Starting phenix.real_space_refine on Tue Feb 3 19:16:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kyb_62643/02_2026/9kyb_62643.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kyb_62643/02_2026/9kyb_62643.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kyb_62643/02_2026/9kyb_62643.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kyb_62643/02_2026/9kyb_62643.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kyb_62643/02_2026/9kyb_62643.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kyb_62643/02_2026/9kyb_62643.map" } resolution = 2.32 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= -0.002 sd= 0.084 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 4072 2.51 5 N 1053 2.21 5 O 1370 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6523 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 1786 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 225, 1780 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 11, 'TRANS': 213} Conformer: "B" Number of residues, atoms: 225, 1780 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 11, 'TRANS': 213} bond proxies already assigned to first conformer: 1814 Chain: "C" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 932 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 5, 'TRANS': 113} Chain: "D" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 932 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 5, 'TRANS': 113} Chain: "E" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 932 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 5, 'TRANS': 113} Chain: "F" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 902 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "G" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 902 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "E" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "G" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ACYS B 194 " occ=0.37 ... (10 atoms not shown) pdb=" SG BCYS B 194 " occ=0.63 Time building chain proxies: 1.34, per 1000 atoms: 0.21 Number of scatterers: 6523 At special positions: 0 Unit cell: (74.88, 79.04, 93.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 1370 8.00 N 1053 7.00 C 4072 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG ACYS B 194 " distance=2.04 Simple disulfide: pdb=" SG CYS C 32 " - pdb=" SG CYS C 49 " distance=2.09 Simple disulfide: pdb=" SG CYS C 107 " - pdb=" SG CYS C 113 " distance=1.99 Simple disulfide: pdb=" SG CYS D 32 " - pdb=" SG CYS D 49 " distance=2.03 Simple disulfide: pdb=" SG CYS D 107 " - pdb=" SG CYS D 113 " distance=2.03 Simple disulfide: pdb=" SG CYS E 32 " - pdb=" SG CYS E 49 " distance=2.03 Simple disulfide: pdb=" SG CYS E 107 " - pdb=" SG CYS E 113 " distance=2.03 Simple disulfide: pdb=" SG CYS F 31 " - pdb=" SG CYS F 47 " distance=2.13 Simple disulfide: pdb=" SG CYS F 105 " - pdb=" SG CYS F 110 " distance=2.04 Simple disulfide: pdb=" SG CYS G 31 " - pdb=" SG CYS G 47 " distance=2.03 Simple disulfide: pdb=" SG CYS G 105 " - pdb=" SG CYS G 110 " distance=2.13 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: 0.56 Conformation dependent library (CDL) restraints added in 220.4 milliseconds 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1516 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 4 sheets defined 24.9% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'B' and resid 16 through 24 Processing helix chain 'B' and resid 33 through 39 Processing helix chain 'B' and resid 58 through 72 removed outlier: 3.550A pdb=" N THR B 62 " --> pdb=" O ASP B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 103 Processing helix chain 'B' and resid 108 through 119 Processing helix chain 'B' and resid 128 through 130 No H-bonds generated for 'chain 'B' and resid 128 through 130' Processing helix chain 'B' and resid 194 through 200 removed outlier: 6.348A pdb=" N ILE B 197 " --> pdb=" O ACYS B 194 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N TYR B 198 " --> pdb=" O PHE B 195 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL B 200 " --> pdb=" O ILE B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 228 Processing helix chain 'C' and resid 57 through 59 No H-bonds generated for 'chain 'C' and resid 57 through 59' Processing helix chain 'C' and resid 60 through 75 Processing helix chain 'C' and resid 89 through 96 Processing helix chain 'D' and resid 57 through 59 No H-bonds generated for 'chain 'D' and resid 57 through 59' Processing helix chain 'D' and resid 60 through 74 Processing helix chain 'D' and resid 89 through 96 Processing helix chain 'E' and resid 57 through 59 No H-bonds generated