Starting phenix.real_space_refine on Tue Aug 4 17:44:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ygf_72922/08_2026/9ygf_72922.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ygf_72922/08_2026/9ygf_72922.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ygf_72922/08_2026/9ygf_72922.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ygf_72922/08_2026/9ygf_72922.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ygf_72922/08_2026/9ygf_72922.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ygf_72922/08_2026/9ygf_72922.map" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.021 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: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 3480 2.51 5 N 942 2.21 5 O 1055 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5501 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 938 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "L" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 829 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "M" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 938 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "N" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 827 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "O" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 938 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "P" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 829 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "G" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 202 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 7, 'TRANS': 20} Time building chain proxies: 1.00, per 1000 atoms: 0.18 Number of scatterers: 5501 At special positions: 0 Unit cell: (63.19, 98.79, 113.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 1055 8.00 N 942 7.00 C 3480 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.25 Conformation dependent library (CDL) restraints added in 119.8 milliseconds 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1266 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 17 sheets defined 3.5% alpha, 37.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.875A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.758A pdb=" N VAL L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.648A pdb=" N THR M 87 " --> pdb=" O ALA M 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'P' and resid 79 through 83 removed outlier: 3.717A pdb=" N VAL P 83 " --> pdb=" O PRO P 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.827A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 45 through 51 removed outlier: 6.732A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 96 through 98 removed outlier: 3.630A pdb=" N PHE H 96 " --> pdb=" O PHE H 100C" (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.801A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.291A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.677A pdb=" N SER M 21 " --> pdb=" O SER M 7 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N THR M 77 " --> pdb=" O ASP M 72 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP M 72 " --> pdb=" O THR M 77 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR M 68 " --> pdb=" O GLN M 81 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 10 through 11 removed outlier: 3.618A pdb=" N THR M 110 " --> pdb=" O GLY M 10 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA M 88 " --> pdb=" O VAL M 109 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N MET M 34 " --> pdb=" O VAL M 50 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 10 through 11 removed outlier: 3.618A pdb=" N THR M 110 " --> pdb=" O GLY M 10 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA M 88 " --> pdb=" O VAL M 109 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 4 through 6 removed outlier: 3.744A pdb=" N THR N 5 " --> pdb=" O ARG N 24 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE N 21 " --> pdb=" O LEU N 73 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU N 73 " --> pdb=" O ILE N 21 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N CYS N 23 " --> pdb=" O PHE N 71 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE N 71 " --> pdb=" O CYS N 23 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 45 through 48 removed outlier: 6.565A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU N 90 " --> pdb=" O THR N 97 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR N 97 " --> pdb=" O GLU N 90 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 45 through 48 removed outlier: 6.565A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'O' and resid 3 through 7 removed outlier: 3.558A pdb=" N VAL O 5 " --> pdb=" O GLU O 23 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL O 78 " --> pdb=" O CYS O 22 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR O 77 " --> pdb=" O ASP O 72 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP O 72 " --> pdb=" O THR O 77 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER O 70 " --> pdb=" O PHE O 79 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'O' and resid 11 through 12 removed outlier: 6.734A pdb=" N MET O 34 " --> pdb=" O VAL O 50 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N VAL O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'O' and resid 11 through 12 removed outlier: 3.770A pdb=" N ARG O 94 " --> pdb=" O TYR O 102 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYR O 102 " --> pdb=" O ARG O 94 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE O 96 " --> pdb=" O PHE O 100C" (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE O 100C" --> pdb=" O PHE O 96 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'P' and resid 4 through 6 Processing sheet with id=AB7, first strand: chain 'P' and resid 10 through 13 removed outlier: 6.726A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'P' and resid 10 through 13 removed outlier: 3.668A pdb=" N THR P 97 " --> pdb=" O GLU P 90 " (cutoff:3.500A) 175 hydrogen bonds defined for protein. 