Starting phenix.real_space_refine on Tue Aug 4 18:13:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r4j_53569/08_2026/9r4j_53569.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r4j_53569/08_2026/9r4j_53569.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9r4j_53569/08_2026/9r4j_53569.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r4j_53569/08_2026/9r4j_53569.map" model { file = "/net/cci-nas-00/data/ceres_data/9r4j_53569/08_2026/9r4j_53569.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r4j_53569/08_2026/9r4j_53569.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 68 5.49 5 S 12 5.16 5 C 3464 2.51 5 N 1002 2.21 5 O 1242 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5788 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1051 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain breaks: 1 Chain: "B" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1134 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 4, 'TRANS': 134} Chain: "C" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1067 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 3, 'TRANS': 127} Chain breaks: 1 Chain: "A" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1143 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 4, 'TRANS': 135} Chain: "Y" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 688 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "Z" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 705 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Time building chain proxies: 1.61, per 1000 atoms: 0.28 Number of scatterers: 5788 At special positions: 0 Unit cell: (72.171, 114.453, 128.304, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 68 15.00 O 1242 8.00 N 1002 7.00 C 3464 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: 0.40 Conformation dependent library (CDL) restraints added in 94.8 milliseconds 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1054 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 8 sheets defined 40.3% alpha, 20.8% beta 26 base pairs and 62 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'D' and resid 44 through 55 removed outlier: 3.625A pdb=" N GLU D 49 " --> pdb=" O PRO D 45 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER D 50 " --> pdb=" O ALA D 46 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR D 54 " --> pdb=" O SER D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 72 removed outlier: 3.858A pdb=" N LEU D 71 " --> pdb=" O THR D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 76 removed outlier: 3.873A pdb=" N ALA D 76 " --> pdb=" O PHE D 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 73 through 76' Processing helix chain 'D' and resid 90 through 95 removed outlier: 4.132A pdb=" N SER D 95 " --> pdb=" O ASN D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 126 Processing helix chain 'D' and resid 129 through 136 removed outlier: 3.680A pdb=" N ARG D 136 " --> pdb=" O THR D 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 25 removed outlier: 4.008A pdb=" N SER B 24 " --> pdb=" O LYS B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 57 removed outlier: 3.815A pdb=" N ASN B 57 " --> pdb=" O GLN B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 73 Processing helix chain 'B' and resid 90 through 98 removed outlier: 3.793A pdb=" N SER B 95 " --> pdb=" O ASN B 91 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASP B 96 " --> pdb=" O ASN B 92 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA B 97 " --> pdb=" O LEU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 127 Processing helix chain 'B' and resid 129 through 134 Processing helix chain 'C' and resid 21 through 25 removed outlier: 3.892A pdb=" N SER C 24 " --> pdb=" O LYS C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 53 Processing helix chain 'C' and resid 64 through 73 removed outlier: 3.581A pdb=" N LYS C 69 " --> pdb=" O THR C 65 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ARG C 70 " --> pdb=" O ARG C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 98 removed outlier: 3.773A pdb=" N SER C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASP C 96 " --> pdb=" O ASN C 92 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA C 97 " --> pdb=" O LEU C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 126 Processing helix chain 'C' and resid 129 through 136 Processing helix chain 'A' and resid 19 through 24 removed outlier: 4.145A pdb=" N SER A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 56 removed outlier: 3.650A pdb=" N PHE A 55 " --> pdb=" O TYR A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 73 Processing helix chain 'A' and resid 90 through 