Starting phenix.real_space_refine on Thu Jul 2 02:24:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r4j_53569/07_2026/9r4j_53569.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r4j_53569/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9r4j_53569/07_2026/9r4j_53569.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r4j_53569/07_2026/9r4j_53569.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9r4j_53569/07_2026/9r4j_53569.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r4j_53569/07_2026/9r4j_53569.map" } 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-dev-6108/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: 1.55, per 1000 atoms: 0.27 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: 0.47 Conformation dependent library (CDL) restraints added in 159.6 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: 0.67 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: 0.90 Time building geometry restraints manager: 0.63 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: 7908 1.91 - 3.81: 466 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: 3.570 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: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.490 Find NCS groups from input model: 0.100 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.530 ------------------------------------------------------------------------------- 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 : 0.955 9.533 8431 Z= 0.662 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 0.95518 / 0.66 ( 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 : 0.221 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: 0.1035 time to fit residues: 22.1921 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 : 0.185 ------------------------------------------------------------------------------- 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: 0.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 5.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- 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 = 0.3508 r_free = 0.3508 target = 0.072093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.060716 restraints weight = 20384.063| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 3.14 r_work: 0.3091 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6028 Z= 0.185 Angle : 0.796 8.520 8431 Z= 0.450 Chirality : 0.049 0.347 960 Planarity : 0.005 0.046 848 Dihedral : 27.153 176.267 1377 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 8.08 % Allowed : 33.13 % Favored : 58.79 % 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: -1.38 (0.37), residues: 527 helix: -1.19 (0.33), residues: 190 sheet: -0.05 (0.42), residues: 168 loop : -1.19 (0.51), 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 0.018 0.003 TRP A 115 HIS 0.009 0.002 HIS D 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.18 ( 6028) covalent geometry : angle 0.79596 / 0.45 ( 8431) hydrogen bonds : bond 0.06808 / 3.98 ( 258) hydrogen bonds : angle 6.33872 / 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 165 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 125 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 21 LYS cc_start: 0.8640 (mptt) cc_final: 0.8349 (tptp) REVERT: D 116 ASP cc_start: 0.7649 (t0) cc_final: 0.7406 (t0) REVERT: D 128 GLU cc_start: 0.8650 (tp30) cc_final: 0.8448 (tp30) REVERT: B 30 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8104 (pp) REVERT: B 43 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.7726 (mtt-85) REVERT: B 110 ASP cc_start: 0.9240 (p0) cc_final: 0.8957 (p0) REVERT: B 118 VAL cc_start: 0.8430 (OUTLIER) cc_final: 0.8064 (m) REVERT: B 128 GLU cc_start: 0.8782 (pt0) cc_final: 0.8480 (tt0) REVERT: C 21 LYS cc_start: 0.8475 (mptt) cc_final: 0.8057 (ttmm) REVERT: C 101 LYS cc_start: 0.7652 (tppp) cc_final: 0.7445 (tppt) REVERT: C 108 GLN cc_start: 0.8476 (mp10) cc_final: 0.8133 (mp10) REVERT: A 98 LYS cc_start: 0.9172 (mtmm) cc_final: 0.8907 (mtmm) REVERT: A 102 GLU cc_start: 0.8602 (pm20) cc_final: 0.8384 (pm20) outliers start: 40 outliers final: 21 residues processed: 156 average time/residue: 0.0718 time to fit residues: 14.0928 Evaluate side-chains 136 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.198 ------------------------------------------------------------------------------- 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 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 137 MET 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: 6.9990 chunk 2 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 56 optimal weight: 20.0000 chunk 12 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 