Starting phenix.real_space_refine on Tue Feb 3 18:12:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mrg_48556/02_2026/9mrg_48556.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mrg_48556/02_2026/9mrg_48556.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mrg_48556/02_2026/9mrg_48556.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mrg_48556/02_2026/9mrg_48556.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mrg_48556/02_2026/9mrg_48556.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mrg_48556/02_2026/9mrg_48556.map" } resolution = 3.69 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= 0.004 sd= 0.047 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 20 5.16 5 C 4026 2.51 5 N 879 2.21 5 O 1028 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5953 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1491 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 5, 'TRANS': 177} Chain breaks: 1 Chain: "B" Number of atoms: 1454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1454 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 4, 'TRANS': 173} Chain breaks: 2 Chain: "C" Number of atoms: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1491 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 5, 'TRANS': 177} Chain breaks: 1 Chain: "D" Number of atoms: 1448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1448 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 5, 'TRANS': 171} Chain breaks: 2 Chain: "B" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'AV0': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.48, per 1000 atoms: 0.25 Number of scatterers: 5953 At special positions: 0 Unit cell: (84.056, 87.248, 101.08, 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 20 16.00 O 1028 8.00 N 879 7.00 C 4026 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.45 Conformation dependent library (CDL) restraints added in 336.7 milliseconds 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1382 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 5 sheets defined 49.8% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 4 through 16 removed outlier: 3.575A pdb=" N LYS A 8 " --> pdb=" O ASN A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 27 Processing helix chain 'A' and resid 45 through 50 Processing helix chain 'A' and resid 50 through 71 removed outlier: 3.819A pdb=" N ILE A 54 " --> pdb=" O ASN A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 102 removed outlier: 3.741A pdb=" N ALA A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR A 100 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 133 removed outlier: 3.931A pdb=" N ASN A 116 " --> pdb=" O ASP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 146 removed outlier: 3.887A pdb=" N PHE A 145 " --> pdb=" O THR A 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 17 removed outlier: 3.701A pdb=" N TYR B 12 " --> pdb=" O LYS B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 27 Processing helix chain 'B' and resid 44 through 50 removed outlier: 3.505A pdb=" N ASN B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 73 Processing helix chain 'B' and resid 93 through 101 removed outlier: 4.155A pdb=" N PHE B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR B 101 " --> pdb=" O PHE B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 108 Processing helix chain 'B' and resid 114 through 130 removed outlier: 3.943A pdb=" N ALA B 118 " --> pdb=" O GLN B 114 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 15 removed outlier: 3.707A pdb=" N TYR C 12 " --> pdb=" O LYS C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 28 removed outlier: 3.530A pdb=" N PHE C 20 " --> pdb=" O LEU C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 50 removed outlier: 3.525A pdb=" N ASN C 50 " --> pdb=" O LEU C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 73 Processing helix chain 'C' and resid 95 through 101 removed outlier: 3.604A pdb=" N THR C 100 " --> pdb=" O THR C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 133 removed outlier: 3.544A pdb=" N ASN C 116 " --> pdb=" O ASP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 146 removed outlier: 3.878A pdb=" N PHE C 145 " --> pdb=" O THR C 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 16 Processing helix chain 'D' and resid 16 through 28 removed outlier: 3.523A pdb=" N PHE D 20 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL D 21 " --> pdb=" O ALA D 17 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE D 22 " --> pdb=" O MET D 18 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA D 28 " --> pdb=" O ILE D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 50 removed outlier: 3.823A pdb=" N VAL D 47 " --> pdb=" O LEU D 43 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASN D 50 " --> pdb=" O LEU D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 71 Processing helix chain 'D' and resid 94 through 101 Processing helix chain 'D' and resid 101 through 108 Processing helix chain 'D' and resid 112 through 132 removed outlier: 3.960A pdb=" N ASN D 116 " --> pdb=" O ASP D 112 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N PHE D 130 " --> pdb=" O ILE D 126 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS D 132 " --> pdb=" O ILE D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 144 Processing sheet with id=AA1, first strand: chain 'A' and resid 178 through 179 removed outlier: 3.688A pdb=" N VAL A 179 " --> pdb=" O VAL A 82 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL A 82 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS A 83 " --> pdb=" O LEU A 155 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 155 " --> pdb=" O LYS A 83 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ASN A 153 " --> pdb=" O THR A 85 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N CYS A 87 " --> pdb=" O ARG A 151 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ARG A 151 " --> pdb=" O CYS A 87 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER A 169 " --> pdb=" O LYS A 148 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE A 189 " --> pdb=" O ILE A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 82 through 83 removed outlier: 4.144A pdb=" N VAL B 82 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL B 179 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE B 189 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU B 165 " --> pdb=" O VAL B 152 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 84 through 89 removed outlier: 3.914A pdb=" N SER C 86 " --> pdb=" O ASN C 153 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ILE C 166 " --> pdb=" O PHE C 189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 83 through 84 removed outlier: 3.739A pdb=" N LYS D 83 " --> pdb=" O LEU D 155 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU D 155 " --> pdb=" O LYS D 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 88 through 89 removed outlier: 3.607A pdb=" N PHE D 189 " --> pdb=" O ILE D 166 " (cutoff:3.500A) 253 hydrogen bonds defined for protein. 726 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: 0.59 Time building geometry restraints manager: 0.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1641 1.34 - 1.46: 1555 1.46 - 1.58: 2863 1.58 - 1.70: 1 1.70 - 1.83: 32 Bond restraints: 6092 Sorted by residual: bond pdb=" CA ASN D 72 " pdb=" CB ASN D 72 " ideal model delta sigma weight residual 1.528 1.589 -0.061 1.49e-02 4.50e+03 1.68e+01 bond pdb=" CB PHE D 189 " pdb=" CG PHE D 189 " ideal model delta sigma weight residual 1.502 1.558 -0.056 2.30e-02 1.89e+03 5.90e+00 bond pdb=" CB MET B 106 " pdb=" CG MET B 106 " ideal model delta sigma weight residual 1.520 1.448 0.072 3.00e-02 1.11e+03 5.73e+00 bond pdb=" CB ASN C 68 " pdb=" CG ASN C 68 " ideal model delta sigma weight residual 1.516 1.564 -0.048 2.50e-02 1.60e+03 3.63e+00 bond pdb=" C ILE A 30 " pdb=" N PRO A 31 " ideal model delta sigma weight residual 1.341 1.371 -0.030 1.60e-02 3.91e+03 3.57e+00 ... (remaining 6087 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.00: 8133 4.00 - 7.99: 89 7.99 - 11.99: 18 11.99 - 15.98: 3 15.98 - 19.98: 1 Bond angle restraints: 8244 Sorted by residual: angle pdb=" CA LEU B 142 " pdb=" CB LEU B 142 " pdb=" CG LEU B 142 " ideal model delta sigma weight residual 116.30 136.28 -19.98 3.50e+00 8.16e-02 3.26e+01 angle pdb=" CB MET B 106 " pdb=" CG MET B 106 " pdb=" SD MET B 106 " ideal model delta sigma weight residual 112.70 97.82 14.88 3.00e+00 1.11e-01 2.46e+01 angle pdb=" C GLY D 158 " pdb=" N SER D 159 " pdb=" CA SER D 159 " ideal model delta sigma weight residual 121.54 130.44 -8.90 1.91e+00 2.74e-01 2.17e+01 angle pdb=" C GLU B 111 " pdb=" CA GLU B 111 " pdb=" CB GLU B 111 " ideal model delta sigma weight residual 115.79 110.25 5.54 1.19e+00 7.06e-01 2.17e+01 angle pdb=" CB ARG B 192 " pdb=" CG ARG B 192 " pdb=" CD ARG B 192 " ideal model delta sigma weight residual 111.30 120.92 -9.62 2.30e+00 1.89e-01 1.75e+01 ... (remaining 8239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.19: 3270 27.19 - 54.38: 327 54.38 - 81.57: 27 81.57 - 108.76: 19 108.76 - 135.96: 9 Dihedral angle restraints: 3652 sinusoidal: 1507 harmonic: 2145 Sorted by residual: dihedral pdb=" CA LYS D 132 " pdb=" C LYS D 132 " pdb=" N THR D 133 " pdb=" CA THR D 133 " ideal model delta harmonic sigma weight residual 180.00 -153.15 -26.85 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA VAL B 82 " pdb=" C VAL B 82 " pdb=" N LYS B 83 " pdb=" CA LYS B 83 " ideal model delta harmonic sigma weight residual 180.00 155.37 24.63 