Starting phenix.real_space_refine on Tue Mar 3 13:56:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p54_71300/03_2026/9p54_71300_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p54_71300/03_2026/9p54_71300.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9p54_71300/03_2026/9p54_71300.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p54_71300/03_2026/9p54_71300.map" model { file = "/net/cci-nas-00/data/ceres_data/9p54_71300/03_2026/9p54_71300_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p54_71300/03_2026/9p54_71300_neut.cif" } resolution = 2.8 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= 0.009 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 34 5.16 5 C 3443 2.51 5 N 927 2.21 5 O 1059 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5463 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 1375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1375 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 7, 'TRANS': 171} Chain breaks: 2 Chain: "D" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1385 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 7, 'TRANS': 172} Chain breaks: 2 Chain: "c" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1357 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain: "d" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1346 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 5, 'TRANS': 170} Chain breaks: 1 Time building chain proxies: 1.45, per 1000 atoms: 0.27 Number of scatterers: 5463 At special positions: 0 Unit cell: (70.8581, 103.335, 106.287, 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 34 16.00 O 1059 8.00 N 927 7.00 C 3443 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: 0.36 Conformation dependent library (CDL) restraints added in 345.3 milliseconds 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1334 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 8 sheets defined 54.6% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'C' and resid 31 through 39 Processing helix chain 'C' and resid 49 through 67 Processing helix chain 'C' and resid 82 through 96 removed outlier: 3.824A pdb=" N ALA C 88 " --> pdb=" O THR C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 119 Processing helix chain 'C' and resid 150 through 173 Processing helix chain 'C' and resid 175 through 185 Processing helix chain 'C' and resid 191 through 197 Processing helix chain 'D' and resid 31 through 39 removed outlier: 3.583A pdb=" N LYS D 35 " --> pdb=" O ASN D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 67 Processing helix chain 'D' and resid 82 through 96 Processing helix chain 'D' and resid 109 through 118 Processing helix chain 'D' and resid 152 through 173 Processing helix chain 'D' and resid 175 through 185 Processing helix chain 'D' and resid 191 through 198 Processing helix chain 'c' and resid 16 through 26 Processing helix chain 'c' and resid 37 through 53 Processing helix chain 'c' and resid 70 through 84 Processing helix chain 'c' and resid 98 through 106 Processing helix chain 'c' and resid 132 through 159 Processing helix chain 'c' and resid 161 through 172 Processing helix chain 'c' and resid 176 through 184 Processing helix chain 'd' and resid 16 through 26 Processing helix chain 'd' and resid 37 through 53 Processing helix chain 'd' and resid 70 through 84 Processing helix chain 'd' and resid 98 through 106 Processing helix chain 'd' and resid 133 through 159 Processing helix chain 'd' and resid 161 through 172 removed outlier: 4.193A pdb=" N ASP d 170 " --> pdb=" O GLU d 166 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG d 171 " --> pdb=" O ALA d 167 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASP d 172 " --> pdb=" O ASP d 168 " (cutoff:3.500A) Processing helix chain 'd' and resid 176 through 184 Processing sheet with id=AA1, first strand: chain 'C' and resid 41 through 44 removed outlier: 6.593A pdb=" N ILE C 72 " --> pdb=" O GLN C 101 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N VAL C 103 " --> pdb=" O ILE C 72 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N MET C 74 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N LEU C 105 " --> pdb=" O MET C 74 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ILE C 76 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N GLN C 107 " --> pdb=" O ILE C 76 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER C 78 " --> pdb=" O GLN C 107 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ALA C 109 " --> pdb=" O SER C 78 