98 Processing helix chain 'A' and resid 116 through 126 Processing helix chain 'A' and resid 129 through 137 removed outlier: 3.739A pdb=" N ARG A 136 " --> pdb=" O THR A 132 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 4 through 9 removed outlier: 4.081A pdb=" N GLY D 4 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU D 40 " --> pdb=" O VAL D 114 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 15 through 16 Processing sheet with id=AA3, first strand: chain 'B' and resid 3 through 8 removed outlier: 4.203A pdb=" N GLY B 4 " --> pdb=" O GLY B 107 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 16 through 17 Processing sheet with id=AA5, first strand: chain 'C' and resid 5 through 9 removed outlier: 3.568A pdb=" N HIS C 111 " --> pdb=" O GLN C 108 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N CYS C 39 " --> pdb=" O GLY C 35 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE C 30 " --> pdb=" O VAL C 79 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 15 through 17 Processing sheet with id=AA7, first strand: chain 'A' and resid 4 through 9 removed outlier: 4.254A pdb=" N GLY A 4 " --> pdb=" O GLY A 107 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 16 through 17 194 hydrogen bonds defined for protein. 537 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 64 hydrogen bonds 124 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 62 stacking parallelities Total time for adding SS restraints: 0.55 Time building geometry restraints manager: 0.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.32: 1012 1.32 - 1.44: 1776 1.44 - 1.56: 3085 1.56 - 1.68: 135 1.68 - 1.80: 20 Bond restraints: 6028 Sorted by residual: bond pdb=" C3' DG Y 2 " pdb=" O3' DG Y 2 " ideal model delta sigma weight residual 1.435 1.386 0.049 1.30e-02 5.92e+03 1.42e+01 bond pdb=" C3' DT Z 24 " pdb=" C2' DT Z 24 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.39e+01 bond pdb=" C1' DC Z 20 " pdb=" N1 DC Z 20 " ideal model delta sigma weight residual 1.468 1.517 -0.049 1.40e-02 5.10e+03 1.20e+01 bond pdb=" C3' DG Y -6 " pdb=" O3' DG Y -6 " ideal model delta sigma weight residual 1.435 1.391 0.044 1.30e-02 5.92e+03 1.15e+01 bond pdb=" C3' DG Z 14 " pdb=" C2' DG Z 14 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 ... (remaining 6023 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 7903 1.91 - 3.81: 471 3.81 - 5.72: 42 5.72 - 7.63: 13 7.63 - 9.53: 2 Bond angle restraints: 8431 Sorted by residual: angle pdb=" N3 DT Y -19 " pdb=" C4 DT Y -19 " pdb=" O4 DT Y -19 " ideal model delta sigma weight residual 119.90 122.77 -2.87 6.00e-01 2.78e+00 2.29e+01 angle pdb=" O4' DT Y -27 " pdb=" C4' DT Y -27 " pdb=" C3' DT Y -27 " ideal model delta sigma weight residual 106.00 103.20 2.80 6.00e-01 2.78e+00 2.18e+01 angle pdb=" N3 DT Z 23 " pdb=" C4 DT Z 23 " pdb=" O4 DT Z 23 " ideal model delta sigma weight residual 119.90 122.68 -2.78 6.00e-01 2.78e+00 2.15e+01 angle pdb=" O4 DT Y -19 " pdb=" C4 DT Y -19 " pdb=" C5 DT Y -19 " ideal model delta sigma weight residual 124.90 121.77 3.13 7.00e-01 2.04e+00 2.00e+01 angle pdb=" N3 DT Y -17 " pdb=" C4 DT Y -17 " pdb=" O4 DT Y -17 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 ... (remaining 8426 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.52: 3056 35.52 - 71.03: 426 71.03 - 106.55: 8 106.55 - 142.06: 2 142.06 - 177.58: 4 Dihedral angle restraints: 3496 sinusoidal: 1897 harmonic: 1599 Sorted by residual: dihedral pdb=" CA GLN B 108 " pdb=" C GLN B 108 " pdb=" N PHE B 109 " pdb=" CA PHE B 109 " ideal model delta harmonic sigma weight residual 180.00 156.88 23.12 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA TRP A 115 " pdb=" C TRP A 115 " pdb=" N ASP A 116 " pdb=" CA ASP A 116 " ideal model delta harmonic sigma weight residual 180.00 158.65 21.35 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA ASN B 12 " pdb=" C ASN B 12 " pdb=" N LYS B 13 " pdb=" CA LYS B 13 " ideal model delta harmonic sigma weight residual 180.00 158.97 21.03 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 3493 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 646 0.051 - 0.102: 230 0.102 - 0.154: 66 0.154 - 0.205: 9 0.205 - 0.256: 9 Chirality restraints: 960 Sorted by residual: chirality pdb=" CB ILE A 42 " pdb=" CA ILE A 42 " pdb=" CG1 ILE A 42 " pdb=" CG2 ILE A 42 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CB ILE A 87 " pdb=" CA ILE A 87 " pdb=" CG1 ILE A 87 " pdb=" CG2 ILE A 87 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA ASN A 38 " pdb=" N ASN A 38 " pdb=" C ASN A 38 " pdb=" CB ASN A 38 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 957 not shown) Planarity restraints: 