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA THR D 133 " pdb=" C THR D 133 " pdb=" N ASP D 134 " pdb=" CA ASP D 134 " ideal model delta harmonic sigma weight residual 180.00 157.30 22.70 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 3649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 870 0.087 - 0.174: 106 0.174 - 0.261: 8 0.261 - 0.348: 1 0.348 - 0.435: 1 Chirality restraints: 986 Sorted by residual: chirality pdb=" CG LEU C 61 " pdb=" CB LEU C 61 " pdb=" CD1 LEU C 61 " pdb=" CD2 LEU C 61 " both_signs ideal model delta sigma weight residual False -2.59 -2.15 -0.43 2.00e-01 2.50e+01 4.72e+00 chirality pdb=" C5 AV0 B 201 " pdb=" C4 AV0 B 201 " pdb=" C6 AV0 B 201 " pdb=" O5 AV0 B 201 " both_signs ideal model delta sigma weight residual False -2.50 -2.24 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CB THR D 49 " pdb=" CA THR D 49 " pdb=" OG1 THR D 49 " pdb=" CG2 THR D 49 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 983 not shown) Planarity restraints: 972 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 156 " -0.050 5.00e-02 4.00e+02 7.63e-02 9.32e+00 pdb=" N PRO D 157 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO D 157 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 157 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 72 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.94e+00 pdb=" C ASN D 72 " -0.046 2.00e-02 2.50e+03 pdb=" O ASN D 72 " 0.017 2.00e-02 2.50e+03 pdb=" N ILE D 73 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 113 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.90e+00 pdb=" C MET B 113 " 0.045 2.00e-02 2.50e+03 pdb=" O MET B 113 " -0.017 2.00e-02 2.50e+03 pdb=" N GLN B 114 " -0.015 2.00e-02 2.50e+03 ... (remaining 969 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1521 2.79 - 3.32: 5188 3.32 - 3.85: 9401 3.85 - 4.37: 9999 4.37 - 4.90: 17420 Nonbonded interactions: 43529 Sorted by model distance: nonbonded pdb=" OG1 THR B 85 " pdb=" O ASN B 153 " model vdw 2.266 3.040 nonbonded pdb=" OG SER C 169 " pdb=" O ALA C 191 " model vdw 2.300 3.040 nonbonded pdb=" OH TYR A 92 " pdb=" O PHE A 147 " model vdw 2.322 3.040 nonbonded pdb=" OG1 THR A 85 " pdb=" O ASN A 153 " model vdw 2.322 3.040 nonbonded pdb=" O SER D 91 " pdb=" OG SER D 91 " model vdw 2.334 3.040 ... (remaining 43524 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 'A' and (resid 5 through 31 or resid 43 through 76 or resid 82 through 15 \ 5 or resid 158 through 195)) selection = (chain 'B' and (resid 5 through 76 or resid 82 through 195)) selection = (chain 'C' and (resid 5 through 31 or resid 43 through 76 or resid 82 through 15 \ 5 or resid 158 through 195)) selection = (chain 'D' and (resid 5 through 31 or resid 43 through 155 or resid 158 through \ 195)) } 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: 0.530 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.620 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 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 : 0.006 0.072 6092 Z= 0.254 Angle : 1.125 19.980 8244 Z= 0.562 Chirality : 0.059 0.435 986 Planarity : 0.007 0.076 972 Dihedral : 22.230 135.955 2270 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 0.76 % Allowed : 37.63 % Favored : 61.61 % 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: -2.75 (0.28), residues: 701 helix: -1.63 (0.23), residues: 326 sheet: -0.57 (0.66), residues: 74 loop : -2.27 (0.34), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 69 TYR 0.030 0.002 TYR D 137 PHE 0.024 0.002 PHE C 105 HIS 0.016 0.004 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00567 ( 6092) covalent geometry : angle 1.12533 ( 8244) hydrogen bonds : bond 0.17857 ( 253) hydrogen bonds : angle 7.08221 ( 726) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 119 time to evaluate : 0.139 Fit side-chains REVERT: A 90 GLU cc_start: 0.8239 (tp30) cc_final: 0.7855 (tp30) REVERT: A 101 TYR cc_start: 0.8934 (m-80) cc_final: 0.8609 (m-80) outliers start: 5 outliers final: 4 residues processed: 121 average time/residue: 0.0659 time to fit residues: 10.6179 Evaluate side-chains 117 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 113 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain D residue 101 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 0.0000 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 153 ASN ** D 156 HIS ** 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 = 0.3868 r_free = 0.3868 target = 0.164567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.116326 restraints weight = 7768.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.119825 restraints weight = 4716.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.121861 restraints weight = 3545.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.123420 restraints weight = 3014.