402 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: 0.53 Time building geometry restraints manager: 0.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1576 1.33 - 1.45: 1098 1.45 - 1.57: 2932 1.57 - 1.70: 0 1.70 - 1.82: 36 Bond restraints: 5642 Sorted by residual: bond pdb=" C PRO L 80 " pdb=" O PRO L 80 " ideal model delta sigma weight residual 1.237 1.211 0.026 1.28e-02 6.10e+03 4.20e+00 bond pdb=" C GLN L 79 " pdb=" N PRO L 80 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.25e-02 6.40e+03 2.93e+00 bond pdb=" CB ASP M 53 " pdb=" CG ASP M 53 " ideal model delta sigma weight residual 1.516 1.549 -0.033 2.50e-02 1.60e+03 1.77e+00 bond pdb=" CA ASP M 53 " pdb=" CB ASP M 53 " ideal model delta sigma weight residual 1.532 1.550 -0.018 1.42e-02 4.96e+03 1.63e+00 bond pdb=" CA PHE M 52A" pdb=" CB PHE M 52A" ideal model delta sigma weight residual 1.527 1.548 -0.021 1.70e-02 3.46e+03 1.53e+00 ... (remaining 5637 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 7523 2.28 - 4.55: 109 4.55 - 6.83: 13 6.83 - 9.11: 3 9.11 - 11.38: 1 Bond angle restraints: 7649 Sorted by residual: angle pdb=" CB LYS P 42 " pdb=" CG LYS P 42 " pdb=" CD LYS P 42 " ideal model delta sigma weight residual 111.30 119.68 -8.38 2.30e+00 1.89e-01 1.33e+01 angle pdb=" CA GLN N 79 " pdb=" CB GLN N 79 " pdb=" CG GLN N 79 " ideal model delta sigma weight residual 114.10 121.03 -6.93 2.00e+00 2.50e-01 1.20e+01 angle pdb=" C PHE M 52A" pdb=" N ASP M 53 " pdb=" CA ASP M 53 " ideal model delta sigma weight residual 123.93 129.10 -5.17 1.54e+00 4.22e-01 1.13e+01 angle pdb=" CA LEU N 54 " pdb=" CB LEU N 54 " pdb=" CG LEU N 54 " ideal model delta sigma weight residual 116.30 127.68 -11.38 3.50e+00 8.16e-02 1.06e+01 angle pdb=" N ALA M 49 " pdb=" CA ALA M 49 " pdb=" C ALA M 49 " ideal model delta sigma weight residual 108.79 113.76 -4.97 1.53e+00 4.27e-01 1.05e+01 ... (remaining 7644 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 2764 17.35 - 34.69: 397 34.69 - 52.04: 103 52.04 - 69.38: 17 69.38 - 86.73: 7 Dihedral angle restraints: 3288 sinusoidal: 1284 harmonic: 2004 Sorted by residual: dihedral pdb=" CB CYS M 22 " pdb=" SG CYS M 22 " pdb=" SG CYS M 92 " pdb=" CB CYS M 92 " ideal model delta sinusoidal sigma weight residual 93.00 30.70 62.30 1 1.00e+01 1.00e-02 5.14e+01 dihedral pdb=" CA SER P 67 " pdb=" C SER P 67 " pdb=" N GLU P 68 " pdb=" CA GLU P 68 " ideal model delta harmonic sigma weight residual 180.00 159.60 20.40 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual -86.00 -119.88 33.88 1 1.00e+01 1.00e-02 1.63e+01 ... (remaining 3285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 524 0.033 - 0.065: 166 0.065 - 0.097: 55 0.097 - 0.130: 56 0.130 - 0.162: 3 Chirality restraints: 804 Sorted by residual: chirality pdb=" CA PRO N 80 " pdb=" N PRO N 80 " pdb=" C PRO N 80 " pdb=" CB PRO N 80 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.58e-01 chirality pdb=" CA PHE M 52A" pdb=" N PHE M 52A" pdb=" C PHE M 52A" pdb=" CB PHE M 52A" both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA ILE L 48 " pdb=" N ILE L 48 " pdb=" C ILE L 48 " pdb=" CB ILE L 48 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.83e-01 ... (remaining 801 not shown) Planarity restraints: 987 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP G 127 " -0.034 5.00e-02 4.00e+02 5.22e-02 4.36e+00 pdb=" N PRO G 128 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO G 128 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO G 128 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN N 79 " -0.034 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO N 80 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO N 80 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO N 80 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR N 49 " -0.019 2.00e-02 2.50e+03 1.14e-02 2.62e+00 pdb=" CG TYR N 49 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR N 49 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR N 49 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR N 49 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR N 49 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR N 49 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR N 49 " -0.006 2.00e-02 2.50e+03 ... (remaining 984 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 90 2.64 - 3.21: 4571 3.21 - 3.77: 7831 3.77 - 4.34: 10853 4.34 - 4.90: 18475 Nonbonded interactions: 41820 Sorted by model distance: nonbonded pdb=" OD1 ASP L 82 " pdb=" OH TYR L 86 " model vdw 2.080 3.040 nonbonded pdb=" OD1 ASP H 98 " pdb=" N GLY H 99 " model vdw 2.192 3.120 nonbonded pdb=" O ASP L 82 " pdb=" OH TYR L 86 " model vdw 2.226 3.040 nonbonded pdb=" O