848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG Y -10 " -0.026 2.00e-02 2.50e+03 1.27e-02 4.83e+00 pdb=" N9 DG Y -10 " 0.026 2.00e-02 2.50e+03 pdb=" C8 DG Y -10 " 0.007 2.00e-02 2.50e+03 pdb=" N7 DG Y -10 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DG Y -10 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG Y -10 " -0.004 2.00e-02 2.50e+03 pdb=" O6 DG Y -10 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DG Y -10 " -0.005 2.00e-02 2.50e+03 pdb=" C2 DG Y -10 " -0.009 2.00e-02 2.50e+03 pdb=" N2 DG Y -10 " 0.017 2.00e-02 2.50e+03 pdb=" N3 DG Y -10 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG Y -10 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT Z 5 " 0.027 2.00e-02 2.50e+03 1.32e-02 4.38e+00 pdb=" N1 DT Z 5 " -0.028 2.00e-02 2.50e+03 pdb=" C2 DT Z 5 " -0.004 2.00e-02 2.50e+03 pdb=" O2 DT Z 5 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DT Z 5 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DT Z 5 " 0.008 2.00e-02 2.50e+03 pdb=" O4 DT Z 5 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DT Z 5 " -0.003 2.00e-02 2.50e+03 pdb=" C7 DT Z 5 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DT Z 5 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 115 " 0.022 2.00e-02 2.50e+03 1.27e-02 4.01e+00 pdb=" CG TRP D 115 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP D 115 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP D 115 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 115 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP D 115 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP D 115 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 115 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 115 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 115 " 0.001 2.00e-02 2.50e+03 ... (remaining 845 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 2189 2.89 - 3.39: 5439 3.39 - 3.90: 10176 3.90 - 4.40: 11559 4.40 - 4.90: 17357 Nonbonded interactions: 46720 Sorted by model distance: nonbonded pdb=" N3 DT Y -27 " pdb=" N4 DC Z 28 " model vdw 2.389 2.560 nonbonded pdb=" OD1 ASN C 38 " pdb=" OE1 GLN C 119 " model vdw 2.431 3.040 nonbonded pdb=" N GLU D 131 " pdb=" OE1 GLU D 131 " model vdw 2.436 3.120 nonbonded pdb=" O5' DT Z -4 " pdb=" O4' DT Z -4 " model vdw 2.462 2.432 nonbonded pdb=" O5' DA Z 17 " pdb=" O4' DA Z 17 " model vdw 2.473 2.432 ... (remaining 46715 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 1 through 53 or resid 65 through 137)) selection = (chain 'B' and (resid 1 through 53 or resid 65 through 137)) selection = (chain 'C' and (resid 1 through 53 or resid 65 through 137)) selection = (chain 'D' and (resid 1 through 53 or resid 65 through 137)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.780 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: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.000 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 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 : 0.008 0.049 6028 Z= 0.527 Angle : 0.958 9.533 8431 Z= 0.666 Chirality : 0.059 0.256 960 Planarity : 0.006 0.044 848 Dihedral : 25.962 177.578 2442 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.63 % Favored : 89.37 % Rotamer: Outliers : 8.08 % Allowed : 44.65 % Favored : 47.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.36), residues: 527 helix: -1.37 (0.35), residues: 175 sheet: 0.03 (0.42), residues: 158 loop : -1.28 (0.46), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 66 TYR 0.018 0.003 TYR D 51 PHE 0.020 0.003 PHE A 36 TRP 0.032 0.005 TRP D 115 HIS 0.006 0.003 HIS B 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00754 / 0.53 ( 6028) covalent geometry : angle 0.95844 / 0.67 ( 8431) hydrogen bonds : bond 0.15289 / 10.05 ( 258) hydrogen bonds : angle 7.60831 / 5.25 ( 661) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 151 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 34 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7431 (ttp-170) REVERT: B 30 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8015 (pp) REVERT: A 105 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8548 (tt) outliers start: 40 outliers final: 18 residues processed: 174 average time/residue: 0.1051 time to fit residues: 22.4555 Evaluate side-chains 134 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 105 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 56 optimal weight: 20.0000 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 53 GLN B 53 GLN B 57 ASN B 119 GLN A 0 HIS A 57 ASN A 122 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.071762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.060429 restraints weight = 20250.114| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 