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.124152 restraints weight = 2730.330| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6092 Z= 0.125 Angle : 0.678 10.815 8244 Z= 0.330 Chirality : 0.046 0.343 986 Planarity : 0.004 0.059 972 Dihedral : 14.956 146.884 908 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 5.16 % Allowed : 33.54 % Favored : 61.31 % 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: -1.69 (0.31), residues: 701 helix: -0.26 (0.27), residues: 327 sheet: -0.57 (0.56), residues: 93 loop : -2.33 (0.36), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 69 TYR 0.013 0.001 TYR C 150 PHE 0.025 0.001 PHE D 189 HIS 0.004 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 6092) covalent geometry : angle 0.67769 ( 8244) hydrogen bonds : bond 0.04040 ( 253) hydrogen bonds : angle 4.83708 ( 726) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 0.282 Fit side-chains REVERT: A 88 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.8172 (mm-40) REVERT: A 163 LYS cc_start: 0.8352 (mttp) cc_final: 0.8113 (tppp) REVERT: B 101 TYR cc_start: 0.7959 (OUTLIER) cc_final: 0.7163 (t80) outliers start: 34 outliers final: 18 residues processed: 143 average time/residue: 0.0617 time to fit residues: 12.3749 Evaluate side-chains 124 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 88 GLN Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 129 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 57 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 chunk 29 optimal weight: 0.4980 chunk 16 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 = 0.3784 r_free = 0.3784 target = 0.153091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.097819 restraints weight = 8022.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.101566 restraints weight = 4217.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.103801 restraints weight = 3004.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.105243 restraints weight = 2522.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.105723 restraints weight = 2285.165| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6092 Z= 0.184 Angle : 0.716 10.748 8244 Z= 0.347 Chirality : 0.046 0.272 986 Planarity : 0.004 0.052 972 Dihedral : 11.951 139.744 903 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 6.37 % Allowed : 33.69 % Favored : 59.94 % 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: -1.15 (0.32), residues: 701 helix: 0.29 (0.28), residues: 328 sheet: -0.25 (0.65), residues: 64 loop : -2.07 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 69 TYR 0.021 0.001 TYR A 181 PHE 0.027 0.001 PHE D 189 HIS 0.002 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00442 ( 6092) covalent geometry : angle 0.71630 ( 8244) hydrogen bonds : bond 0.03943 ( 253) hydrogen bonds : angle 4.74912 ( 726) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 118 time to evaluate : 0.235 Fit side-chains REVERT: A 65 TYR cc_start: 0.8501 (t80) cc_final: 0.8104 (t80) REVERT: A 88 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7950 (mm-40) REVERT: A 101 TYR cc_start: 0.8747 (m-80) cc_final: 0.8449 (m-80) REVERT: B 101 TYR cc_start: 0.8091 (OUTLIER) cc_final: 0.7234 (t80) REVERT: C 16 LEU cc_start: 0.7097 (OUTLIER) cc_final: 0.6703 (tt) REVERT: D 72 ASN cc_start: 0.8355 (t0) cc_final: 0.7847 (t0) REVERT: D 136 TYR cc_start: 0.7819 (t80) cc_final: 0.7495 (t80) outliers start: 42 outliers final: 26 residues processed: 147 average time/residue: 0.0594 time to fit residues: 12.4052 Evaluate side-chains 135 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 106 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 56 CYS Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 88 GLN Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 129 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 29 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 17 optimal weight: 0.0470 chunk 7 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 153 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.156902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.101716 restraints weight = 8077.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.105740 restraints weight = 4189.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.108322 restraints weight = 2945.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.109691 restraints weight = 2436.