TYR L 49 " pdb=" OH TYR L 91 " model vdw 2.228 3.040 nonbonded pdb=" OE2 GLU M 23 " pdb=" OG1 THR M 77 " model vdw 2.231 3.040 ... (remaining 41815 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 Found NCS groups: ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'O' } ncs_group { reference = (chain 'L' and (resid 1 through 59 or resid 61 through 107)) selection = (chain 'N' and (resid 1 through 59 or resid 61 through 107)) selection = (chain 'P' and (resid 1 through 59 or resid 61 through 107)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.800 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.950 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 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 : 0.003 0.035 5648 Z= 0.135 Angle : 0.658 11.383 7661 Z= 0.355 Chirality : 0.045 0.162 804 Planarity : 0.005 0.052 987 Dihedral : 17.125 86.725 2004 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.25 % Favored : 90.61 % Rotamer: Outliers : 0.17 % Allowed : 31.53 % Favored : 68.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.34), residues: 692 helix: None (None), residues: 0 sheet: -0.15 (0.33), residues: 281 loop : -1.00 (0.34), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG P 18 TYR 0.025 0.001 TYR N 49 PHE 0.024 0.001 PHE O 100C TRP 0.012 0.001 TRP O 36 HIS 0.002 0.001 HIS H 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 ( 5642) covalent geometry : angle 0.65814 / 0.35 ( 7649) SS BOND : bond 0.00342 / 0.17 ( 6) SS BOND : angle 0.69167 / 0.50 ( 12) hydrogen bonds : bond 0.25846 / 17.74 ( 152) hydrogen bonds : angle 9.86456 / 6.89 ( 402) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 0.151 Fit side-chains revert: symmetry clash REVERT: H 86 ASP cc_start: 0.8057 (m-30) cc_final: 0.7776 (m-30) REVERT: L 32 TRP cc_start: 0.8098 (m-10) cc_final: 0.6226 (m-10) REVERT: L 55 GLU cc_start: 0.6789 (tm-30) cc_final: 0.6530 (tm-30) REVERT: O 16 ARG cc_start: 0.8334 (mmm-85) cc_final: 0.8126 (ttm110) REVERT: O 77 THR cc_start: 0.7426 (p) cc_final: 0.7145 (p) REVERT: O 95 ASN cc_start: 0.7832 (t0) cc_final: 0.7489 (t0) REVERT: O 105 GLN cc_start: 0.6903 (pt0) cc_final: 0.6665 (pt0) REVERT: P 26 SER cc_start: 0.8239 (m) cc_final: 0.7860 (p) outliers start: 1 outliers final: 1 residues processed: 151 average time/residue: 0.0637 time to fit residues: 12.4983 Evaluate side-chains 118 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 56 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.0020 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 overall best weight: 0.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 35 HIS M 76 ASN N 27 GLN O 76 ASN ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 113 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.165382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.136829 restraints weight = 8048.589| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.52 r_work: 0.3567 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5648 Z= 0.170 Angle : 0.670 8.701 7661 Z= 0.357 Chirality : 0.049 0.182 804 Planarity : 0.005 0.058 987 Dihedral : 4.751 23.448 776 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.97 % Favored : 89.88 % Rotamer: Outliers : 6.07 % Allowed : 27.15 % Favored : 66.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.34), residues: 692 helix: None (None), residues: 0 sheet: 0.22 (0.33), residues: 264 loop : -1.04 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 83 TYR 0.033 0.002 TYR N 49 PHE 0.017 0.002 PHE M 96 TRP 0.007 0.001 TRP O 103 HIS 0.004 0.001 HIS M 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 ( 5642) covalent geometry : angle 0.66955 / 0.36 ( 7649) SS BOND : bond 0.00495 / 0.26 ( 6) SS BOND : angle 1.05187 / 0.77 ( 12) hydrogen bonds : bond 0.03956 / 2.66 ( 152) hydrogen bonds : angle 6.57711 / 4.46 ( 402) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 130 time to evaluate : 0.162 Fit side-chains revert: symmetry clash REVERT: H 13 GLN cc_start: 0.8477 (mm-40) cc_final: 0.8164 (mm-40) REVERT: H 43 LYS cc_start: 0.8061 (mmmt) cc_final: 0.7403 (mttt) REVERT: H 108 LEU cc_start: 0.7028 (OUTLIER) cc_final: 0.6810 (tt) REVERT: L 4 MET cc_start: 0.8316 (tpp) cc_final: 0.8111 (tpp) REVERT: L 32 TRP cc_start: 0.8484 (m-10) cc_final: 0.6795 (m-10) REVERT: L 100 GLN cc_start: 0.8705 (pt0) cc_final: 0.7889 (mm110) REVERT: M 23 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.6265 (tm-30) REVERT: O 16 ARG cc_start: 0.8445 (mmm-85) cc_final: 0.8102 (ttm110) REVERT: O 95 ASN cc_start: 0.8110 (t0) cc_final: 0.7714 (t0) REVERT: O 105 GLN cc_start: 0.7209 (pt0) cc_final: 0.6775 (pt0) REVERT: P 4 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8146 (mmm) REVERT: P 26 SER cc_start: 0.8257 (m) cc_final: 0.7913 (p) REVERT: P 27 GLN cc_start: 0.7122 (tp-100) cc_final: 0.6887 (tt0) REVERT: P 61 ARG cc_start: 0.7346 (OUTLIER) cc_final: 0.6995 (ptt180) outliers start: 36 outliers final: 18 residues processed: 155 average time/residue: 0.0668 time to fit residues: 13.3507 Evaluate side-chains 138 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain M residue 23 GLU Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 62 SER Chi-restraints excluded: chain O residue 102 TYR Chi-restraints excluded: chain P residue 4 MET Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 61 ARG Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 37 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 31 optimal weight: 0.0470 chunk 10 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 76 ASN M 93 HIS N 27 GLN O 76 ASN ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.164304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.136305 restraints weight = 7952.839| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.50 r_work: 0.3570 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5648 Z= 0.140 Angle : 0.620 7.314 7661 Z= 0.328 Chirality : 0.048 0.174 804 Planarity : 0.005 0.053 987 Dihedral : 4.564 22.273 774 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 5.73 % Allowed : 29.34 % Favored : 64.