for 'chain 'E' and resid 57 through 59' Processing helix chain 'E' and resid 60 through 75 Processing helix chain 'E' and resid 89 through 96 Processing helix chain 'F' and resid 58 through 73 Processing helix chain 'F' and resid 87 through 94 Processing helix chain 'G' and resid 58 through 73 Processing helix chain 'G' and resid 87 through 94 Processing sheet with id=AA1, first strand: chain 'B' and resid 9 through 13 removed outlier: 7.279A pdb=" N LEU B 79 " --> pdb=" O ALA B 137 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ALA B 137 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ARG B 81 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ALA B 135 " --> pdb=" O ARG B 81 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LYS B 83 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N GLN B 133 " --> pdb=" O ILE B 154 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ILE B 154 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ALA B 135 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER B 152 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ALA B 137 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASP B 141 " --> pdb=" O GLN B 146 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN B 146 " --> pdb=" O ASP B 141 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA3, first strand: chain 'B' and resid 191 through 192 Processing sheet with id=AA4, first strand: chain 'C' and resid 10 through 25 removed outlier: 5.429A pdb=" N ILE C 17 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL C 36 " --> pdb=" O ILE C 17 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 46 through 51 current: chain 'C' and resid 100 through 106 removed outlier: 8.487A pdb=" N VAL C 102 " --> pdb=" O GLN D 24 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN D 24 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N PHE D 20 " --> pdb=" O SER C 106 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ILE D 17 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL D 36 " --> pdb=" O ILE D 17 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 46 through 51 current: chain 'D' and resid 100 through 106 removed outlier: 8.464A pdb=" N VAL D 102 " --> pdb=" O GLN E 24 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN E 24 " --> pdb=" O VAL D 102 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N PHE E 20 " --> pdb=" O SER D 106 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LYS E 34 " --> pdb=" O SER E 18 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N PHE E 20 " --> pdb=" O CYS E 32 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N CYS E 32 " --> pdb=" O PHE E 20 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL E 22 " --> pdb=" O TYR E 30 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N TYR E 30 " --> pdb=" O VAL E 22 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLN E 24 " --> pdb=" O GLY E 28 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N GLY E 28 " --> pdb=" O GLN E 24 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 46 through 51 current: chain 'E' and resid 100 through 106 removed outlier: 8.488A pdb=" N VAL E 102 " --> pdb=" O GLN F 23 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN F 23 " --> pdb=" O VAL E 102 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N PHE F 19 " --> pdb=" O SER E 106 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ILE F 16 " --> pdb=" O VAL F 35 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL F 35 " --> pdb=" O ILE F 16 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 44 through 49 current: chain 'F' and resid 98 through 104 removed outlier: 8.650A pdb=" N VAL F 100 " --> pdb=" O GLN G 23 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN G 23 " --> pdb=" O VAL F 100 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N PHE G 19 " --> pdb=" O SER F 104 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ILE G 16 " --> pdb=" O VAL G 35 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL G 35 " --> pdb=" O ILE G 16 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 44 through 49 current: chain 'G' and resid 98 through 104 216 hydrogen bonds defined for protein. 