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.110040 restraints weight = 2208.647| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6092 Z= 0.118 Angle : 0.632 10.568 8244 Z= 0.310 Chirality : 0.043 0.239 986 Planarity : 0.004 0.046 972 Dihedral : 9.897 135.299 903 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 5.61 % Allowed : 35.20 % Favored : 59.18 % 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: -0.89 (0.32), residues: 701 helix: 0.60 (0.29), residues: 330 sheet: 0.20 (0.62), residues: 73 loop : -2.23 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 69 TYR 0.019 0.001 TYR A 181 PHE 0.023 0.001 PHE D 189 HIS 0.003 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 6092) covalent geometry : angle 0.63163 ( 8244) hydrogen bonds : bond 0.03440 ( 253) hydrogen bonds : angle 4.46748 ( 726) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 119 time to evaluate : 0.138 Fit side-chains REVERT: A 65 TYR cc_start: 0.8592 (t80) cc_final: 0.8388 (t80) REVERT: A 88 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7881 (mm-40) REVERT: A 105 PHE cc_start: 0.6594 (m-10) cc_final: 0.6314 (m-10) REVERT: B 101 TYR cc_start: 0.7934 (OUTLIER) cc_final: 0.7078 (t80) REVERT: B 183 PHE cc_start: 0.7001 (OUTLIER) cc_final: 0.6789 (t80) REVERT: C 16 LEU cc_start: 0.7008 (OUTLIER) cc_final: 0.6595 (tt) REVERT: C 192 ARG cc_start: 0.8207 (ptt-90) cc_final: 0.7904 (ptt-90) REVERT: D 63 SER cc_start: 0.8993 (t) cc_final: 0.8411 (p) REVERT: D 72 ASN cc_start: 0.8286 (t0) cc_final: 0.7679 (m-40) outliers start: 37 outliers final: 28 residues processed: 145 average time/residue: 0.0594 time to fit residues: 11.9235 Evaluate side-chains 142 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 56 CYS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 88 GLN Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 130 PHE Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 165 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 7 optimal weight: 3.9990 chunk 6 optimal weight: 0.4980 chunk 38 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3838 r_free = 0.3838 target = 0.157377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.101885 restraints weight = 8179.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.105912 restraints weight = 4240.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.108455 restraints weight = 2986.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.109439 restraints weight = 2473.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.110612 restraints weight = 2273.585| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6092 Z= 0.116 Angle : 0.618 11.252 8244 Z= 0.301 Chirality : 0.042 0.173 986 Planarity : 0.004 0.044 972 Dihedral : 9.143 127.606 903 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 6.53 % Allowed : 33.99 % Favored : 59.48 % 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: -0.69 (0.33), residues: 701 helix: 0.77 (0.29), residues: 330 sheet: 0.07 (0.57), residues: 89 loop : -2.17 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 69 TYR 0.018 0.001 TYR A 181 PHE 0.020 0.001 PHE D 189 HIS 0.002 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 6092) covalent geometry : angle 0.61782 ( 8244) hydrogen bonds : bond 0.03359 ( 253) hydrogen bonds : angle 4.36292 ( 726) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 117 time to evaluate : 0.234 Fit side-chains REVERT: A 88 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7923 (mm-40) REVERT: A 101 TYR cc_start: 0.8630 (m-80) cc_final: 0.8404 (m-80) REVERT: A 163 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.8093 (tppp) REVERT: B 101 TYR cc_start: 0.8018 (OUTLIER) cc_final: 0.7153 (t80) REVERT: C 16 LEU cc_start: 0.7009 (OUTLIER) cc_final: 0.6586 (tt) REVERT: D 72 ASN cc_start: 0.8253 (t0) cc_final: 0.7689 (m-40) REVERT: D 73 ILE cc_start: 0.7599 (OUTLIER) cc_final: 0.7326 (mm) outliers start: 43 outliers final: 31 residues processed: 146 average time/residue: 0.0475 time to fit residues: 9.8462 Evaluate side-chains 139 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 103 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 56 CYS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 GLN Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 110 PHE Chi-restraints excluded: chain B residue 130 PHE Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 165 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 1 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 38 optimal weight: 0.5980 chunk 62 optimal weight: 0.0040 chunk 24 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- 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 = 0.3818 r_free = 0.3818 target = 0.155778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.100074 restraints weight = 8099.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.103864 restraints weight = 4362.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.106319 restraints weight = 3138.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.107606 restraints weight = 2626.