0 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.069841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.058435 restraints weight = 20755.428| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 3.09 r_work: 0.3041 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 6028 Z= 0.240 Angle : 0.782 7.706 8431 Z= 0.443 Chirality : 0.049 0.334 960 Planarity : 0.005 0.037 848 Dihedral : 27.242 174.762 1358 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 10.10 % Allowed : 31.31 % Favored : 58.59 % 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: -1.41 (0.36), residues: 527 helix: -0.85 (0.34), residues: 190 sheet: -0.18 (0.43), residues: 166 loop : -1.56 (0.47), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 34 TYR 0.019 0.002 TYR C 51 PHE 0.017 0.002 PHE B 58 TRP 0.019 0.004 TRP B 115 HIS 0.007 0.002 HIS D 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.24 ( 6028) covalent geometry : angle 0.78182 / 0.44 ( 8431) hydrogen bonds : bond 0.06813 / 3.97 ( 258) hydrogen bonds : angle 6.25675 / 4.27 ( 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 166 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 116 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 11 ASP cc_start: 0.8342 (t0) cc_final: 0.7921 (p0) REVERT: D 100 ASP cc_start: 0.8950 (t0) cc_final: 0.8719 (t0) REVERT: D 116 ASP cc_start: 0.7683 (t0) cc_final: 0.7397 (t0) REVERT: B 30 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8274 (pp) REVERT: B 43 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.7833 (mtt-85) REVERT: B 110 ASP cc_start: 0.9231 (p0) cc_final: 0.8961 (p0) REVERT: B 118 VAL cc_start: 0.8408 (OUTLIER) cc_final: 0.8078 (m) REVERT: B 128 GLU cc_start: 0.8948 (pt0) cc_final: 0.8565 (pt0) REVERT: C 21 LYS cc_start: 0.8590 (mptt) cc_final: 0.8252 (mmmt) REVERT: C 101 LYS cc_start: 0.7652 (tppp) cc_final: 0.7312 (tppt) REVERT: C 108 GLN cc_start: 0.8649 (mp10) cc_final: 0.8124 (mp10) REVERT: A 98 LYS cc_start: 0.9394 (mtmm) cc_final: 0.9027 (mtmm) REVERT: A 110 ASP cc_start: 0.9007 (p0) cc_final: 0.8653 (p0) outliers start: 50 outliers final: 31 residues processed: 154 average time/residue: 0.0710 time to fit residues: 13.8926 Evaluate side-chains 145 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 111 time to evaluate : 0.138 ------------------------------------------------------------------------------- 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 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 B residue 118 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 87 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 14 ASN Chi-restraints excluded: chain A residue 17 SER 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 55 optimal weight: 20.0000 chunk 24 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- 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 = 0.3470 r_free = 0.3470 target = 0.070152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.058787 restraints weight = 20915.649| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 3.10 r_work: 0.3050 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6028 Z= 0.204 Angle : 0.756 7.821 8431 Z= 0.429 Chirality : 0.049 0.340 960 Planarity : 0.004 0.034 848 Dihedral : 27.132 174.305 1356 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 10.10 % Allowed : 31.52 % Favored : 58.38 % 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 (0.44), residues: 163 loop : -1.41 (0.47), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 34 TYR 0.017 0.002 TYR C 51 PHE 0.012 0.002 PHE D 52 TRP 0.018 0.003 TRP B 115 HIS 0.006 0.002 HIS A 0 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.20 ( 6028) covalent geometry : angle 0.75586 / 0.43 ( 8431) hydrogen bonds : bond 0.06557 / 3.82 ( 258) hydrogen bonds : angle 6.00976 / 4.11 ( 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 163 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 113 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 11 ASP cc_start: 0.8361 (t0) cc_final: 0.8002 (p0) REVERT: D 106 ILE cc_start: 0.8247 (OUTLIER) cc_final: 0.8000 (mp) REVERT: D 116 ASP cc_start: 0.7616 (t0) cc_final: 0.7305 (t0) REVERT: D 124 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8686 (pp) REVERT: D 128 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7914 (tm-30) REVERT: B 30 ILE cc_start: 0.8718 (OUTLIER) cc_final: 0.8286 (pp) REVERT: B 43 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.7764 (mtt-85) REVERT: B 100 ASP cc_start: 0.8222 (m-30) cc_final: 0.7930 (m-30) REVERT: B 110 ASP cc_start: 0.9266 (p0) cc_final: 0.9003 (p0) REVERT: B 118 VAL cc_start: 0.8332 (OUTLIER) cc_final: 0.8120 (m) REVERT: B 128 GLU cc_start: 0.8972 (pt0) cc_final: 0.8541 (pt0) REVERT: C 21 LYS cc_start: 0.8625 (mptt) cc_final: 0.8287 (mmmt) REVERT: C 101 LYS cc_start: 0.7453 (tppp) cc_final: 0.7078 (tptp) REVERT: C 102 GLU cc_start: 0.8367 (mp0) cc_final: 0.8148 (mp0) REVERT: C 108 GLN cc_start: 0.8646 (mp10) cc_final: 0.8230 (mp10) REVERT: C 117 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.7868 (ptpp) REVERT: A 33 ASN cc_start: 0.8715 (OUTLIER) cc_final: 0.8407 (p0) REVERT: A 98 LYS cc_start: 0.9389 (mtmm) cc_final: 0.9021 (mtmm) REVERT: A 110 ASP cc_start: 0.9004 (p0) cc_final: 0.8550 (p0) outliers start: 50 outliers final: 31 residues processed: 147 average time/residue: 0.0658 time to fit residues: 12.2069 Evaluate side-chains 149 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 111 time to evaluate : 0.110 ------------------------------------------------------------------------------- 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 106 ILE 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 54 THR 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 103 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 B residue 137 MET Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 41 GLU 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 0 HIS Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 41 GLU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 34 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 1 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 chunk 22 optimal weight: 8.9990 chunk 57 optimal weight: 20.0000 chunk 43 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.3493 r_free = 0.3493 target = 0.071043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.059730 restraints weight = 21053.134| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 3.15 r_work: 0.3074 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6028 Z= 0.160 Angle : 0.721 8.256 8431 Z= 0.408 Chirality : 0.048 0.341 960 Planarity : 0.004 0.036 848 Dihedral : 27.022 172.612 1354 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 : 7.68 % Allowed : 33.33 % 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: -1.02 (0.37), residues: 527 helix: -0.45 (0.36), residues: 191 sheet: -0.05 (0.44), residues: 163 loop : -1.34 (0.48), residues: 173 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 0.035 0.002 PHE B 58 TRP 0.016 0.003 TRP A 115 HIS 0.004 0.001 HIS A 0 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.16 ( 6028) covalent geometry : angle 0.72051 / 0.41 ( 8431) hydrogen bonds : bond 0.06211 / 3.56 ( 258) hydrogen bonds : angle 5.80275 / 3.98 ( 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: 38 poor density : 118 time to evaluate : 0.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 11 ASP cc_start: 0.8368 (t0) cc_final: 0.7993 (p0) REVERT: D 43 ARG cc_start: 0.8114 (mtt90) cc_final: 0.7858 (mtt-85) REVERT: D 106 ILE cc_start: 0.8286 (OUTLIER) cc_final: 0.8068 (mp) REVERT: D 116 ASP cc_start: 0.7459 (t0) cc_final: 0.7154 (t0) REVERT: B 30 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8232 (pp) REVERT: B 43 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.7784 (mtt-85) REVERT: B 100 ASP cc_start: 0.8175 (m-30) cc_final: 0.7934 (m-30) REVERT: B 110 ASP cc_start: 0.9276 (p0) cc_final: 0.8986 (p0) REVERT: B 128 GLU cc_start: 0.8991 (pt0) cc_final: 0.8437 (pt0) REVERT: C 21 LYS cc_start: 0.8601 (mptt) cc_final: 0.8258 (mmmt) REVERT: C 30 ILE cc_start: 0.7643 (OUTLIER) cc_final: 0.7436 (pp) REVERT: C 43 ARG cc_start: 0.8558 (mtt90) cc_final: 0.8290 (mtt90) REVERT: C 101 LYS cc_start: 0.7495 (tppp) cc_final: 0.7081 (tppt) REVERT: C 102 GLU cc_start: 0.8401 (mp0) cc_final: 0.8095 (mp0) REVERT: C 108 GLN cc_start: 0.8614 (mp10) cc_final: 0.8156 (mp10) REVERT: C 117 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.7834 (ptpp) REVERT: A 33 ASN cc_start: 0.8653 (OUTLIER) cc_final: 0.8368 (p0) REVERT: A 98 LYS cc_start: 0.9404 (mtmm) cc_final: 0.9048 (mtmm) REVERT: A 110 ASP cc_start: 0.9001 (p0) cc_final: 0.8571 (p0) outliers start: 38 outliers final: 24 residues processed: 146 average time/residue: 0.0675 time to fit residues: 12.4443 Evaluate side-chains 141 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 0.183 ------------------------------------------------------------------------------- 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 106 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 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 133 VAL 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 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 117 LYS Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 