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.34), residues: 692 helix: None (None), residues: 0 sheet: 0.31 (0.33), residues: 263 loop : -1.03 (0.32), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 83 TYR 0.031 0.002 TYR N 49 PHE 0.015 0.001 PHE M 96 TRP 0.008 0.001 TRP O 103 HIS 0.003 0.001 HIS P 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 5642) covalent geometry : angle 0.61777 / 0.33 ( 7649) SS BOND : bond 0.00425 / 0.23 ( 6) SS BOND : angle 1.32393 / 1.03 ( 12) hydrogen bonds : bond 0.03426 / 2.28 ( 152) hydrogen bonds : angle 6.01245 / 4.05 ( 402) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 0.163 Fit side-chains revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7969 (mmmt) cc_final: 0.7402 (mttt) REVERT: L 4 MET cc_start: 0.8289 (tpp) cc_final: 0.8086 (tpp) REVERT: L 27 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.6956 (mt0) REVERT: L 55 GLU cc_start: 0.6259 (tm-30) cc_final: 0.5940 (tm-30) REVERT: L 100 GLN cc_start: 0.8673 (pt0) cc_final: 0.7902 (mm110) REVERT: M 23 GLU cc_start: 0.7003 (OUTLIER) cc_final: 0.6341 (tm-30) REVERT: M 79 PHE cc_start: 0.7720 (m-80) cc_final: 0.6843 (m-80) REVERT: M 83 ARG cc_start: 0.7823 (mpt180) cc_final: 0.7563 (mpt180) REVERT: N 32 TRP cc_start: 0.8346 (m100) cc_final: 0.8093 (m100) REVERT: O 16 ARG cc_start: 0.8453 (mmm-85) cc_final: 0.8095 (ttm110) REVERT: O 95 ASN cc_start: 0.7990 (t0) cc_final: 0.7599 (t0) REVERT: P 4 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8143 (mmm) REVERT: P 26 SER cc_start: 0.8239 (m) cc_final: 0.7924 (p) REVERT: P 27 GLN cc_start: 0.7194 (tp-100) cc_final: 0.6850 (tt0) REVERT: P 61 ARG cc_start: 0.7177 (OUTLIER) cc_final: 0.6830 (ptt180) outliers start: 34 outliers final: 21 residues processed: 146 average time/residue: 0.0644 time to fit residues: 12.2753 Evaluate side-chains 138 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain M residue 23 GLU Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 62 SER Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 101 ASP Chi-restraints excluded: chain O residue 102 TYR Chi-restraints excluded: chain P residue 4 MET Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 61 ARG Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 72 THR Chi-restraints excluded: chain P residue 104 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 49 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.2980 chunk 47 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 76 ASN ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 GLN O 76 ASN ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.163494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.134701 restraints weight = 8123.302| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.54 r_work: 0.3544 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5648 Z= 0.147 Angle : 0.617 7.421 7661 Z= 0.327 Chirality : 0.048 0.178 804 Planarity : 0.005 0.048 987 Dihedral : 4.556 22.504 774 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer: Outliers : 7.93 % Allowed : 26.64 % Favored : 65.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.34), residues: 692 helix: None (None), residues: 0 sheet: 0.26 (0.33), residues: 265 loop : -1.07 (0.32), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 31 TYR 0.031 0.002 TYR N 49 PHE 0.012 0.001 PHE M 96 TRP 0.008 0.001 TRP O 103 HIS 0.003 0.001 HIS H 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 5642) covalent geometry : angle 0.61680 / 0.33 ( 7649) SS BOND : bond 0.00372 / 0.20 ( 6) SS BOND : angle 0.68569 / 0.45 ( 12) hydrogen bonds : bond 0.03111 / 2.08 ( 152) hydrogen bonds : angle 5.85144 / 3.94 ( 402) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 121 time to evaluate : 0.115 Fit side-chains revert: symmetry clash REVERT: H 13 GLN cc_start: 0.8387 (mm-40) cc_final: 0.8104 (mm-40) REVERT: H 43 LYS cc_start: 0.7877 (mmmt) cc_final: 0.7286 (mttt) REVERT: L 4 MET cc_start: 0.8341 (tpp) cc_final: 0.8132 (tpp) REVERT: L 27 GLN cc_start: 0.7624 (OUTLIER) cc_final: 0.6891 (mt0) REVERT: L 55 GLU cc_start: 0.6238 (tm-30) cc_final: 0.6033 (tm-30) REVERT: L 94 TYR cc_start: 0.8468 (OUTLIER) cc_final: 0.7169 (m-80) REVERT: L 100 GLN cc_start: 0.8695 (pt0) cc_final: 0.7912 (mm110) REVERT: M 23 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6415 (tm-30) REVERT: N 32 TRP cc_start: 0.8413 (m100) cc_final: 0.8212 (m100) REVERT: O 16 ARG cc_start: 0.8461 (mmm-85) cc_final: 0.8099 (ttm110) REVERT: P 4 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8133 (mmm) REVERT: P 26 SER cc_start: 0.8202 (m) cc_final: 0.7828 (p) REVERT: P 38 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.7728 (tt0) outliers