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.108030 restraints weight = 2385.940| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 6092 Z= 0.127 Angle : 0.634 11.246 8244 Z= 0.309 Chirality : 0.043 0.196 986 Planarity : 0.004 0.042 972 Dihedral : 8.840 125.130 903 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 6.37 % Allowed : 34.90 % Favored : 58.73 % 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: -0.63 (0.33), residues: 701 helix: 0.82 (0.29), residues: 328 sheet: 0.17 (0.55), residues: 93 loop : -2.18 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 69 TYR 0.020 0.001 TYR A 181 PHE 0.018 0.001 PHE D 189 HIS 0.001 0.000 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 6092) covalent geometry : angle 0.63413 ( 8244) hydrogen bonds : bond 0.03379 ( 253) hydrogen bonds : angle 4.41336 ( 726) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 111 time to evaluate : 0.272 Fit side-chains REVERT: A 88 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7919 (mm-40) REVERT: A 163 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.8121 (tppp) REVERT: B 101 TYR cc_start: 0.8029 (OUTLIER) cc_final: 0.7133 (t80) REVERT: C 16 LEU cc_start: 0.7092 (OUTLIER) cc_final: 0.6669 (tt) REVERT: D 72 ASN cc_start: 0.8224 (t0) cc_final: 0.7871 (t0) REVERT: D 73 ILE cc_start: 0.7585 (OUTLIER) cc_final: 0.7280 (mm) REVERT: D 106 MET cc_start: 0.7786 (tpp) cc_final: 0.7572 (tpp) outliers start: 42 outliers final: 35 residues processed: 140 average time/residue: 0.0600 time to fit residues: 11.9539 Evaluate side-chains 144 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 104 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 56 CYS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 88 GLN Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 110 PHE Chi-restraints excluded: chain B residue 130 PHE Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 165 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 41 optimal weight: 6.9990 chunk 21 optimal weight: 0.6980 chunk 54 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 60 optimal weight: 0.2980 chunk 15 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 24 optimal weight: 0.1980 chunk 46 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3849 r_free = 0.3849 target = 0.158437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.103753 restraints weight = 8089.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.107650 restraints weight = 4361.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.110160 restraints weight = 3115.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.111417 restraints weight = 2592.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.111724 restraints weight = 2360.319| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6092 Z= 0.109 Angle : 0.614 11.284 8244 Z= 0.300 Chirality : 0.042 0.169 986 Planarity : 0.003 0.043 972 Dihedral : 8.457 119.104 903 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 6.53 % Allowed : 35.05 % Favored : 58.42 % 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: -0.50 (0.33), residues: 701 helix: 0.94 (0.29), residues: 328 sheet: 0.31 (0.55), residues: 93 loop : -2.17 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 69 TYR 0.020 0.001 TYR A 181 PHE 0.018 0.001 PHE D 189 HIS 0.001 0.000 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 6092) covalent geometry : angle 0.61356 ( 8244) hydrogen bonds : bond 0.03205 ( 253) hydrogen bonds : angle 4.27443 ( 726) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 108 time to evaluate : 0.194 Fit side-chains REVERT: A 88 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7877 (mm-40) REVERT: B 101 TYR cc_start: 0.7923 (OUTLIER) cc_final: 0.6807 (t80) REVERT: B 192 ARG cc_start: 0.7882 (tmm-80) cc_final: 0.7539 (tmm-80) REVERT: C 16 LEU cc_start: 0.6995 (OUTLIER) cc_final: 0.6576 (tt) REVERT: D 72 ASN cc_start: 0.8231 (t0) cc_final: 0.7681 (m-40) REVERT: D 73 ILE cc_start: 0.7507 (OUTLIER) cc_final: 0.7269 (mm) outliers start: 43 outliers final: 32 residues processed: 138 average time/residue: 0.0470 time to fit residues: 9.1525 Evaluate side-chains 137 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 101 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 56 CYS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 88 GLN Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 110 PHE Chi-restraints excluded: chain B residue 130 PHE Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 153 ASN Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 154 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 39 optimal weight: 0.0570 chunk 8 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 17 optimal weight: 0.0170 chunk 43 optimal weight: 0.9980 chunk 10 optimal weight: 0.0270 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 overall best weight: 0.3594 ------------------------------------------------------------------------------- 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 = 0.3854 r_free = 0.3854 target = 0.159062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.104184 restraints weight = 8045.