606 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.74 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1037 1.27 - 1.41: 1812 1.41 - 1.54: 3640 1.54 - 1.68: 39 1.68 - 1.82: 32 Bond restraints: 6560 Sorted by residual: bond pdb=" C ILE F 32 " pdb=" O ILE F 32 " ideal model delta sigma weight residual 1.235 1.145 0.090 1.05e-02 9.07e+03 7.36e+01 bond pdb=" C ILE F 45 " pdb=" O ILE F 45 " ideal model delta sigma weight residual 1.237 1.146 0.091 1.07e-02 8.73e+03 7.18e+01 bond pdb=" C SER C 50 " pdb=" O SER C 50 " ideal model delta sigma weight residual 1.234 1.141 0.093 1.11e-02 8.12e+03 7.05e+01 bond pdb=" C LYS F 33 " pdb=" O LYS F 33 " ideal model delta sigma weight residual 1.236 1.135 0.101 1.20e-02 6.94e+03 7.04e+01 bond pdb=" C LYS C 34 " pdb=" O LYS C 34 " ideal model delta sigma weight residual 1.236 1.143 0.093 1.14e-02 7.69e+03 6.66e+01 ... (remaining 6555 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 8720 2.52 - 5.04: 172 5.04 - 7.56: 27 7.56 - 10.08: 0 10.08 - 12.61: 2 Bond angle restraints: 8921 Sorted by residual: angle pdb=" C SER G 106 " pdb=" N THR G 107 " pdb=" CA THR G 107 " ideal model delta sigma weight residual 121.54 134.15 -12.61 1.91e+00 2.74e-01 4.36e+01 angle pdb=" C THR C 111 " pdb=" N ASP C 112 " pdb=" CA ASP C 112 " ideal model delta sigma weight residual 121.54 133.28 -11.74 1.91e+00 2.74e-01 3.78e+01 angle pdb=" C PRO C 45 " pdb=" CA PRO C 45 " pdb=" CB PRO C 45 " ideal model delta sigma weight residual 111.64 105.33 6.31 1.26e+00 6.30e-01 2.51e+01 angle pdb=" C ASP C 112 " pdb=" N CYS C 113 " pdb=" CA CYS C 113 " ideal model delta sigma weight residual 122.81 115.89 6.92 1.57e+00 4.06e-01 1.94e+01 angle pdb=" C THR C 44 " pdb=" CA THR C 44 " pdb=" CB THR C 44 " ideal model delta sigma weight residual 108.61 102.07 6.54 1.53e+00 4.27e-01 1.82e+01 ... (remaining 8916 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 3287 17.12 - 34.25: 395 34.25 - 51.37: 119 51.37 - 68.49: 26 68.49 - 85.62: 14 Dihedral angle restraints: 3841 sinusoidal: 1469 harmonic: 2372 Sorted by residual: dihedral pdb=" C THR C 44 " pdb=" N THR C 44 " pdb=" CA THR C 44 " pdb=" CB THR C 44 " ideal model delta harmonic sigma weight residual -122.00 -110.58 -11.42 0 2.50e+00 1.60e-01 2.09e+01 dihedral pdb=" C THR G 107 " pdb=" N THR G 107 " pdb=" CA THR G 107 " pdb=" CB THR G 107 " ideal model delta harmonic sigma weight residual -122.00 -133.38 11.38 0 2.50e+00 1.60e-01 2.07e+01 dihedral pdb=" N THR G 107 " pdb=" C THR G 107 " pdb=" CA THR G 107 " pdb=" CB THR G 107 " ideal model delta harmonic sigma weight residual 123.40 133.84 -10.44 0 2.50e+00 1.60e-01 1.75e+01 ... (remaining 3838 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 854 0.088 - 0.176: 94 0.176 - 0.264: 8 0.264 - 0.351: 2 0.351 - 0.439: 2 Chirality restraints: 960 Sorted by residual: chirality pdb=" CA THR G 107 " pdb=" N THR G 107 " pdb=" C THR G 107 " pdb=" CB THR G 107 " both_signs ideal model delta sigma weight residual False 2.53 2.09 0.44 2.00e-01 2.50e+01 4.83e+00 chirality pdb=" CA THR C 44 " pdb=" N THR C 44 " pdb=" C THR C 44 " pdb=" CB THR C 44 " both_signs ideal model delta sigma weight residual False 2.53 2.89 -0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" CB ILE F 32 " pdb=" CA ILE F 32 " pdb=" CG1 ILE F 32 " pdb=" CG2 ILE F 32 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.76e+00 ... (remaining 957 not shown) Planarity restraints: 1149 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER G 103 " 0.015 2.00e-02 2.50e+03 2.90e-02 8.43e+00 pdb=" C SER G 103 " -0.050 2.00e-02 2.50e+03 pdb=" O SER G 103 " 0.019 2.00e-02 2.50e+03 pdb=" N SER G 104 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 108 " -0.013 2.00e-02 2.50e+03 2.64e-02 6.99e+00 pdb=" C SER C 108 " 0.046 2.00e-02 2.50e+03 pdb=" O SER C 108 " -0.018 2.00e-02 2.50e+03 pdb=" N ALA C 109 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 44 " 0.038 5.00e-02 4.00e+02 5.69e-02 5.19e+00 pdb=" N PRO D 45 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO D 45 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 45 " 0.032 5.00e-02 4.00e+02 ... (remaining 1146 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 290 2.70 - 3.25: 6773 3.25 - 3.80: 12764 3.80 - 4.35: 16526 4.35 - 4.90: 25745 Nonbonded interactions: 62098 Sorted by model distance: nonbonded pdb=" N ASP C 39 " pdb=" OD1 ASP C 39 " model vdw 2.153 3.120 nonbonded pdb=" N ASP D 39 " pdb=" OD1 ASP D 39 " model vdw 2.155 3.120 nonbonded pdb=" O SER B 162 " pdb=" OG SER B 162 " model vdw 2.181 3.040 nonbonded pdb=" OD2 ASP E 5 " pdb=" ND2 ASN E 8 " model vdw 2.237 3.120 nonbonded pdb=" O ASP B 185 " pdb=" O HOH B 301 " model vdw 2.272 3.040 ... (remaining 62093 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 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' } 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=0.37 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: 2.690 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.230 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 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 : 