start: 47 outliers final: 32 residues processed: 153 average time/residue: 0.0640 time to fit residues: 12.5715 Evaluate side-chains 150 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 113 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain M residue 23 GLU Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 23 CYS Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 69 ILE Chi-restraints excluded: chain O residue 82 LEU Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 101 ASP Chi-restraints excluded: chain O residue 102 TYR Chi-restraints excluded: chain O residue 105 GLN Chi-restraints excluded: chain P residue 4 MET Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 38 GLN Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 72 THR Chi-restraints excluded: chain P residue 104 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 58 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 76 ASN ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 GLN O 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.158980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.129428 restraints weight = 8301.285| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.60 r_work: 0.3470 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5648 Z= 0.229 Angle : 0.710 9.324 7661 Z= 0.376 Chirality : 0.050 0.178 804 Planarity : 0.005 0.045 987 Dihedral : 5.051 23.109 774 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.84 % Favored : 89.02 % Rotamer: Outliers : 9.44 % Allowed : 24.28 % Favored : 66.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.33), residues: 692 helix: None (None), residues: 0 sheet: 0.03 (0.33), residues: 266 loop : -1.19 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG N 31 TYR 0.043 0.002 TYR N 49 PHE 0.021 0.002 PHE O 67 TRP 0.011 0.002 TRP O 103 HIS 0.005 0.001 HIS O 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.23 ( 5642) covalent geometry : angle 0.71024 / 0.38 ( 7649) SS BOND : bond 0.00439 / 0.22 ( 6) SS BOND : angle 0.72665 / 0.45 ( 12) hydrogen bonds : bond 0.03387 / 2.28 ( 152) hydrogen bonds : angle 6.16913 / 4.18 ( 402) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 143 time to evaluate : 0.124 Fit side-chains revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7844 (mmmt) cc_final: 0.7286 (mttt) REVERT: H 75 LYS cc_start: 0.6264 (tmtt) cc_final: 0.6048 (tmtt) REVERT: L 4 MET cc_start: 0.8436 (tpp) cc_final: 0.8217 (tpp) REVERT: L 27 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.6979 (mt0) REVERT: L 94 TYR cc_start: 0.8622 (OUTLIER) cc_final: 0.7277 (m-80) REVERT: M 13 GLN cc_start: 0.8121 (tt0) cc_final: 0.7789 (tt0) REVERT: M 23 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6854 (tm-30) REVERT: M 77 THR cc_start: 0.8109 (OUTLIER) cc_final: 0.7425 (m) REVERT: N 32 TRP cc_start: 0.8497 (m100) cc_final: 0.8264 (m100) REVERT: O 16 ARG cc_start: 0.8542 (mmm-85) cc_final: 0.8114 (ttm110) REVERT: O 70 SER cc_start: 0.7735 (t) cc_final: 0.7377 (p) REVERT: O 71 ARG cc_start: 0.7359 (tmm-80) cc_final: 0.6819 (tmm-80) REVERT: P 4 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8163 (mmm) REVERT: P 26 SER cc_start: 0.8177 (m) cc_final: 0.7960 (p) REVERT: P 27 GLN cc_start: 0.7219 (tp-100) cc_final: 0.6904 (tt0) REVERT: P 38 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.7734 (tt0) REVERT: P 39 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7323 (mmtp) outliers start: 56 outliers final: 42 residues processed: 179 average time/residue: 0.0438 time to fit residues: 10.3907 Evaluate side-chains 183 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 134 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 23 GLU Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 76 ASN Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 23 CYS Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 62 SER Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 69 ILE Chi-restraints excluded: chain O residue 82 LEU Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 101 ASP Chi-restraints excluded: chain O residue 102 TYR Chi-restraints excluded: chain O residue 105 GLN Chi-restraints excluded: chain P residue 4 MET Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 38 GLN Chi-restraints excluded: chain P residue 39 LYS Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 72 THR Chi-restraints excluded: chain P residue 90 GLU Chi-restraints excluded: chain P residue 104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 20 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 48 optimal weight: 0.0970 chunk 27 optimal weight: 0.0070 chunk 6 optimal weight: 0.3980 chunk 54 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 GLN O 76 ASN P 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.164119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.135007 restraints weight = 8105.525| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.58 r_work: 0.3537 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5648 Z= 0.125 Angle : 0.624 8.510 7661 Z= 0.328 Chirality : 0.048 0.180 804 Planarity : 0.004 0.046 987 Dihedral : 4.618 21.889 774 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 6.24 % Allowed : 29.68 % Favored : 64.