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.108071 restraints weight = 4252.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.110389 restraints weight = 3028.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.112171 restraints weight = 2514.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.112777 restraints weight = 2252.380| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 6092 Z= 0.109 Angle : 0.612 11.258 8244 Z= 0.300 Chirality : 0.042 0.161 986 Planarity : 0.003 0.042 972 Dihedral : 8.291 115.182 903 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 6.22 % Allowed : 35.81 % Favored : 57.97 % 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: -0.47 (0.33), residues: 701 helix: 0.98 (0.29), residues: 328 sheet: 0.31 (0.55), residues: 93 loop : -2.17 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 69 TYR 0.020 0.001 TYR A 181 PHE 0.017 0.001 PHE D 189 HIS 0.001 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 6092) covalent geometry : angle 0.61238 ( 8244) hydrogen bonds : bond 0.03147 ( 253) hydrogen bonds : angle 4.22128 ( 726) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 104 time to evaluate : 0.241 Fit side-chains REVERT: A 88 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7862 (mm-40) REVERT: B 101 TYR cc_start: 0.7797 (OUTLIER) cc_final: 0.6661 (t80) REVERT: B 114 GLN cc_start: 0.7347 (OUTLIER) cc_final: 0.7130 (tt0) REVERT: B 192 ARG cc_start: 0.7891 (tmm-80) cc_final: 0.7543 (tmm-80) REVERT: C 16 LEU cc_start: 0.6956 (OUTLIER) cc_final: 0.6517 (tt) REVERT: D 72 ASN cc_start: 0.8246 (t0) cc_final: 0.7675 (m-40) REVERT: D 73 ILE cc_start: 0.7508 (OUTLIER) cc_final: 0.7253 (mm) outliers start: 41 outliers final: 30 residues processed: 132 average time/residue: 0.0692 time to fit residues: 12.5663 Evaluate side-chains 139 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 104 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 56 CYS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 88 GLN Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 110 PHE Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 154 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 7 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 66 optimal weight: 0.0170 chunk 50 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 17 optimal weight: 0.0070 chunk 49 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.8038 ------------------------------------------------------------------------------- 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 = 0.3841 r_free = 0.3841 target = 0.157629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.102962 restraints weight = 8165.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.106952 restraints weight = 4287.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.109429 restraints weight = 3029.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.110760 restraints weight = 2508.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.111091 restraints weight = 2270.836| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6092 Z= 0.119 Angle : 0.617 11.303 8244 Z= 0.302 Chirality : 0.042 0.148 986 Planarity : 0.003 0.042 972 Dihedral : 8.302 115.270 903 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 6.07 % Allowed : 35.81 % Favored : 58.12 % 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: -0.47 (0.33), residues: 701 helix: 0.97 (0.29), residues: 328 sheet: 0.26 (0.55), residues: 93 loop : -2.13 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 69 TYR 0.020 0.001 TYR A 181 PHE 0.017 0.001 PHE D 189 HIS 0.002 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 6092) covalent geometry : angle 0.61676 ( 8244) hydrogen bonds : bond 0.03162 ( 253) hydrogen bonds : angle 4.24565 ( 726) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 106 time to evaluate : 0.304 Fit side-chains REVERT: A 88 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7918 (mm-40) REVERT: B 101 TYR cc_start: 0.7933 (OUTLIER) cc_final: 0.6809 (t80) REVERT: B 114 GLN cc_start: 0.7406 (OUTLIER) cc_final: 0.7164 (tt0) REVERT: B 192 ARG cc_start: 0.7915 (tmm-80) cc_final: 0.7563 (tmm-80) REVERT: C 16 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6731 (tt) REVERT: D 72 ASN cc_start: 0.8188 (t0) cc_final: 0.7876 (t0) REVERT: D 73 ILE cc_start: 0.7533 (OUTLIER) cc_final: 0.7244 (mm) outliers start: 40 outliers final: 34 residues processed: 134 average time/residue: 0.0695 time to fit residues: 12.9954 Evaluate side-chains 143 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 104 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 