3.10 r_work: 0.3085 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 6028 Z= 0.191 Angle : 0.803 8.451 8431 Z= 0.452 Chirality : 0.050 0.362 960 Planarity : 0.005 0.047 848 Dihedral : 27.122 176.136 1377 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 8.28 % Allowed : 32.73 % Favored : 58.99 % 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: -1.37 (0.37), residues: 527 helix: -1.18 (0.34), residues: 190 sheet: -0.06 (0.42), residues: 168 loop : -1.18 (0.52), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 43 TYR 0.011 0.001 TYR B 51 PHE 0.015 0.002 PHE B 25 TRP 0.019 0.003 TRP A 115 HIS 0.009 0.002 HIS D 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.19 ( 6028) covalent geometry : angle 0.80332 / 0.45 ( 8431) hydrogen bonds : bond 0.06829 / 3.99 ( 258) hydrogen bonds : angle 6.33930 / 4.35 ( 661) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 125 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 116 ASP cc_start: 0.7654 (t0) cc_final: 0.7403 (t0) REVERT: B 43 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.7739 (mtt-85) REVERT: B 110 ASP cc_start: 0.9244 (p0) cc_final: 0.8975 (p0) REVERT: B 118 VAL cc_start: 0.8426 (OUTLIER) cc_final: 0.8066 (m) REVERT: B 128 GLU cc_start: 0.8805 (pt0) cc_final: 0.8504 (tt0) REVERT: C 21 LYS cc_start: 0.8499 (mptt) cc_final: 0.8084 (ttmm) REVERT: C 30 ILE cc_start: 0.7864 (OUTLIER) cc_final: 0.7647 (pp) REVERT: C 108 GLN cc_start: 0.8529 (mp10) cc_final: 0.8131 (mp10) outliers start: 41 outliers final: 21 residues processed: 157 average time/residue: 0.0902 time to fit residues: 17.8915 Evaluate side-chains 135 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 111 HIS Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain A residue 0 HIS Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 105 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 1 optimal weight: 20.0000 chunk 43 optimal weight: 6.9990 chunk 52 optimal weight: 30.0000 chunk 24 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 2 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 56 optimal weight: 20.0000 chunk 12 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 0 HIS ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.071409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.060021 restraints weight = 20997.235| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 3.17 r_work: 0.3077 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6028 Z= 0.174 Angle : 0.763 7.767 8431 Z= 0.433 Chirality : 0.049 0.359 960 Planarity : 0.005 0.035 848 Dihedral : 27.116 173.935 1356 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 9.09 % Allowed : 31.72 % Favored : 59.19 % 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: -1.42 (0.37), residues: 527 helix: -0.96 (0.34), residues: 193 sheet: -0.17 (0.43), residues: 162 loop : -1.42 (0.49), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 34 TYR 0.008 0.001 TYR B 51 PHE 0.013 0.002 PHE A 73 TRP 0.017 0.003 TRP A 115 HIS 0.003 0.001 HIS D 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.17 ( 6028) covalent geometry : angle 0.76276 / 0.43 ( 8431) hydrogen bonds : bond 0.06633 / 3.90 ( 258) hydrogen bonds : angle 6.11156 / 4.17 ( 661) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 119 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 11 ASP cc_start: 0.8347 (t0) cc_final: 0.7980 (p0) REVERT: D 100 ASP cc_start: 0.8901 (t0) cc_final: 0.8675 (t0) REVERT: D 116 ASP cc_start: 0.7506 (t0) cc_final: 0.7176 (t0) REVERT: D 133 VAL cc_start: 0.9184 (t) cc_final: 0.8896 (m) REVERT: B 30 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8182 (pp) REVERT: B 43 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.7838 (mtt-85) REVERT: B 100 ASP cc_start: 0.8456 (m-30) cc_final: 0.8206 (m-30) REVERT: B 118 VAL cc_start: 0.8412 (OUTLIER) cc_final: 0.8097 (m) REVERT: B 128 GLU cc_start: 0.8958 (pt0) cc_final: 0.8476 (pt0) REVERT: C 21 LYS cc_start: 0.8531 (mptt) cc_final: 0.8169 (mmmt) REVERT: C 101 LYS cc_start: 0.7247 (tppt) cc_final: 0.6977 (tptp) REVERT: C 108 GLN cc_start: 0.8578 (mp10) cc_final: 0.8181 (mp10) REVERT: A 88 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8416 (tt) REVERT: A 110 ASP cc_start: 0.8974 (p0) cc_final: 0.8616 (p0) outliers start: 45 outliers final: 24 residues processed: 153 average time/residue: 0.0895 time to fit residues: 17.0894 Evaluate side-chains 141 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 93 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 2.9990 chunk 40 optimal weight: 0.0770 chunk 12 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 55 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 