0.4397 target = 0.133299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.093988 restraints weight = 21600.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.087992 restraints weight = 16275.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.089264 restraints weight = 12269.252| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.4990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 7282 Z= 0.221 Angle : 0.575 5.699 9897 Z= 0.310 Chirality : 0.043 0.167 1137 Planarity : 0.004 0.048 1240 Dihedral : 4.717 22.186 972 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % 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 (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: 0.52 (0.28), residues: 900 helix: 2.14 (0.28), residues: 314 sheet: -0.79 (0.33), residues: 238 loop : -0.39 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 182 HIS 0.004 0.001 HIS A 630 PHE 0.026 0.002 PHE A 562 TYR 0.013 0.001 TYR H 60 ARG 0.004 0.001 ARG A 410 Details of bonding type rmsd hydrogen bonds : bond 0.04097 ( 363) hydrogen bonds : angle 4.84095 ( 1044) SS BOND : bond 0.00434 ( 3) SS BOND : angle 0.60188 ( 6) covalent geometry : bond 0.00494 ( 7279) covalent geometry : angle 0.57494 ( 9891) *********************** 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 59 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 44 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.2040 (tpt) cc_final: 0.0843 (mtt) REVERT: A 64 PHE cc_start: 0.8016 (t80) cc_final: 0.7543 (t80) REVERT: A 65 MET cc_start: 0.7195 (mtp) cc_final: 0.6445 (tpp) REVERT: A 183 LEU cc_start: 0.7798 (tt) cc_final: 0.7444 (mm) REVERT: A 495 THR cc_start: 0.8917 (OUTLIER) cc_final: 0.8658 (p) outliers start: 15 outliers final: 10 residues processed: 55 average time/residue: 0.2031 time to fit residues: 16.8812 Evaluate side-chains 54 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 495 THR 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 769 PHE Chi-restraints excluded: chain A residue 773 ILE 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 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 51 optimal weight: 0.0770 chunk 9 optimal weight: 20.0000 chunk 12 optimal weight: 20.0000 chunk 39 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 68 optimal weight: 0.3980 chunk 69 optimal weight: 1.9990 chunk 8 optimal weight: 40.0000 chunk 45 optimal weight: 5.9990 overall best weight: 0.6942 ------------------------------------------------------------------------------- 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 = 0.4432 r_free = 0.4432 target = 0.135662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.095865 restraints weight = 21434.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.091288 restraints weight = 15282.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.092560 restraints weight = 11343.448| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7282 Z= 0.113 Angle : 0.520 7.728 9897 Z= 0.278 Chirality : 0.042 0.179 1137 Planarity : 0.004 0.037 1240 Dihedral : 4.454 21.656 972 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.31 % Allowed : 16.19 % 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 (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: 0.80 (0.29), residues: 900 helix: 2.35 (0.28), residues: 311 sheet: -0.55 (0.34), residues: 228 loop : -0.28 (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 0.021 0.001 PHE A 782 TYR 0.009 0.001 TYR A 46 ARG 0.004 0.000 ARG A 410 Details of bonding type rmsd hydrogen bonds : bond 0.03729 ( 363) hydrogen bonds : angle 4.62898 ( 1044) SS BOND : bond 0.00198 ( 3) SS BOND : angle 0.40717 ( 6) covalent geometry : bond 0.00243 ( 7279) covalent geometry : angle 0.51961 ( 9891) *********************** 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 54 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.2076 (tpt) cc_final: 0.0931 (mtt) REVERT: A 64 PHE cc_start: 0.8164 (t80) cc_final: 0.7766 (t80) REVERT: A 65 MET cc_start: 0.7082 (mtp) cc_final: 0.6426 (tpp) REVERT: A 183 LEU cc_start: 0.7962 (tt) cc_final: 0.7601 (mm) REVERT: A 495 THR cc_start: 0.8897 (OUTLIER) cc_final: 0.8658 (p) outliers start: 10 outliers final: 9 residues processed: 52 average time/residue: 0.1737 time to fit residues: 13.4790 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 : 0.813 ------------------------------------------------------------------------------- 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 607 LEU Chi-restraints excluded: chain A residue 610 LEU 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 78 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 47 optimal weight: 7.9990 chunk 69 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 15 optimal weight: 20.0000 chunk 29 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 61 optimal weight: 9.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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 = 0.4394 r_free = 0.4394 target = 0.133095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.093724 restraints weight = 21711.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.086753 restraints weight = 15416.