0.007 0.102 6571 Z= 0.523 Angle : 0.837 12.822 8943 Z= 0.500 Chirality : 0.058 0.439 960 Planarity : 0.006 0.057 1149 Dihedral : 17.298 85.615 2292 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.50 % Favored : 93.12 % Rotamer: Outliers : 3.53 % Allowed : 22.88 % Favored : 73.59 % Cbeta Deviations : 0.26 % 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: -0.27 (0.28), residues: 803 helix: 0.02 (0.38), residues: 176 sheet: 0.46 (0.30), residues: 228 loop : -0.57 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 26 TYR 0.018 0.001 TYR D 6 PHE 0.030 0.001 PHE C 31 TRP 0.008 0.001 TRP G 55 HIS 0.007 0.001 HIS D 84 Details of bonding type rmsd covalent geometry : bond 0.00720 ( 6560) covalent geometry : angle 0.81419 ( 8921) SS BOND : bond 0.04765 ( 11) SS BOND : angle 3.97533 ( 22) hydrogen bonds : bond 0.14654 ( 216) hydrogen bonds : angle 6.95241 ( 606) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 0.260 Fit side-chains REVERT: C 37 LYS cc_start: 0.7899 (mmtt) cc_final: 0.7660 (mmtm) REVERT: C 66 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7518 (mt-10) REVERT: C 85 ASN cc_start: 0.8179 (m-40) cc_final: 0.7899 (m-40) REVERT: F 36 LYS cc_start: 0.8342 (mmtp) cc_final: 0.8077 (mmtm) outliers start: 25 outliers final: 21 residues processed: 174 average time/residue: 0.4211 time to fit residues: 77.6013 Evaluate side-chains 169 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain G residue 109 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 0.4980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN C 14 HIS D 76 GLN D 94 ASN F 23 GLN F 60 ASN G 25 ASN G 51 HIS G 74 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.145326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.107945 restraints weight = 12774.792| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.72 r_work: 0.2974 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2973 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.0825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6571 Z= 0.153 Angle : 0.572 6.209 8943 Z= 0.309 Chirality : 0.046 0.140 960 Planarity : 0.004 0.049 1149 Dihedral : 7.536 68.507 914 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 3.25 % Allowed : 21.19 % Favored : 75.56 % 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: 0.10 (0.28), residues: 803 helix: 1.06 (0.38), residues: 178 sheet: 0.53 (0.30), residues: 226 loop : -0.62 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 220 TYR 0.014 0.001 TYR E 72 PHE 0.010 0.001 PHE B 225 TRP 0.006 0.001 TRP F 55 HIS 0.006 0.001 HIS D 84 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 6560) covalent geometry : angle 0.57129 ( 8921) SS BOND : bond 0.00233 ( 11) SS BOND : angle 0.82579 ( 22) hydrogen bonds : bond 0.04224 ( 216) hydrogen bonds : angle 4.88348 ( 606) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 0.250 Fit side-chains REVERT: B 33 ASP cc_start: 0.7835 (t70) cc_final: 0.7512 (t70) REVERT: B 181 GLN cc_start: 0.5481 (OUTLIER) cc_final: 0.4892 (mm110) REVERT: B 218 ASP cc_start: 0.9048 (t0) cc_final: 0.8291 (t0) REVERT: C 62 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8430 (mptt) REVERT: E 54 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7864 (tm-30) REVERT: E 62 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8170 (mmtt) outliers start: 23 outliers final: 11 residues processed: 177 average time/residue: 0.4301 time to fit residues: 80.7177 Evaluate side-chains 172 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 157 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 62 LYS Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain G residue 91 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 35 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 58 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN C 14 HIS D 76 GLN D 94 ASN F 51 HIS F 60 ASN G 51 HIS G 74 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.140448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.102454 restraints weight = 8197.421| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.20 r_work: 0.2990 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2839 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2839 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 6571 Z= 0.322 Angle : 0.684 7.775 8943 Z= 0.374 Chirality : 0.053 0.196 960 Planarity : 0.005 0.054 1149 Dihedral : 7.000 66.932 896 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 4.52 % Allowed : 20.34 % Favored : 75.14 % 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: 0.17 (0.27), residues: 803 helix: 1.14 (0.37), residues: 176 sheet: 0.67 (0.30), residues: 