93 LEU 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: 10.0000 chunk 27 optimal weight: 0.0970 chunk 26 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 53 optimal weight: 20.0000 chunk 9 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 0 HIS B 53 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.068512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.057263 restraints weight = 21048.207| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 3.07 r_work: 0.3014 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 6028 Z= 0.279 Angle : 0.807 6.944 8431 Z= 0.448 Chirality : 0.050 0.352 960 Planarity : 0.005 0.051 848 Dihedral : 27.193 172.115 1354 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 18.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 8.69 % Allowed : 32.32 % 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: -1.08 (0.36), residues: 527 helix: -0.37 (0.36), residues: 191 sheet: 0.02 (0.46), residues: 140 loop : -1.49 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 136 TYR 0.024 0.002 TYR C 51 PHE 0.020 0.002 PHE A 36 TRP 0.018 0.004 TRP A 115 HIS 0.006 0.002 HIS D 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00613 / 0.28 ( 6028) covalent geometry : angle 0.80678 / 0.45 ( 8431) hydrogen bonds : bond 0.07016 / 4.12 ( 258) hydrogen bonds : angle 6.03232 / 4.11 ( 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 157 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 114 time to evaluate : 0.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 11 ASP cc_start: 0.8398 (t0) cc_final: 0.7987 (p0) REVERT: D 21 LYS cc_start: 0.8789 (mptt) cc_final: 0.8553 (tptm) REVERT: D 34 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.7997 (ttp-170) REVERT: D 102 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7123 (mm-30) REVERT: D 106 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8161 (mp) REVERT: D 116 ASP cc_start: 0.7704 (t0) cc_final: 0.7382 (t0) REVERT: D 133 VAL cc_start: 0.9273 (t) cc_final: 0.9032 (m) REVERT: B 43 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.7701 (mtt-85) REVERT: B 100 ASP cc_start: 0.8236 (m-30) cc_final: 0.7871 (m-30) REVERT: B 110 ASP cc_start: 0.9267 (p0) cc_final: 0.8858 (p0) REVERT: B 128 GLU cc_start: 0.9044 (pt0) cc_final: 0.8729 (pt0) REVERT: C 21 LYS cc_start: 0.8753 (mptt) cc_final: 0.8432 (mmmt) REVERT: C 101 LYS cc_start: 0.7712 (tppp) cc_final: 0.7423 (tppt) REVERT: C 102 GLU cc_start: 0.8452 (mp0) cc_final: 0.8053 (mp0) REVERT: C 108 GLN cc_start: 0.8733 (mp10) cc_final: 0.8478 (mm110) REVERT: C 117 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8082 (pttm) REVERT: A 33 ASN cc_start: 0.8771 (OUTLIER) cc_final: 0.8415 (p0) REVERT: A 110 ASP cc_start: 0.9076 (p0) cc_final: 0.8628 (p0) outliers start: 43 outliers final: 28 residues processed: 151 average time/residue: 0.0738 time to fit residues: 13.9713 Evaluate side-chains 145 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 111 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain B residue 27 ASP 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 2 LEU Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 41 GLU 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 18 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 54 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 48 optimal weight: 7.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.3477 r_free = 0.3477 target = 0.070253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.058943 restraints weight = 21293.380| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 3.12 r_work: 0.3057 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6028 Z= 0.169 Angle : 0.733 7.400 8431 Z= 0.415 Chirality : 0.047 0.353 960 Planarity : 0.004 0.032 848 Dihedral : 27.015 171.593 1352 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.97 % Favored : 91.84 % Rotamer: Outliers : 7.27 % Allowed : 33.74 % 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: -0.92 (0.37), residues: 527 helix: -0.25 (0.37), residues: 192 sheet: 0.15 (0.46), residues: 139 loop : -1.42 (0.43), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 136 TYR 0.023 0.002 TYR C 51 PHE 0.035 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 0.00348 / 0.17 ( 6028) covalent geometry : angle 0.73265 / 0.41 ( 8431) hydrogen bonds : bond 0.06135 / 3.51 ( 258) hydrogen bonds : angle 5.69666 / 3.92 ( 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 156 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 120 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 11 ASP cc_start: 0.8376 (t0) cc_final: 0.7945 (p0) REVERT: D 21 LYS cc_start: 0.8816 (mptt) cc_final: 0.8548 (tptp) REVERT: D 34 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.7979 (ttp-170) REVERT: D 43 ARG cc_start: 0.8115 (mtt90) cc_final: 0.7847 (mtt-85) REVERT: D 102 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6913 (mm-30) REVERT: D 116 ASP cc_start: 0.7546 (t0) cc_final: 0.7172 (t0) REVERT: D 124 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8643 (pp) REVERT: D 133 VAL cc_start: 0.9228 (t) cc_final: 0.8975 (m) REVERT: B 30 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8266 (pp) REVERT: B 43 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.7719 (mtt-85) REVERT: B 100 ASP cc_start: 0.8221 (m-30) cc_final: 0.7958 (m-30) REVERT: B 110 ASP cc_start: 0.9257 (p0) cc_final: 0.8841 (p0) REVERT: B 128 GLU cc_start: 0.9059 (pt0) cc_final: 0.8707 (pt0) REVERT: C 21 LYS cc_start: 0.8696 (mptt) cc_final: 0.8376 (mmmt) REVERT: C 101 LYS cc_start: 0.7594 (tppp) cc_final: 0.7261 (tppt) REVERT: C 102 GLU cc_start: 0.8466 (mp0) cc_final: 0.8134 (mp0) REVERT: C 108 GLN cc_start: 0.8774 (mp10) cc_final: 0.8425 (mm110) REVERT: C 117 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.7762 (ptpp) REVERT: A 33 ASN cc_start: 0.8674 (OUTLIER) cc_final: 0.8402 (p0) REVERT: A 98 LYS cc_start: 0.9438 (mtmm) cc_final: 0.8948 (mtmm) REVERT: A 110 ASP cc_start: 0.9053 (p0) cc_final: 0.8631 (p0) REVERT: A 113 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7856 (mm-30) outliers start: 36 outliers final: 22 residues processed: 148 average time/residue: 0.0744 time to fit residues: 13.7739 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 : 0.131 ------------------------------------------------------------------------------- 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 34 ARG 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 124 LEU Chi-restraints excluded: chain B residue 14 ASN 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 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 33 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 17 optimal weight: 0.7980 chunk 19 optimal weight: 0.3980 chunk 3 optimal weight: 8.9990 chunk 40 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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** A 122 GLN 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 = 0.071017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.059668 restraints weight = 21076.489| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 3.14 r_work: 0.3075 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6028 Z= 0.158 Angle : 0.744 7.664 8431 Z= 0.418 Chirality : 0.047 0.353 960 Planarity : 0.004 0.031 848 Dihedral : 27.004 169.602 1350 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 6.46 % Allowed : 35.56 % Favored : 57.98 % 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: -0.84 (0.37), residues: 527 helix: -0.14 (0.38), residues: 191 sheet: 0.28 (0.45), residues: 150 loop : -1.59 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 136 TYR 0.021 0.001 TYR C 51 PHE 0.010 0.001 PHE C 48 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 0.00322 / 0.16 ( 6028) covalent geometry : angle 0.74408 / 0.42 ( 8431) hydrogen bonds : bond 0.06036 / 3.44 ( 258) hydrogen bonds : angle 5.56330 / 3.84 ( 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 153 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 11 ASP cc_start: 0.8315 (t0) cc_final: 0.7966 (p0) REVERT: D 21 LYS cc_start: 0.8826 (mptt) cc_final: 0.8553 (tptp) REVERT: D 43 ARG cc_start: 0.8141 (mtt90) cc_final: 0.7884 (mtt-85) REVERT: D 116 ASP cc_start: 0.7407 (t0) cc_final: 0.7147 (t0) REVERT: B 30 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8233 (pp) REVERT: B 43 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.7757 (mtt-85) REVERT: B 99 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7992 (mp) REVERT: B 100 ASP cc_start: 0.8173 (m-30) cc_final: 0.7907 (m-30) REVERT: B 110 ASP cc_start: 0.9257 (p0) cc_final: 0.8995 (p0) REVERT: B 128 GLU cc_start: 0.9012 (pt0) cc_final: 0.8703 (pt0) REVERT: C 21 LYS cc_start: 0.8641 (mptt) cc_final: 0.8338 (mmmt) REVERT: C 43 ARG cc_start: 0.8415 (mtt90) cc_final: 0.7911 (mtt-85) REVERT: C 101 LYS cc_start: 0.7582 (tppp) cc_final: 0.7261 (tppt) REVERT: C 102 GLU cc_start: 0.8456 (mp0) cc_final: 0.8111 (mp0) REVERT: C 108 GLN cc_start: 0.8707 (mp10) cc_final: 0.8420 (mm110) REVERT: C 117 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.7752 (ptpp) REVERT: A 33 ASN cc_start: 0.8613 (OUTLIER) cc_final: 0.8339 (p0) REVERT: A 98 LYS cc_start: 0.9447 (mtmm) cc_final: 0.8946 (mtmm) REVERT: A 106 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8106 (pt) REVERT: A 110 ASP