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.087956 restraints weight = 11872.326| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.5281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 7282 Z= 0.227 Angle : 0.571 6.398 9897 Z= 0.307 Chirality : 0.043 0.148 1137 Planarity : 0.004 0.048 1240 Dihedral : 4.625 21.901 972 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.83 % Allowed : 16.06 % 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 (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: 0.60 (0.29), residues: 900 helix: 2.24 (0.28), residues: 319 sheet: -0.70 (0.34), residues: 229 loop : -0.48 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 36 HIS 0.005 0.001 HIS A 630 PHE 0.025 0.002 PHE A 562 TYR 0.012 0.001 TYR L 33 ARG 0.004 0.001 ARG A 410 Details of bonding type rmsd hydrogen bonds : bond 0.03941 ( 363) hydrogen bonds : angle 4.73916 ( 1044) SS BOND : bond 0.00442 ( 3) SS BOND : angle 0.69648 ( 6) covalent geometry : bond 0.00509 ( 7279) covalent geometry : angle 0.57044 ( 9891) *********************** 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 59 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.2062 (tpt) cc_final: 0.1509 (mtt) REVERT: A 53 MET cc_start: 0.3116 (ttp) cc_final: 0.2595 (ptt) REVERT: A 64 PHE cc_start: 0.8183 (t80) cc_final: 0.7742 (t80) REVERT: A 65 MET cc_start: 0.7084 (mtp) cc_final: 0.6459 (tpp) REVERT: A 183 LEU cc_start: 0.7935 (tt) cc_final: 0.7584 (mm) outliers start: 14 outliers final: 13 residues processed: 56 average time/residue: 0.1744 time to fit residues: 14.5643 Evaluate side-chains 56 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 ILE 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 769 PHE Chi-restraints excluded: chain A residue 773 ILE 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 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 15 optimal weight: 20.0000 chunk 21 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 13 optimal weight: 30.0000 chunk 47 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 20 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 76 optimal weight: 0.4980 chunk 78 optimal weight: 0.7980 chunk 66 optimal weight: 20.0000 overall best weight: 2.1984 ------------------------------------------------------------------------------- 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 = 0.4397 r_free = 0.4397 target = 0.133232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.094255 restraints weight = 21929.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.088330 restraints weight = 16342.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.089232 restraints weight = 12805.142| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.5447 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= 0.203 Angle : 0.568 9.819 9897 Z= 0.304 Chirality : 0.043 0.196 1137 Planarity : 0.004 0.041 1240 Dihedral : 4.616 21.744 972 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.96 % Allowed : 16.58 % Favored : 81.46 % 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: 0.59 (0.29), residues: 900 helix: 2.30 (0.28), residues: 312 sheet: -0.76 (0.34), residues: 229 loop : -0.45 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 182 HIS 0.004 0.001 HIS A 674 PHE 0.020 0.002 PHE A 505 TYR 0.011 0.001 TYR H 60 ARG 0.003 0.000 ARG A 668 Details of bonding type rmsd hydrogen bonds : bond 0.03850 ( 363) hydrogen bonds : angle 4.75596 ( 1044) SS BOND : bond 0.00385 ( 3) SS BOND : angle 0.60056 ( 6) covalent geometry : bond 0.00454 ( 7279) covalent geometry : angle 0.56767 ( 9891) ********************** 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 60 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.2107 (tpt) cc_final: 0.1537 (mtt) REVERT: A 53 MET cc_start: 0.3166 (ttp) cc_final: 0.2757 (ptt) REVERT: A 64 PHE cc_start: 0.8063 (t80) cc_final: 0.7596 (t80) REVERT: A 65 MET cc_start: 0.7064 (mtp) cc_final: 0.6455 (tpp) REVERT: A 495 THR cc_start: 0.8970 (OUTLIER) cc_final: 0.8669 (p) outliers start: 15 outliers final: 14 residues processed: 56 average time/residue: 0.1749 time to fit residues: 14.5795 Evaluate side-chains 56 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 769 PHE Chi-restraints excluded: chain A residue 773 ILE 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 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 46 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 10 optimal weight: 30.0000 chunk 83 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 88 optimal weight: 0.9990 chunk 61 optimal weight: 0.0970 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4418 r_free = 0.4418 target = 0.134865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.095427 restraints weight = 21441.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.091405 restraints weight = 14621.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.092544 restraints weight = 11127.823| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.5480 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= 0.120 Angle : 0.541 9.071 9897 Z= 0.289 Chirality : 0.043 0.266 1137 Planarity : 0.004 0.036 1240 Dihedral : 4.397 22.000 972 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.09 % Allowed : 16.84 % Favored : 81.07 % 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: 0.75 (0.29), residues: 900 helix: 2.31 (0.28), residues: 317 sheet: -0.58 (0.34), residues: 224 loop : -0.36 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 851 HIS 0.004 0.001 HIS A 674 PHE 0.027 0.002 PHE A 884 TYR 0.009 0.001 TYR A 46 ARG 0.003 0.000 ARG A 410 Details of bonding type rmsd hydrogen bonds : bond 0.03693 ( 363) hydrogen bonds : angle 4.65541 ( 1044) SS BOND : bond 0.00204 ( 3) SS BOND : angle 0.42110 ( 6) covalent geometry : bond 0.00259 ( 7279) covalent geometry : angle 0.54089 ( 9891) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3091.47 seconds wall clock time: 55 minutes 26.85 seconds (3326.85 seconds total)