56 CYS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 88 GLN Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 110 PHE Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 154 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 5 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 26 optimal weight: 0.1980 chunk 19 optimal weight: 0.9990 chunk 49 optimal weight: 0.2980 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 43 optimal weight: 0.7980 chunk 41 optimal weight: 9.9990 chunk 55 optimal weight: 0.0570 overall best weight: 0.4298 ------------------------------------------------------------------------------- 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 = 0.3850 r_free = 0.3850 target = 0.158770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.104323 restraints weight = 8060.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.108237 restraints weight = 4250.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.110782 restraints weight = 3018.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.112024 restraints weight = 2497.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.112998 restraints weight = 2264.196| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 6092 Z= 0.107 Angle : 0.612 11.270 8244 Z= 0.299 Chirality : 0.042 0.152 986 Planarity : 0.003 0.042 972 Dihedral : 8.100 112.069 903 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 5.77 % Allowed : 36.12 % Favored : 58.12 % 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: -0.41 (0.33), residues: 701 helix: 0.98 (0.29), residues: 328 sheet: 0.29 (0.56), residues: 91 loop : -2.05 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 69 TYR 0.020 0.001 TYR A 181 PHE 0.016 0.001 PHE D 189 HIS 0.003 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 6092) covalent geometry : angle 0.61177 ( 8244) hydrogen bonds : bond 0.03084 ( 253) hydrogen bonds : angle 4.17037 ( 726) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 103 time to evaluate : 0.225 Fit side-chains REVERT: A 88 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7873 (mm-40) REVERT: A 163 LYS cc_start: 0.8485 (tppp) cc_final: 0.8209 (tppp) REVERT: B 101 TYR cc_start: 0.7809 (OUTLIER) cc_final: 0.6651 (t80) REVERT: B 114 GLN cc_start: 0.7275 (OUTLIER) cc_final: 0.7053 (tt0) REVERT: B 192 ARG cc_start: 0.8009 (tmm-80) cc_final: 0.7573 (tmm-80) REVERT: C 16 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6556 (tt) REVERT: D 72 ASN cc_start: 0.8175 (t0) cc_final: 0.7886 (t0) REVERT: D 73 ILE cc_start: 0.7492 (OUTLIER) cc_final: 0.7203 (mm) outliers start: 38 outliers final: 32 residues processed: 130 average time/residue: 0.0702 time to fit residues: 12.4778 Evaluate side-chains 138 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 101 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 56 CYS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 88 GLN Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 110 PHE Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 154 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 9 optimal weight: 0.0020 chunk 31 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 69 optimal weight: 0.6980 chunk 64 optimal weight: 0.3980 chunk 18 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 overall best weight: 0.7990 ------------------------------------------------------------------------------- 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 = 0.3836 r_free = 0.3836 target = 0.157519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.102458 restraints weight = 8065.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.106341 restraints weight = 4289.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.108800 restraints weight = 3053.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.110033 restraints weight = 2543.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.110990 restraints weight = 2313.627| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6092 Z= 0.119 Angle : 0.620 11.306 8244 Z= 0.302 Chirality : 0.042 0.150 986 Planarity : 0.003 0.042 972 Dihedral : 7.698 112.709 901 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 6.37 % Allowed : 35.36 % Favored : 58.27 % 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: -0.39 (0.33), residues: 701 helix: 1.01 (0.29), residues: 328 sheet: 0.26 (0.56), residues: 91 loop : -2.02 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 69 TYR 0.020 0.001 TYR A 181 PHE 0.016 0.001 PHE D 189 HIS 0.001 0.000 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 6092) covalent geometry : angle 0.61985 ( 8244) hydrogen bonds : bond 0.03109 ( 253) hydrogen bonds : angle 4.20449 ( 726) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1097.80 seconds wall clock time: 19 minutes 37.78 seconds (1177.78 seconds total)