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ARG C 131 " --> pdb=" O CYS C 104 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLY C 106 " --> pdb=" O ARG C 131 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU C 133 " --> pdb=" O GLY C 106 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ALA C 108 " --> pdb=" O LEU C 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 41 through 44 removed outlier: 6.593A pdb=" N ILE C 72 " --> pdb=" O GLN C 101 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N VAL C 103 " --> pdb=" O ILE C 72 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N MET C 74 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N LEU C 105 " --> pdb=" O MET C 74 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ILE C 76 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N GLN C 107 " --> pdb=" O ILE C 76 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER C 78 " --> pdb=" O GLN C 107 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ALA C 109 " --> pdb=" O SER C 78 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N MET C 125 " --> pdb=" O ILE C 100 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N THR C 102 " --> pdb=" O MET C 125 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA C 126 " --> pdb=" O THR C 202 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 41 through 44 removed outlier: 8.065A pdb=" N MET D 125 " --> pdb=" O ILE D 100 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N THR D 102 " --> pdb=" O MET D 125 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA D 126 " --> pdb=" O THR D 202 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 107 through 108 removed outlier: 6.444A pdb=" N ALA D 108 " --> pdb=" O LEU D 133 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'c' and resid 29 through 32 removed outlier: 6.275A pdb=" N ILE c 60 " --> pdb=" O ALA c 89 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N TYR c 91 " --> pdb=" O ILE c 60 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU c 62 " --> pdb=" O TYR c 91 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N MET c 93 " --> pdb=" O LEU c 62 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ILE c 64 " --> pdb=" O MET c 93 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N MET c 95 " --> pdb=" O ILE c 64 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'c' and resid 29 through 32 removed outlier: 6.275A pdb=" N ILE c 60 " --> pdb=" O ALA c 89 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N TYR c 91 " --> pdb=" O ILE c 60 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU c 62 " --> pdb=" O TYR c 91 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N MET c 93 " --> pdb=" O LEU c 62 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ILE c 64 " --> pdb=" O MET c 93 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N MET c 95 " --> pdb=" O ILE c 64 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N TYR c 113 " --> pdb=" O ILE c 88 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N THR c 90 " --> pdb=" O TYR c 113 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ARG c 112 " --> pdb=" O HIS c 188 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'd' and resid 29 through 32 removed outlier: 6.392A pdb=" N ILE d 60 " --> pdb=" O ALA d 89 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N TYR d 91 " --> pdb=" O ILE d 60 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU d 62 " --> pdb=" O TYR d 91 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N MET d 93 " --> pdb=" O LEU d 62 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ILE d 64 " --> pdb=" O MET d 93 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N MET d 95 " --> pdb=" O ILE d 64 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'd' and resid 29 through 32 removed outlier: 6.392A pdb=" N ILE d 60 " --> pdb=" O ALA d 89 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N TYR d 91 " --> pdb=" O ILE d 60 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU d 62 " --> pdb=" O TYR d 91 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N MET d 93 " --> pdb=" O LEU d 62 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ILE d 64 " --> pdb=" O MET d 93 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N MET d 95 " --> pdb=" O ILE d 64 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N TYR d 113 " --> pdb=" O ILE d 88 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N THR d 90 " --> pdb=" O TYR d 113 " (cutoff:3.500A) 328 hydrogen bonds defined for protein. 