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.34), residues: 692 helix: None (None), residues: 0 sheet: -0.01 (0.33), residues: 267 loop : -1.13 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 38 TYR 0.014 0.001 TYR P 91 PHE 0.009 0.001 PHE M 96 TRP 0.012 0.001 TRP P 32 HIS 0.003 0.001 HIS P 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 ( 5642) covalent geometry : angle 0.62450 / 0.33 ( 7649) SS BOND : bond 0.00309 / 0.17 ( 6) SS BOND : angle 0.54553 / 0.33 ( 12) hydrogen bonds : bond 0.02896 / 1.98 ( 152) hydrogen bonds : angle 5.71771 / 3.86 ( 402) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 135 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7923 (mmmt) cc_final: 0.7419 (mttt) REVERT: L 94 TYR cc_start: 0.8491 (OUTLIER) cc_final: 0.7168 (m-80) REVERT: M 13 GLN cc_start: 0.8133 (tt0) cc_final: 0.7843 (tt0) REVERT: M 23 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6678 (tm-30) REVERT: M 77 THR cc_start: 0.8113 (m) cc_final: 0.7438 (m) REVERT: M 83 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.7438 (mpt180) REVERT: O 16 ARG cc_start: 0.8429 (mmm-85) cc_final: 0.8059 (ttm110) REVERT: O 70 SER cc_start: 0.7664 (t) cc_final: 0.7332 (p) REVERT: P 26 SER cc_start: 0.8157 (m) cc_final: 0.7897 (p) REVERT: P 27 GLN cc_start: 0.7135 (tp-100) cc_final: 0.6869 (tt0) REVERT: P 38 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.7695 (tt0) REVERT: P 39 LYS cc_start: 0.7609 (OUTLIER) cc_final: 0.7311 (mmtp) REVERT: P 68 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8218 (pt0) outliers start: 37 outliers final: 28 residues processed: 157 average time/residue: 0.0552 time to fit residues: 11.1630 Evaluate side-chains 166 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 132 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 23 GLU Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 73 ASN Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 83 ARG Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 62 SER Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 101 ASP Chi-restraints excluded: chain O residue 102 TYR Chi-restraints excluded: chain P residue 38 GLN Chi-restraints excluded: chain P residue 39 LYS Chi-restraints excluded: chain P residue 68 GLU Chi-restraints excluded: chain P residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 57 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 47 optimal weight: 0.0170 chunk 18 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 overall best weight: 0.8620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.161768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.132857 restraints weight = 8176.608| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.59 r_work: 0.3519 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5648 Z= 0.154 Angle : 0.648 8.050 7661 Z= 0.343 Chirality : 0.049 0.179 804 Planarity : 0.005 0.044 987 Dihedral : 4.696 22.255 774 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.83 % Favored : 90.03 % Rotamer: Outliers : 7.76 % Allowed : 28.16 % Favored : 64.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.34), residues: 692 helix: None (None), residues: 0 sheet: 0.16 (0.34), residues: 255 loop : -1.26 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 38 TYR 0.017 0.002 TYR N 49 PHE 0.011 0.001 PHE M 96 TRP 0.009 0.001 TRP O 103 HIS 0.003 0.001 HIS H 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 ( 5642) covalent geometry : angle 0.64762 / 0.34 ( 7649) SS BOND : bond 0.00381 / 0.19 ( 6) SS BOND : angle 0.63248 / 0.36 ( 12) hydrogen bonds : bond 0.02918 / 1.98 ( 152) hydrogen bonds : angle 5.77477 / 3.90 ( 402) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 134 time to evaluate : 0.117 Fit side-chains revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7895 (mmmt) cc_final: 0.7376 (mttt) REVERT: L 27 GLN cc_start: 0.7570 (OUTLIER) cc_final: 0.6836 (mt0) REVERT: L 81 ASP cc_start: 0.8089 (t0) cc_final: 0.7886 (t0) REVERT: L 94 TYR cc_start: 0.8536 (OUTLIER) cc_final: 0.7186 (m-80) REVERT: L 100 GLN cc_start: 0.8556 (pt0) cc_final: 0.7721 (mm-40) REVERT: M 13 GLN cc_start: 0.8168 (tt0) cc_final: 0.7925 (tt0) REVERT: M 23 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.6831 (tm-30) REVERT: M 83 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7329 (mpt180) REVERT: O 13 GLN cc_start: 0.7263 (tp-100) cc_final: 0.6787 (mp10) REVERT: O 16 ARG cc_start: 0.8378 (mmm-85) cc_final: 0.8017 (ttm110) REVERT: O 70 SER cc_start: 0.7793 (t) cc_final: 0.7546 (p) REVERT: P 26 SER cc_start: 0.8179 (m) cc_final: 0.7921 (p) REVERT: P 27 GLN cc_start: 0.7191 (tp-100) cc_final: 0.6913 (tt0) REVERT: P 38 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.7699 (tt0) REVERT: P 39 LYS cc_start: 0.7623 (OUTLIER) cc_final: 0.7366 (mmtp) outliers start: 46 outliers final: 37 residues processed: 163 average time/residue: 0.0589 time to fit residues: 12.4072 Evaluate side-chains 174 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 131 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 23 GLU Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 83 ARG Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 69 ILE Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 82 SER Chi-restraints excluded: chain O residue 82 LEU Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 101 ASP Chi-restraints excluded: chain O residue 102 TYR Chi-restraints excluded: chain O residue 105 GLN Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 38 GLN Chi-restraints excluded: chain P residue 39 LYS Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain P residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 33 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 42 optimal weight: 7.9990 chunk 40 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 63 optimal weight: 0.0040 chunk 46 optimal weight: 0.8980 chunk 57 optimal weight: 0.0070 overall best weight: 0.3810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 GLN O 76 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.165639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.136977 restraints weight = 8065.268| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.58 r_work: 0.3574 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5648 Z= 0.117 Angle : 0.617 8.290 7661 Z= 0.324 Chirality : 0.047 0.181 804 Planarity : 0.004 0.044 987 Dihedral : 4.418 22.337 774 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 6.91 % Allowed : 29.01 % Favored : 64.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.33), residues: 692 helix: None (None), residues: 0 sheet: 0.13 (0.35), residues: 249 loop : -1.20 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG N 31 TYR 0.013 0.001 TYR N 49 PHE 0.009 0.001 PHE O 100C TRP 0.013 0.001 TRP P 32 HIS 0.002 0.001 HIS P 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 5642) covalent geometry : angle 0.61726 / 0.32 ( 7649) SS BOND : bond 0.00305 / 0.17 ( 6) SS BOND : angle 0.47252 / 0.27 ( 12) hydrogen bonds : bond 0.02717 / 1.85 ( 152) hydrogen bonds : angle 5.49568 / 3.72 ( 402) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 132 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7914 (mmmt) cc_final: 0.7390 (mttt) REVERT: L 5 THR cc_start: 0.9091 (m) cc_final: 0.8845 (p) REVERT: M 5 VAL cc_start: 0.7160 (t) cc_final: 0.6399 (t) REVERT: M 13 GLN cc_start: 0.8177 (tt0) cc_final: 0.7954 (tt0) REVERT: M 23 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6678 (tm-30) REVERT: M 82 MET cc_start: 0.6988 (mmm) cc_final: 0.6479 (mmm) REVERT: M 83 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.7240 (mpt180) REVERT: O 16 ARG cc_start: 0.8296 (mmm-85) cc_final: 0.8007 (ttm110) REVERT: O 67 PHE cc_start: 0.6577 (m-80) cc_final: 0.6153 (m-80) REVERT: O 80 MET cc_start: 0.7509 (mtp) cc_final: 0.7231 (mtp) REVERT: O 95 ASN cc_start: 0.8039 (t0) cc_final: 0.7751 (t0) REVERT: P 26 SER cc_start: 0.8198 (m) cc_final: 0.7921 (p) REVERT: P 27 GLN cc_start: 0.7089 (tp-100) cc_final: 0.6845 (tt0) outliers start: 41 outliers final: 34 residues processed: 159 average time/residue: 0.0557 time to fit residues: 11.5084 Evaluate side-chains 158 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 122 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 23 GLU Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 83 ARG Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 62 SER Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 69 ILE Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 82 LEU Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 101 ASP Chi-restraints excluded: chain O residue 102 TYR Chi-restraints excluded: chain O residue 105 GLN Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain P residue 72 THR Chi-restraints excluded: chain P residue 104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 13 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 11 optimal weight: 0.0060 chunk 40 optimal weight: 0.7980 chunk 54 optimal weight: 0.0970 chunk 27 optimal weight: 4.9990 chunk 52 optimal weight: 0.0470 overall best weight: 0.3692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 6 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 35 HIS ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 GLN O 76 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.166922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.138213 restraints weight = 8134.137| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.60 r_work: 0.3581 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5648 Z= 0.118 Angle : 0.620 7.790 7661 Z= 0.326 Chirality : 0.048 0.226 804 Planarity : 0.005 0.041 987 Dihedral : 4.336 22.453 774 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 5.90 % Allowed : 30.19 % Favored : 63.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.34), residues: 692 helix: None (None), residues: 0 sheet: 0.18 (0.35), residues: 249 loop : -1.16 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 38 TYR 0.013 0.001 TYR P 91 PHE 0.012 0.001 PHE O 100C TRP 0.009 0.001 TRP P 32 HIS 0.004 0.001 HIS M 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 5642) covalent geometry : angle 0.62001 / 0.33 ( 7649) SS BOND : bond 0.00324 / 0.17 ( 6) SS BOND : angle 0.53176 / 0.29 ( 12) hydrogen bonds : bond 0.02613 / 1.76 ( 152) hydrogen bonds : angle 5.42282 / 3.68 ( 402) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 126 time to evaluate : 0.130 Fit side-chains revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7901 (mmmt) cc_final: 0.7384 (mttt) REVERT: L 5 THR cc_start: 0.9049 (m) cc_final: 0.8835 (p) REVERT: M 5 VAL cc_start: 0.7198 (t) cc_final: 0.6441 (t) REVERT: M 13 GLN cc_start: 0.8171 (tt0) cc_final: 0.7948 (tt0) REVERT: M 23 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6656 (tm-30) REVERT: M 83 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.7209 (mpt180) REVERT: O 16 