38 ASN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.071010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.059692 restraints weight = 20804.413| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 3.11 r_work: 0.3073 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6028 Z= 0.184 Angle : 0.757 8.319 8431 Z= 0.425 Chirality : 0.049 0.362 960 Planarity : 0.004 0.033 848 Dihedral : 27.077 172.844 1352 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 9.49 % Allowed : 31.31 % Favored : 59.19 % 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 (0.37), residues: 527 helix: -0.58 (0.36), residues: 190 sheet: -0.09 (0.43), residues: 163 loop : -1.40 (0.49), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 136 TYR 0.019 0.002 TYR C 51 PHE 0.040 0.002 PHE B 58 TRP 0.016 0.003 TRP B 115 HIS 0.005 0.002 HIS A 0 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 ( 6028) covalent geometry : angle 0.75714 / 0.42 ( 8431) hydrogen bonds : bond 0.06435 / 3.72 ( 258) hydrogen bonds : angle 5.89306 / 4.03 ( 661) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 115 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.8055 (ttt) REVERT: D 11 ASP cc_start: 0.8326 (t0) cc_final: 0.7938 (p0) REVERT: D 21 LYS cc_start: 0.8728 (mptt) cc_final: 0.8443 (tptp) REVERT: D 116 ASP cc_start: 0.7577 (t0) cc_final: 0.7272 (t0) REVERT: D 124 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8649 (pp) REVERT: D 133 VAL cc_start: 0.9089 (t) cc_final: 0.8817 (m) REVERT: B 30 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8221 (pp) REVERT: B 43 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.7804 (mtt-85) REVERT: B 100 ASP cc_start: 0.8461 (m-30) cc_final: 0.8172 (m-30) REVERT: B 110 ASP cc_start: 0.9242 (p0) cc_final: 0.8944 (p0) REVERT: B 118 VAL cc_start: 0.8386 (OUTLIER) cc_final: 0.8091 (m) REVERT: C 21 LYS cc_start: 0.8571 (mptt) cc_final: 0.8220 (mmmt) REVERT: C 101 LYS cc_start: 0.7213 (tppt) cc_final: 0.6659 (tptp) REVERT: C 108 GLN cc_start: 0.8619 (mp10) cc_final: 0.8214 (mp10) REVERT: C 117 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.7850 (ptpt) REVERT: A 33 ASN cc_start: 0.8654 (OUTLIER) cc_final: 0.8394 (p0) REVERT: A 110 ASP cc_start: 0.8993 (p0) cc_final: 0.8656 (p0) outliers start: 47 outliers final: 25 residues processed: 146 average time/residue: 0.0845 time to fit residues: 15.6020 Evaluate side-chains 142 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 93 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 chunk 57 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 chunk 8 optimal weight: 8.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 38 ASN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.070398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.059032 restraints weight = 21181.904| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 3.11 r_work: 0.3059 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6028 Z= 0.202 Angle : 0.756 7.318 8431 Z= 0.425 Chirality : 0.050 0.370 960 Planarity : 0.004 0.033 848 Dihedral : 27.039 171.866 1352 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 8.69 % Allowed : 31.92 % Favored : 59.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.38), residues: 527 helix: -0.46 (0.36), residues: 191 sheet: -0.08 (0.44), residues: 163 loop : -1.35 (0.49), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 136 TYR 0.025 0.002 TYR C 51 PHE 0.014 0.001 PHE A 36 TRP 0.017 0.003 TRP B 115 HIS 0.004 0.002 HIS A 0 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.20 ( 6028) covalent geometry : angle 0.75603 / 0.43 ( 8431) hydrogen bonds : bond 0.06436 / 3.72 ( 258) hydrogen bonds : angle 5.89375 / 4.02 ( 661) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 113 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 11 ASP cc_start: 0.8382 (t0) cc_final: 0.8034 (p0) REVERT: D 116 ASP cc_start: 0.7588 (t0) cc_final: 0.7239 (t0) REVERT: D 124 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8652 (pp) REVERT: B 30 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8202 (pp) REVERT: B 43 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.7778 (mtt-85) REVERT: B 100 ASP cc_start: 0.8372 (m-30) cc_final: 0.8116 (m-30) REVERT: B 110 ASP cc_start: 0.9271 (p0) cc_final: 0.8968 (p0) REVERT: C 21 LYS cc_start: 0.8604 (mptt) cc_final: 0.8276 (mmmt) REVERT: C 108 GLN cc_start: 0.8634 (mp10) cc_final: 0.8174 (mp10) REVERT: A 33 ASN cc_start: 0.8689 (OUTLIER) cc_final: 0.8441 (p0) REVERT: A 110 ASP cc_start: 0.9020 (p0) cc_final: 0.8573 (p0) outliers start: 43 outliers final: 30 residues processed: 145 average time/residue: 0.0938 time to fit residues: 17.1314 Evaluate side-chains 