cc_start: 0.9014 (p0) cc_final: 0.8600 (p0) REVERT: A 113 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7741 (mm-30) outliers start: 32 outliers final: 21 residues processed: 144 average time/residue: 0.0676 time to fit residues: 12.1414 Evaluate side-chains 144 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 0.110 ------------------------------------------------------------------------------- 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 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 99 LEU 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 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 1 MET Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 33 ASN 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: 7.9990 chunk 54 optimal weight: 20.0000 chunk 25 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 57 optimal weight: 20.0000 chunk 19 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- 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 = 0.3467 r_free = 0.3467 target = 0.069646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.058184 restraints weight = 21386.998| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 3.16 r_work: 0.3043 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6028 Z= 0.209 Angle : 0.777 8.463 8431 Z= 0.435 Chirality : 0.048 0.361 960 Planarity : 0.005 0.043 848 Dihedral : 27.042 168.930 1348 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 6.26 % Allowed : 36.16 % Favored : 57.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.37), residues: 527 helix: -0.18 (0.37), residues: 192 sheet: 0.17 (0.45), residues: 149 loop : -1.54 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 136 TYR 0.022 0.002 TYR C 51 PHE 0.034 0.002 PHE B 58 TRP 0.014 0.003 TRP B 115 HIS 0.004 0.002 HIS D 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.21 ( 6028) covalent geometry : angle 0.77677 / 0.44 ( 8431) hydrogen bonds : bond 0.06305 / 3.63 ( 258) hydrogen bonds : angle 5.63846 / 3.87 ( 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 147 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 116 time to evaluate : 0.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 21 LYS cc_start: 0.8856 (mptt) cc_final: 0.8580 (tptm) REVERT: D 34 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.7954 (ttp-170) REVERT: D 43 ARG cc_start: 0.8162 (mtt90) cc_final: 0.7857 (mtt-85) REVERT: D 116 ASP cc_start: 0.7672 (t0) cc_final: 0.7370 (t0) REVERT: B 30 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8229 (pp) REVERT: B 43 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.7716 (mtt-85) REVERT: B 100 ASP cc_start: 0.8260 (m-30) cc_final: 0.7880 (m-30) REVERT: B 110 ASP cc_start: 0.9251 (p0) cc_final: 0.8996 (p0) REVERT: B 128 GLU cc_start: 0.9047 (pt0) cc_final: 0.8616 (pt0) REVERT: C 21 LYS cc_start: 0.8703 (mptt) cc_final: 0.8401 (mmmt) REVERT: C 101 LYS cc_start: 0.7654 (tppp) cc_final: 0.7348 (tppt) REVERT: C 102 GLU cc_start: 0.8506 (mp0) cc_final: 0.8159 (mp0) REVERT: C 117 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.7737 (ptpp) REVERT: A 33 ASN cc_start: 0.8732 (OUTLIER) cc_final: 0.8434 (p0) REVERT: A 98 LYS cc_start: 0.9457 (mtmm) cc_final: 0.9044 (mtmm) REVERT: A 106 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8160 (pt) REVERT: A 110 ASP cc_start: 0.9069 (p0) cc_final: 0.8640 (p0) REVERT: A 113 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7819 (mm-30) outliers start: 31 outliers final: 24 residues processed: 142 average time/residue: 0.0685 time to fit residues: 12.2440 Evaluate side-chains 144 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 0.133 ------------------------------------------------------------------------------- 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 34 ARG 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 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 99 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 16 ILE Chi-restraints excluded: chain C residue 41 GLU 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 30 ILE Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 50 SER 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: 0.8980 chunk 12 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 25 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 54 optimal weight: 20.0000 chunk 31 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 51 optimal weight: 8.