ARG cc_start: 0.8238 (mmm-85) cc_final: 0.7966 (ttm110) REVERT: O 80 MET cc_start: 0.7401 (mtp) cc_final: 0.7126 (mtp) REVERT: O 95 ASN cc_start: 0.8044 (t0) cc_final: 0.7759 (t0) REVERT: P 26 SER cc_start: 0.8176 (m) cc_final: 0.7884 (p) outliers start: 35 outliers final: 33 residues processed: 147 average time/residue: 0.0582 time to fit residues: 11.1552 Evaluate side-chains 157 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 122 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 23 GLU Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 83 ARG Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 62 SER Chi-restraints excluded: chain O residue 69 ILE Chi-restraints excluded: chain O residue 76 ASN Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 82 LEU Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 101 ASP Chi-restraints excluded: chain O residue 102 TYR Chi-restraints excluded: chain O residue 105 GLN Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain P residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 25 optimal weight: 2.9990 chunk 33 optimal weight: 0.2980 chunk 64 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 0.0970 chunk 1 optimal weight: 0.2980 chunk 35 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 56 ASN ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 ASN ** 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 = 0.4007 r_free = 0.4007 target = 0.163563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.134239 restraints weight = 8261.906| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.65 r_work: 0.3528 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5648 Z= 0.166 Angle : 0.671 7.790 7661 Z= 0.355 Chirality : 0.049 0.181 804 Planarity : 0.005 0.043 987 Dihedral : 4.552 23.819 774 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer: Outliers : 5.90 % Allowed : 30.52 % Favored : 63.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.33), residues: 692 helix: None (None), residues: 0 sheet: 0.12 (0.35), residues: 249 loop : -1.25 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 31 TYR 0.018 0.002 TYR N 49 PHE 0.012 0.001 PHE O 100C TRP 0.009 0.001 TRP O 103 HIS 0.003 0.001 HIS H 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 ( 5642) covalent geometry : angle 0.67064 / 0.36 ( 7649) SS BOND : bond 0.00382 / 0.19 ( 6) SS BOND : angle 0.62573 / 0.35 ( 12) hydrogen bonds : bond 0.02802 / 1.90 ( 152) hydrogen bonds : angle 5.63156 / 3.81 ( 402) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 118 time to evaluate : 0.199 Fit side-chains REVERT: H 43 LYS cc_start: 0.7902 (mmmt) cc_final: 0.7348 (mttt) REVERT: L 55 GLU cc_start: 0.6045 (tm-30) cc_final: 0.5774 (tm-30) REVERT: L 100 GLN cc_start: 0.8541 (pt0) cc_final: 0.7712 (mm-40) REVERT: M 23 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.6894 (tm-30) REVERT: M 83 ARG cc_start: 0.7632 (mpt180) cc_final: 0.7240 (mpt180) REVERT: O 16 ARG cc_start: 0.8256 (mmm-85) cc_final: 0.7971 (ttm110) REVERT: O 80 MET cc_start: 0.7499 (mtp) cc_final: 0.7260 (mtp) REVERT: P 26 SER cc_start: 0.8243 (m) cc_final: 0.7919 (p) outliers start: 35 outliers final: 32 residues processed: 141 average time/residue: 0.0650 time to fit residues: 11.9661 Evaluate side-chains 149 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 116 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 23 GLU Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 69 ILE Chi-restraints excluded: chain O residue 82 LEU Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 101 ASP Chi-restraints excluded: chain O residue 102 TYR Chi-restraints excluded: chain O residue 105 GLN Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain P residue 72 THR Chi-restraints excluded: chain P residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 36 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 chunk 56 optimal weight: 2.9990 chunk 32 optimal weight: 0.0040 chunk 58 optimal weight: 0.6980 chunk 22 optimal weight: 0.0050 chunk 41 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 overall best weight: 0.4606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 73 ASN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.166443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.137566 restraints weight = 8138.273| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.62 r_work: 0.3574 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5648 Z= 0.126 Angle : 0.639 7.587 7661 Z= 0.336 Chirality : 0.048 0.179 804 Planarity : 0.005 0.041 987 Dihedral : 4.392 22.655 774 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 5.73 % Allowed : 30.35 % Favored : 63.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.33), residues: 692 helix: None (None), residues: 0 sheet: 0.14 (0.34), residues: 249 loop : -1.24 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 31 TYR 0.014 0.001 TYR N 49 PHE 0.012 0.001 PHE O 100C TRP 0.010 0.001 TRP P 32 HIS 0.003 0.001 HIS H 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 5642) covalent geometry : angle 0.63915 / 0.34 ( 7649) SS BOND : bond 0.00316 / 0.17 ( 6) SS BOND : angle 0.52344 / 0.30 ( 12) hydrogen bonds : bond 0.02656 / 1.80 ( 152) hydrogen bonds : angle 5.48108 / 3.72 ( 402) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1097.82 seconds wall clock time: 19 minutes 25.52 seconds (1165.52 seconds total)