144 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 110 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 138 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 30 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 53 optimal weight: 20.0000 chunk 9 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.070156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.058806 restraints weight = 21189.755| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 3.13 r_work: 0.3051 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6028 Z= 0.202 Angle : 0.751 7.665 8431 Z= 0.423 Chirality : 0.049 0.376 960 Planarity : 0.004 0.032 848 Dihedral : 27.006 171.162 1352 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 8.48 % Allowed : 32.32 % Favored : 59.19 % 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: -0.94 (0.37), residues: 527 helix: -0.35 (0.37), residues: 191 sheet: 0.22 (0.47), residues: 136 loop : -1.38 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 136 TYR 0.024 0.002 TYR C 51 PHE 0.043 0.002 PHE B 58 TRP 0.017 0.003 TRP B 115 HIS 0.005 0.002 HIS D 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.20 ( 6028) covalent geometry : angle 0.75109 / 0.42 ( 8431) hydrogen bonds : bond 0.06310 / 3.64 ( 258) hydrogen bonds : angle 5.77848 / 3.96 ( 661) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 117 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 11 ASP cc_start: 0.8390 (t0) cc_final: 0.7997 (p0) REVERT: D 102 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6927 (mm-30) REVERT: D 116 ASP cc_start: 0.7567 (t0) cc_final: 0.7231 (t0) REVERT: D 124 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8655 (pp) REVERT: B 30 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8232 (pp) REVERT: B 43 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.7751 (mtt-85) REVERT: B 110 ASP cc_start: 0.9276 (p0) cc_final: 0.8979 (p0) REVERT: C 21 LYS cc_start: 0.8660 (mptt) cc_final: 0.8339 (mmmt) REVERT: C 102 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7795 (tm-30) REVERT: C 108 GLN cc_start: 0.8651 (mp10) cc_final: 0.8424 (mm110) REVERT: C 117 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8076 (ptpt) REVERT: A 33 ASN cc_start: 0.8764 (OUTLIER) cc_final: 0.8428 (p0) REVERT: A 110 ASP cc_start: 0.9035 (p0) cc_final: 0.8604 (p0) outliers start: 42 outliers final: 32 residues processed: 149 average time/residue: 0.0916 time to fit residues: 17.1949 Evaluate side-chains 148 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 110 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain C residue 2 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 138 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 18 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 54 optimal weight: 20.0000 chunk 45 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 8 optimal weight: 0.0170 chunk 41 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 38 ASN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.071274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.060005 restraints weight = 21034.630| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 3.12 r_work: 0.3087 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6028 Z= 0.155 Angle : 0.739 7.523 8431 Z= 0.417 Chirality : 0.049 0.376 960 Planarity : 0.004 0.031 848 Dihedral : 26.914 169.819 1350 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 7.88 % Allowed : 32.32 % Favored : 59.80 % 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: -0.85 (0.37), residues: 527 helix: -0.30 (0.37), residues: 191 sheet: 0.39 (0.47), residues: 136 loop : -1.39 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 136 TYR 0.023 0.001 TYR C 51 PHE 0.010 0.001 PHE C 25 TRP 0.018 0.003 TRP A 115 HIS 0.003 0.001 HIS A 0 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.16 ( 6028) covalent geometry : angle 0.73914 / 0.42 ( 8431) hydrogen bonds : bond 0.06076 / 3.47 ( 258) hydrogen bonds : angle 5.65364 / 3.88 ( 661) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 121 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 11 ASP cc_start: 0.8331 (t0) cc_final: 0.7912 (p0) REVERT: D 116 ASP cc_start: 0.7394 (t0) cc_final: 0.7053 (t0) REVERT: D 124 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8630 (pp) REVERT: B 30 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8244 (pp) REVERT: B 43 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.7790 (mtt-85) REVERT: B 110 ASP cc_start: 0.9277 (p0) cc_final: 0.8957 (p0) REVERT: B 122 GLN cc_start: 0.8610 (mm-40) cc_final: 0.8324 (mm-40) REVERT: C 21 LYS cc_start: 0.8618 (mptt) cc_final: 0.8302 (mmmt) REVERT: C 30 ILE cc_start: 0.7653 (OUTLIER) cc_final: 0.7434 (pp) REVERT: C 101 LYS cc_start: 0.7368 (tppt) cc_final: 0.7096 (tppt) REVERT: C 108 GLN cc_start: 0.8647 (mp10) cc_final: 0.8334 (mm110) REVERT: A 33 ASN cc_start: 0.8639 (OUTLIER) cc_final: 0.8365 (p0) REVERT: A 63 LYS cc_start: 0.9131 (tppt) cc_final: 0.8709 (tppt) REVERT: A 98 LYS cc_start: 0.9180 (mtmm) cc_final: 0.8487 (ptpp) REVERT: A 106 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8296 (pt) REVERT: A 110 ASP cc_start: 0.9025 (p0) cc_final: 0.8609 (p0) outliers start: 39 outliers final: 24 residues processed: 147 average time/residue: 0.0874 time to fit residues: 16.2217 Evaluate side-chains 145 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 115 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain C residue 2 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 106 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 17 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 40 optimal weight: 0.2980 chunk 43 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.071357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.060082 restraints weight = 21025.430| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 3.12 r_work: 0.3094 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6028 Z= 0.163 Angle : 0.740 7.571 8431 Z= 0.417 Chirality : 0.048 0.380 960 Planarity : 0.004 0.029 848 Dihedral : 26.938 168.318 1350 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 6.87 % Allowed : 33.13 % Favored : 60.00 % 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: -0.78 (0.37), residues: 527 helix: -0.21 (0.37), residues: 191 sheet: 0.44 (0.45), residues: 146 loop : -1.51 (0.44), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 15 TYR 0.023 0.001 TYR C 51 PHE 0.039 0.002 PHE B 58 TRP 0.018 0.003 TRP A 115 HIS 0.003 0.001 HIS D 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.16 ( 6028) covalent geometry : angle 0.73987 / 0.42 ( 8431) hydrogen bonds : bond 0.06043 / 3.43 ( 258) hydrogen bonds : angle 5.56164 / 3.82 ( 661) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 11 ASP cc_start: 0.8308 (t0) cc_final: 0.7922 (p0) REVERT: D 116 ASP cc_start: 0.7525 (t0) cc_final: 0.7281 (t0) REVERT: B 30 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8182 (pp) REVERT: B 43 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.7776 (mtt-85) REVERT: B 110 ASP cc_start: 0.9268 (p0) cc_final: 0.8957 (p0) REVERT: C 21 LYS cc_start: 0.8600 (mptt) cc_final: 0.8305 (mmmt) REVERT: C 30 ILE cc_start: 0.7667 (OUTLIER) cc_final: 0.7464 (pp) REVERT: C 101 LYS cc_start: 0.7333 (tppt) cc_final: 0.7077 (tppt) REVERT: C 108 GLN cc_start: 0.8616 (mp10) cc_final: 0.8354 (mm110) REVERT: A 33 ASN cc_start: 0.8683 (OUTLIER) cc_final: 0.8387 (p0) REVERT: A 98 LYS cc_start: 0.9207 (mtmm) cc_final: 0.8879 (mtmm) REVERT: A 106 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8312 (pt) REVERT: A 110 ASP cc_start: 0.8996 (p0) cc_final: 0.8578 (p0) REVERT: A 117 LYS cc_start: 0.9282 (tttm) cc_final: 0.8727 (tttm) REVERT: A 121 GLU cc_start: 0.9127 (mm-30) cc_final: 0.8563 (mt-10) outliers start: 34 outliers final: 25 residues processed: 144 average time/residue: 0.0759 time to fit residues: 13.8655 Evaluate side-chains 147 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain C residue 2 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 106 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 5 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 chunk 54 optimal weight: 20.0000 chunk 25 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 57 optimal weight: 20.0000 chunk 19 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.071049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.059721 restraints weight = 21140.536| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 3.15 r_work: 0.3079 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6028 Z= 0.176 Angle : 0.778 7.791 8431 Z= 0.436 Chirality : 0.048 0.385 960 Planarity : 0.004 0.038 848 Dihedral : 26.914 167.726 1348 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 6.46 % Allowed : 34.34 % Favored : 59.19 % 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: -0.78 (0.37), residues: 527 helix: -0.19 (0.37), residues: 190 sheet: 0.48 (0.45), residues: 146 loop : -1.55 (0.44), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 136 TYR 0.024 0.002 TYR C 51 PHE 0.012 0.001 PHE A 36 TRP 0.016 0.003 TRP A 115 HIS 0.003 0.001 HIS D 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.18 ( 6028) covalent geometry : angle 0.77804 / 0.44 ( 8431) hydrogen bonds : bond 0.06118 / 3.52 ( 258) hydrogen bonds : angle 5.54766 / 3.82 ( 661) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 117 