226 loop : -0.66 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 69 TYR 0.017 0.002 TYR E 72 PHE 0.014 0.002 PHE B 225 TRP 0.009 0.002 TRP F 55 HIS 0.008 0.002 HIS D 84 Details of bonding type rmsd covalent geometry : bond 0.00708 ( 6560) covalent geometry : angle 0.68140 ( 8921) SS BOND : bond 0.00353 ( 11) SS BOND : angle 1.43495 ( 22) hydrogen bonds : bond 0.05034 ( 216) hydrogen bonds : angle 5.21379 ( 606) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 0.184 Fit side-chains REVERT: B 33 ASP cc_start: 0.7967 (t70) cc_final: 0.7618 (t70) REVERT: B 180 THR cc_start: 0.3749 (OUTLIER) cc_final: 0.3417 (p) REVERT: C 76 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8240 (pt0) REVERT: D 6 TYR cc_start: 0.7844 (p90) cc_final: 0.7513 (p90) REVERT: D 80 ILE cc_start: 0.9488 (OUTLIER) cc_final: 0.9266 (mt) REVERT: E 62 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8170 (mmtt) REVERT: E 75 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8267 (mt-10) REVERT: F 81 GLN cc_start: 0.9029 (tt0) cc_final: 0.8825 (tt0) outliers start: 32 outliers final: 17 residues processed: 179 average time/residue: 0.4313 time to fit residues: 81.7078 Evaluate side-chains 173 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain E residue 62 LYS Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 107 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 58 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 60 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN D 94 ASN F 51 HIS F 60 ASN G 51 HIS G 74 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.144836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.105423 restraints weight = 11623.263| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.87 r_work: 0.2995 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2846 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2846 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6571 Z= 0.151 Angle : 0.562 6.532 8943 Z= 0.304 Chirality : 0.046 0.140 960 Planarity : 0.004 0.050 1149 Dihedral : 6.545 68.925 896 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 3.81 % Allowed : 20.62 % Favored : 75.56 % 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: 0.10 (0.27), residues: 803 helix: 1.18 (0.36), residues: 178 sheet: 0.61 (0.30), residues: 226 loop : -0.75 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 220 TYR 0.011 0.001 TYR B 198 PHE 0.009 0.001 PHE B 187 TRP 0.007 0.001 TRP F 55 HIS 0.005 0.001 HIS D 84 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 6560) covalent geometry : angle 0.56101 ( 8921) SS BOND : bond 0.00182 ( 11) SS BOND : angle 0.99129 ( 22) hydrogen bonds : bond 0.03947 ( 216) hydrogen bonds : angle 4.82221 ( 606) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 0.161 Fit side-chains REVERT: B 33 ASP cc_start: 0.7950 (t70) cc_final: 0.7659 (t70) REVERT: B 181 GLN cc_start: 0.5338 (OUTLIER) cc_final: 0.4903 (mm110) REVERT: B 218 ASP cc_start: 0.9075 (t0) cc_final: 0.8145 (t0) REVERT: C 16 VAL cc_start: 0.9000 (OUTLIER) cc_final: 0.8763 (t) REVERT: C 66 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7971 (mt-10) REVERT: D 6 TYR cc_start: 0.7784 (p90) cc_final: 0.7495 (p90) REVERT: E 54 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7847 (tm-30) REVERT: E 62 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8215 (mmtt) REVERT: F 36 LYS cc_start: 0.8108 (mmmt) cc_final: 0.7760 (mmtm) outliers start: 27 outliers final: 13 residues processed: 178 average time/residue: 0.3889 time to fit residues: 73.1454 Evaluate side-chains 167 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 62 LYS Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 91 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 35 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 60 optimal weight: 0.0010 chunk 56 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 69 optimal weight: 0.0970 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 HIS D 76 GLN D 94 ASN F 51 HIS F 60 ASN F 74 HIS G 51 HIS G 74 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.145434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.106587 restraints weight = 11175.569| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.81 r_work: 0.3020 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2874 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6571 Z= 0.138 Angle : 0.547 6.409 8943 Z= 0.294 Chirality : 0.046 0.139 960 Planarity : 0.004 0.049 1149 Dihedral : 6.316 69.772 896 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 4.52 % Allowed : 20.34 % Favored : 75.14 % 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: 0.11 (0.28), residues: 803 helix: 1.27 (0.36), residues: 178 sheet: 0.58 (0.30), residues: 226 loop : -0.76 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 81 TYR 0.010 0.001 TYR B 198 PHE 0.009 0.001 PHE B 225 TRP 0.007 0.001 TRP F 55 HIS 0.004 0.001 HIS D 84 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 6560) covalent geometry : angle 0.54560 ( 8921) SS BOND : bond 0.00164 ( 11) SS BOND : angle 0.93580 ( 22) hydrogen bonds : bond 0.03719 ( 216) hydrogen bonds : angle 4.71730 ( 606) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 0.166 Fit side-chains REVERT: B 33 ASP cc_start: 0.7992 (t70) cc_final: 0.7699 (t70) REVERT: B 181 GLN cc_start: 0.5316 (OUTLIER) cc_final: 0.4915 (mm110) REVERT: C 80 ILE cc_start: 0.9380 (OUTLIER) cc_final: 0.9095 (mm) REVERT: D 6 TYR cc_start: 0.7826 (p90) cc_final: 0.7551 (p90) REVERT: E 54 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7830 (tm-30) REVERT: E 62 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8255 (mmtt) REVERT: F 92 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8158 (mp0) outliers start: 32 outliers final: 17 residues processed: 177 average time/residue: 0.3871 time to fit residues: 72.5589 Evaluate side-chains 174 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 62 LYS Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 107 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 45 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 HIS D 76 GLN D 94 ASN F 51 HIS F 60 ASN G 51 HIS G 74 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.144288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.106441 restraints weight = 9222.998| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.31 r_work: 0.3048 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2895 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2895 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6571 Z= 0.158 Angle : 0.559 6.515 8943 Z= 0.300 Chirality : 0.046 0.139 960 Planarity : 0.004 0.049 1149 Dihedral : 6.303 69.663 895 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 3.53 % Allowed : 21.05 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.27), residues: 803 helix: 1.30 (0.36), residues: 178 sheet: 0.63 (0.30), residues: 226 loop : -0.71 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 81 TYR 0.011 0.001 TYR G 11 PHE 0.009 0.001 PHE B 225 TRP 0.008 0.001 TRP F 55 HIS 0.005 0.001 HIS E 84 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 6560) covalent geometry : angle 0.55788 ( 8921) SS BOND : bond 0.00193 ( 11) SS BOND : angle 0.97722 ( 22) hydrogen bonds : bond 0.03850 ( 216) hydrogen bonds : angle 4.75984 ( 606) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 0.257 Fit side-chains REVERT: B 33 ASP cc_start: 0.7909 (t70) cc_final: 0.7605 (t70) REVERT: B 181 GLN cc_start: 0.5325 (OUTLIER) cc_final: 0.4965 (mm110) REVERT: C 66 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7944 (mt-10) REVERT: C 80 ILE cc_start: 0.9395 (OUTLIER) cc_final: 0.9071 (mm) REVERT: D 6 TYR cc_start: 0.7815 (p90) cc_final: 0.7553 (p90) REVERT: E 54 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7743 (tm-30) REVERT: E 62 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8188 (mmtt) REVERT: F 92 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8078 (mp0) outliers start: 25 outliers final: 15 residues processed: 173 average time/residue: 0.4194 time to fit residues: 76.5612 Evaluate side-chains 171 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 62 LYS Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain G residue 107 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 34 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 13 optimal weight: 10.0000 chunk 20 optimal weight: 0.3980 chunk 24 optimal weight: 8.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN C 14 HIS D 76 GLN D 94 ASN F 51 HIS F 60 ASN G 51 HIS G 74 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.143697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.104101 restraints weight = 10774.486| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.80 r_work: 0.2983 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2839 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2839 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6571 Z= 0.191 Angle : 0.585 6.868 8943 Z= 0.316 Chirality : 0.047 0.159 960 Planarity : 0.004 0.050 1149 Dihedral : 6.375 69.074 894 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.53 % Allowed : 21.61 % Favored : 74.86 % 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: 0.16 (0.27), residues: 803 helix: 1.25 (0.36), residues: 178 sheet: 0.64 (0.30), residues: 