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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 = 0.3485 r_free = 0.3485 target = 0.070440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.058919 restraints weight = 21460.902| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 3.18 r_work: 0.3061 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6028 Z= 0.176 Angle : 0.768 8.906 8431 Z= 0.431 Chirality : 0.047 0.358 960 Planarity : 0.004 0.036 848 Dihedral : 26.962 168.741 1348 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 6.26 % Allowed : 35.76 % Favored : 57.98 % 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: -0.88 (0.36), residues: 527 helix: -0.21 (0.37), residues: 193 sheet: 0.27 (0.45), residues: 149 loop : -1.59 (0.43), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 136 TYR 0.021 0.002 TYR C 51 PHE 0.012 0.001 PHE C 26 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 0.00373 / 0.18 ( 6028) covalent geometry : angle 0.76843 / 0.43 ( 8431) hydrogen bonds : bond 0.06059 / 3.46 ( 258) hydrogen bonds : angle 5.53186 / 3.81 ( 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 147 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 116 time to evaluate : 0.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 11 ASP cc_start: 0.8218 (t0) cc_final: 0.7852 (p0) REVERT: D 21 LYS cc_start: 0.8864 (mptt) cc_final: 0.8581 (tptp) REVERT: D 34 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.7940 (ttp-170) REVERT: D 43 ARG cc_start: 0.8158 (mtt90) cc_final: 0.7886 (mtt-85) REVERT: D 116 ASP cc_start: 0.7694 (t0) cc_final: 0.7406 (t0) REVERT: B 30 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8225 (pp) REVERT: B 43 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.7696 (mtt-85) REVERT: B 100 ASP cc_start: 0.8218 (m-30) cc_final: 0.7840 (m-30) REVERT: B 110 ASP cc_start: 0.9253 (p0) cc_final: 0.8997 (p0) REVERT: B 122 GLN cc_start: 0.8550 (mm-40) cc_final: 0.8273 (mm-40) REVERT: B 128 GLU cc_start: 0.9018 (pt0) cc_final: 0.8678 (pt0) REVERT: C 21 LYS cc_start: 0.8697 (mptt) cc_final: 0.8394 (mmmt) REVERT: C 101 LYS cc_start: 0.7605 (tppp) cc_final: 0.7329 (tppt) REVERT: C 102 GLU cc_start: 0.8502 (mp0) cc_final: 0.8152 (mp0) REVERT: C 117 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.7737 (ptpp) REVERT: A 33 ASN cc_start: 0.8659 (OUTLIER) cc_final: 0.8378 (p0) REVERT: A 98 LYS cc_start: 0.9451 (mtmm) cc_final: 0.8962 (mtmm) REVERT: A 106 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8117 (pt) REVERT: A 110 ASP cc_start: 0.9059 (p0) cc_final: 0.8662 (p0) REVERT: A 113 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7750 (mm-30) REVERT: A 121 GLU cc_start: 0.9131 (mm-30) cc_final: 0.8578 (mt-10) outliers start: 31 outliers final: 23 residues processed: 141 average time/residue: 0.0919 time to fit residues: 16.1568 Evaluate side-chains 142 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 113 time to evaluate : 0.196 ------------------------------------------------------------------------------- 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 34 ARG 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 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 99 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 16 ILE Chi-restraints excluded: chain C residue 41 GLU 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 30 ILE Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 50 SER 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 24 optimal weight: 0.0970 chunk 30 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 54 optimal weight: 20.0000 chunk 12 optimal weight: 0.4980 chunk 33 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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 = 0.3493 r_free = 0.3493 target = 0.070793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.059368 restraints weight = 20792.968| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 3.14 r_work: 0.3074 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3974 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= 0.167 Angle : 0.767 8.868 8431 Z= 0.429 Chirality : 0.047 0.360 960 Planarity : 0.004 0.052 848 Dihedral : 26.938 167.367 1348 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 5.86 % Allowed : 35.76 % Favored : 58.38 % 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: -0.90 (0.36), residues: 527 helix: -0.20 (0.37), residues: 196 sheet: 0.24 (0.43), residues: 159 loop : -1.74 (0.43), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 136 TYR 0.021 0.002 TYR C 51 PHE 0.035 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 0.00355 / 0.17 ( 6028) covalent geometry : angle 0.76683 / 0.43 ( 8431) hydrogen bonds : bond 0.05999 / 3.42 ( 258) hydrogen bonds : angle 5.44808 / 3.75 ( 661) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1174.95 seconds wall clock time: 20 minutes 50.44 seconds (1250.44 seconds total)