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 11 ASP cc_start: 0.8303 (t0) cc_final: 0.7922 (p0) REVERT: D 116 ASP cc_start: 0.7586 (t0) cc_final: 0.7303 (t0) REVERT: B 30 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.8187 (pp) REVERT: B 43 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.7732 (mtt-85) REVERT: B 110 ASP cc_start: 0.9257 (p0) cc_final: 0.8962 (p0) REVERT: C 21 LYS cc_start: 0.8616 (mptt) cc_final: 0.8316 (mmmt) REVERT: C 30 ILE cc_start: 0.7706 (OUTLIER) cc_final: 0.7496 (pp) REVERT: C 101 LYS cc_start: 0.7305 (tppt) cc_final: 0.7073 (tppt) REVERT: C 108 GLN cc_start: 0.8636 (mp10) cc_final: 0.8359 (mm110) REVERT: A 33 ASN cc_start: 0.8704 (OUTLIER) cc_final: 0.8408 (p0) REVERT: A 98 LYS cc_start: 0.9210 (mtmm) cc_final: 0.8541 (ptpp) REVERT: A 106 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8337 (pt) REVERT: A 110 ASP cc_start: 0.9035 (p0) cc_final: 0.8616 (p0) REVERT: A 117 LYS cc_start: 0.9296 (tttm) cc_final: 0.8750 (tttm) REVERT: A 121 GLU cc_start: 0.9133 (mm-30) cc_final: 0.8562 (mt-10) outliers start: 32 outliers final: 24 residues processed: 141 average time/residue: 0.0819 time to fit residues: 14.5280 Evaluate side-chains 145 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain C residue 2 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 12 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 54 optimal weight: 20.0000 chunk 31 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.069894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.058829 restraints weight = 21587.118| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 3.01 r_work: 0.3081 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6028 Z= 0.233 Angle : 0.821 9.059 8431 Z= 0.457 Chirality : 0.050 0.391 960 Planarity : 0.005 0.038 848 Dihedral : 26.961 167.865 1348 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 6.06 % Allowed : 34.34 % Favored : 59.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.36), residues: 527 helix: -0.29 (0.37), residues: 188 sheet: 0.24 (0.42), residues: 160 loop : -1.70 (0.44), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 136 TYR 0.024 0.002 TYR C 51 PHE 0.032 0.002 PHE B 58 TRP 0.016 0.003 TRP D 115 HIS 0.004 0.002 HIS A 0 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.23 ( 6028) covalent geometry : angle 0.82104 / 0.46 ( 8431) hydrogen bonds : bond 0.06460 / 3.76 ( 258) hydrogen bonds : angle 5.67308 / 3.89 ( 661) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 116 ASP cc_start: 0.7847 (t0) cc_final: 0.7592 (t0) REVERT: B 30 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8281 (pp) REVERT: B 43 ARG cc_start: 0.9026 (OUTLIER) cc_final: 0.7719 (mtt-85) REVERT: B 110 ASP cc_start: 0.9184 (p0) cc_final: 0.8779 (p0) REVERT: C 21 LYS cc_start: 0.8659 (mptt) cc_final: 0.8397 (mmmt) REVERT: C 101 LYS cc_start: 0.7533 (tppt) cc_final: 0.7307 (tppt) REVERT: C 110 ASP cc_start: 0.9157 (p0) cc_final: 0.8931 (p0) REVERT: A 33 ASN cc_start: 0.8732 (OUTLIER) cc_final: 0.8390 (p0) REVERT: A 110 ASP cc_start: 0.9053 (p0) cc_final: 0.8638 (p0) outliers start: 30 outliers final: 23 residues processed: 134 average time/residue: 0.0835 time to fit residues: 14.0499 Evaluate side-chains 133 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain C residue 2 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 71 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 24 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 54 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.071644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.060983 restraints weight = 21070.419| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.96 r_work: 0.3159 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6028 Z= 0.171 Angle : 0.793 9.245 8431 Z= 0.442 Chirality : 0.048 0.388 960 Planarity : 0.004 0.031 848 Dihedral : 26.831 167.503 1348 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.16 % Favored : 91.65 % Rotamer: Outliers : 5.05 % Allowed : 35.56 % Favored : 59.39 % 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 (0.36), residues: 527 helix: -0.32 (0.37), residues: 193 sheet: 0.34 (0.42), residues: 160 loop : -1.66 (0.44), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 136 TYR 0.022 0.002 TYR C 51 PHE 0.011 0.001 PHE C 109 TRP 0.019 0.003 TRP A 115 HIS 0.003 0.001 HIS A 0 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.17 ( 6028) covalent geometry : angle 0.79317 / 0.44 ( 8431) hydrogen bonds : bond 0.06050 / 3.49 ( 258) hydrogen bonds : angle 5.45483 / 3.76 ( 661) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1382.76 seconds wall clock time: 24 minutes 22.78 seconds (1462.78 seconds total)