226 loop : -0.71 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 69 TYR 0.013 0.002 TYR G 11 PHE 0.010 0.001 PHE B 225 TRP 0.008 0.002 TRP F 55 HIS 0.006 0.001 HIS D 84 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 6560) covalent geometry : angle 0.58395 ( 8921) SS BOND : bond 0.00191 ( 11) SS BOND : angle 1.03732 ( 22) hydrogen bonds : bond 0.04117 ( 216) hydrogen bonds : angle 4.86389 ( 606) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.266 Fit side-chains REVERT: B 33 ASP cc_start: 0.8007 (t70) cc_final: 0.7726 (t70) REVERT: B 181 GLN cc_start: 0.5305 (OUTLIER) cc_final: 0.4935 (mm110) REVERT: D 6 TYR cc_start: 0.7852 (p90) cc_final: 0.7595 (p90) REVERT: E 54 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7811 (tm-30) REVERT: E 62 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8254 (mmtt) REVERT: F 92 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8188 (mp0) outliers start: 25 outliers final: 16 residues processed: 172 average time/residue: 0.3968 time to fit residues: 72.5632 Evaluate side-chains 172 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 62 LYS Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain G residue 107 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 53 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN C 14 HIS D 94 ASN F 51 HIS F 60 ASN F 74 HIS G 51 HIS G 74 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.143837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.104683 restraints weight = 9764.259| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.41 r_work: 0.3016 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2865 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2865 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6571 Z= 0.189 Angle : 0.587 6.557 8943 Z= 0.317 Chirality : 0.047 0.162 960 Planarity : 0.004 0.051 1149 Dihedral : 6.254 69.115 892 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 3.53 % Allowed : 21.61 % Favored : 74.86 % 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: 0.13 (0.27), residues: 803 helix: 1.22 (0.36), residues: 178 sheet: 0.63 (0.30), residues: 226 loop : -0.74 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 69 TYR 0.015 0.002 TYR G 11 PHE 0.010 0.001 PHE B 225 TRP 0.008 0.002 TRP F 55 HIS 0.006 0.001 HIS D 84 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 6560) covalent geometry : angle 0.58519 ( 8921) SS BOND : bond 0.00222 ( 11) SS BOND : angle 1.19927 ( 22) hydrogen bonds : bond 0.04115 ( 216) hydrogen bonds : angle 4.88105 ( 606) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.166 Fit side-chains REVERT: B 33 ASP cc_start: 0.7912 (t70) cc_final: 0.7574 (t70) REVERT: B 181 GLN cc_start: 0.5289 (OUTLIER) cc_final: 0.4958 (mm110) REVERT: C 85 ASN cc_start: 0.8449 (m-40) cc_final: 0.8145 (m-40) REVERT: D 6 TYR cc_start: 0.7831 (p90) cc_final: 0.7567 (p90) REVERT: E 54 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7776 (tm-30) REVERT: E 62 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8198 (mmtt) REVERT: F 92 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8116 (mp0) outliers start: 25 outliers final: 17 residues processed: 170 average time/residue: 0.3690 time to fit residues: 66.5724 Evaluate side-chains 172 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 62 LYS Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain G residue 107 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 15 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 63 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 28 optimal weight: 0.3980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN C 14 HIS D 94 ASN F 51 HIS F 60 ASN G 51 HIS G 74 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.144811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.104478 restraints weight = 11714.065| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.99 r_work: 0.2995 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2843 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2843 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6571 Z= 0.163 Angle : 0.574 6.497 8943 Z= 0.309 Chirality : 0.047 0.152 960 Planarity : 0.004 0.050 1149 Dihedral : 6.183 69.286 892 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 3.25 % Allowed : 22.32 % Favored : 74.44 % 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: 0.15 (0.27), residues: 803 helix: 1.22 (0.36), residues: 178 sheet: 0.66 (0.30), residues: 226 loop : -0.73 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 81 TYR 0.012 0.001 TYR G 11 PHE 0.011 0.001 PHE C 12 TRP 0.008 0.001 TRP G 55 HIS 0.006 0.001 HIS D 84 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 6560) covalent geometry : angle 0.57197 ( 8921) SS BOND : bond 0.00189 ( 11) SS BOND : angle 1.09641 ( 22) hydrogen bonds : bond 0.03934 ( 216) hydrogen bonds : angle 4.82689 ( 606) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 0.188 Fit side-chains REVERT: B 33 ASP cc_start: 0.7993 (t70) cc_final: 0.7650 (t70) REVERT: B 181 GLN cc_start: 0.5243 (OUTLIER) cc_final: 0.4899 (mm110) REVERT: D 6 TYR cc_start: 0.7835 (p90) cc_final: 0.7550 (p90) REVERT: E 54 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8062 (tt0) REVERT: E 62 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8238 (mmtt) REVERT: F 92 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8150 (mp0) outliers start: 23 outliers final: 17 residues processed: 166 average time/residue: 0.3651 time to fit residues: 64.2392 Evaluate side-chains 171 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 62 LYS Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain G residue 107 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 55 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 20 optimal weight: 20.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 HIS D 94 ASN F 51 HIS F 60 ASN G 25 ASN G 51 HIS G 74 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.144741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.105918 restraints weight = 9431.413| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.38 r_work: 0.3040 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2889 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2889 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6571 Z= 0.169 Angle : 0.580 6.537 8943 Z= 0.312 Chirality : 0.047 0.170 960 Planarity : 0.004 0.051 1149 Dihedral : 6.206 69.198 892 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 2.97 % Allowed : 22.46 % Favored : 74.58 % 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: 0.15 (0.27), residues: 803 helix: 1.23 (0.37), residues: 178 sheet: 0.63 (0.30), residues: 228 loop : -0.72 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 81 TYR 0.014 0.001 TYR G 11 PHE 0.010 0.001 PHE B 225 TRP 0.008 0.001 TRP G 55 HIS 0.006 0.001 HIS D 84 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 6560) covalent geometry : angle 0.57855 ( 8921) SS BOND : bond 0.00197 ( 11) SS BOND : angle 1.09472 ( 22) hydrogen bonds : bond 0.03973 ( 216) hydrogen bonds : angle 4.83580 ( 606) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 0.182 Fit side-chains REVERT: B 33 ASP cc_start: 0.7938 (t70) cc_final: 0.7588 (t70) REVERT: B 181 GLN cc_start: 0.5290 (OUTLIER) cc_final: 0.4867 (mm110) REVERT: D 6 TYR cc_start: 0.7845 (p90) cc_final: 0.7549 (p90) REVERT: E 54 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7983 (tt0) REVERT: E 62 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8196 (mmtt) REVERT: F 92 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8042 (mp0) outliers start: 21 outliers final: 17 residues processed: 163 average time/residue: 0.3748 time to fit residues: 64.6028 Evaluate side-chains 169 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 62 LYS Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain G residue 107 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 31 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 chunk 71 optimal weight: 0.0270 chunk 0 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN D 94 ASN F 51 HIS F 60 ASN G 51 HIS G 74 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.146557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.109847 restraints weight = 7405.664| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.11 r_work: 0.3097 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6571 Z= 0.134 Angle : 0.552 6.493 8943 Z= 0.296 Chirality : 0.046 0.150 960 Planarity : 0.004 0.050 1149 Dihedral : 6.040 69.691 892 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 3.39 % Allowed : 22.03 % Favored : 74.58 % 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: 0.21 (0.28), residues: 803 helix: 1.32 (0.37), residues: 178 sheet: 0.71 (0.30), residues: 226 loop : -0.73 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 81 TYR 0.010 0.001 TYR B 198 PHE 0.012 0.001 PHE C 12 TRP 0.008 0.001 TRP G 55 HIS 0.005 0.001 HIS D 84 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 6560) covalent geometry : angle 0.55045 ( 8921) SS BOND : bond 0.00178 ( 11) SS BOND : angle 1.01213 ( 22) hydrogen bonds : bond 0.03672 ( 216) hydrogen bonds : angle 4.72962 ( 606) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2892.29 seconds wall clock time: 49 minutes 55.73 seconds (2995.73 seconds total)