972 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: 0.84 Time building geometry restraints manager: 0.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1179 1.33 - 1.45: 1104 1.45 - 1.57: 3193 1.57 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 5538 Sorted by residual: bond pdb=" CA SER d 72 " pdb=" CB SER d 72 " ideal model delta sigma weight residual 1.528 1.460 0.068 1.59e-02 3.96e+03 1.82e+01 bond pdb=" CA SER c 72 " pdb=" CB SER c 72 " ideal model delta sigma weight residual 1.528 1.461 0.068 1.59e-02 3.96e+03 1.81e+01 bond pdb=" CA SER c 70 " pdb=" CB SER c 70 " ideal model delta sigma weight residual 1.529 1.465 0.064 1.70e-02 3.46e+03 1.41e+01 bond pdb=" CA SER d 70 " pdb=" CB SER d 70 " ideal model delta sigma weight residual 1.529 1.466 0.064 1.70e-02 3.46e+03 1.40e+01 bond pdb=" CA SER c 26 " pdb=" CB SER c 26 " ideal model delta sigma weight residual 1.532 1.471 0.062 1.79e-02 3.12e+03 1.19e+01 ... (remaining 5533 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 5957 1.83 - 3.67: 1386 3.67 - 5.50: 123 5.50 - 7.34: 16 7.34 - 9.17: 2 Bond angle restraints: 7484 Sorted by residual: angle pdb=" CA ARG d 171 " pdb=" CB ARG d 171 " pdb=" CG ARG d 171 " ideal model delta sigma weight residual 114.10 123.27 -9.17 2.00e+00 2.50e-01 2.10e+01 angle pdb=" N GLU d 54 " pdb=" CA GLU d 54 " pdb=" C GLU d 54 " ideal model delta sigma weight residual 112.93 107.02 5.91 1.33e+00 5.65e-01 1.98e+01 angle pdb=" N GLU c 54 " pdb=" CA GLU c 54 " pdb=" C GLU c 54 " ideal model delta sigma weight residual 112.93 107.05 5.88 1.33e+00 5.65e-01 1.95e+01 angle pdb=" N GLU c 27 " pdb=" CA GLU c 27 " pdb=" C GLU c 27 " ideal model delta sigma weight residual 112.88 107.22 5.66 1.29e+00 6.01e-01 1.93e+01 angle pdb=" N GLU d 27 " pdb=" CA GLU d 27 " pdb=" C GLU d 27 " ideal model delta sigma weight residual 112.88 107.23 5.65 1.29e+00 6.01e-01 1.92e+01 ... (remaining 7479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.62: 3153 16.62 - 33.23: 165 33.23 - 49.85: 29 49.85 - 66.46: 37 66.46 - 83.08: 4 Dihedral angle restraints: 3388 sinusoidal: 1326 harmonic: 2062 Sorted by residual: dihedral pdb=" CA PHE D 19 " pdb=" C PHE D 19 " pdb=" N ILE D 20 " pdb=" CA ILE D 20 " ideal model delta harmonic sigma weight residual 180.00 -157.35 -22.65 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" N ARG D 131 " pdb=" CA ARG D 131 " pdb=" CB ARG D 131 " pdb=" CG ARG D 131 " ideal model delta sinusoidal sigma weight residual -180.00 -120.87 -59.13 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB MET c 93 " pdb=" CG MET c 93 " pdb=" SD MET c 93 " pdb=" CE MET c 93 " ideal model delta sinusoidal sigma weight residual -60.00 -1.74 -58.26 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 3385 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 619 0.103 - 0.205: 230 0.205 - 0.307: 25 0.307 - 0.409: 0 0.409 - 0.512: 1 Chirality restraints: 875 Sorted by residual: chirality pdb=" CG LEU D 86 " pdb=" CB LEU D 86 " pdb=" CD1 LEU D 86 " pdb=" CD2 LEU D 86 " both_signs ideal model delta sigma weight residual False -2.59 -2.08 -0.51 2.00e-01 2.50e+01 6.54e+00 chirality pdb=" CA ILE d 30 " pdb=" N ILE d 30 " pdb=" C ILE d 30 " pdb=" CB ILE d 30 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CA ILE c 30 " pdb=" N ILE c 30 " pdb=" C ILE c 30 " pdb=" CB ILE c 30 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 872 not shown) Planarity restraints: 968 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS D 171 " 0.037 2.00e-02 2.50e+03 2.79e-02 1.17e+01 pdb=" CG HIS D 171 " -0.045 2.00e-02 2.50e+03 pdb=" ND1 HIS D 171 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 HIS D 171 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 HIS D 171 " 0.014 2.00e-02 2.50e+03 pdb=" NE2 HIS D 171 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 124 " 0.285 9.50e-02 1.11e+02 1.28e-01 9.99e+00 pdb=" NE ARG D 124 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG D 124 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG D 124 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG D 124 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 40 " -0.281 9.50e-02 1.11e+02 1.26e-01 9.74e+00 pdb=" NE ARG C 40 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG C 40 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG C 40 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 40 " -0.010 2.00e-02 2.50e+03 ... (remaining 965 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 201 2.71 - 3.26: 5509 3.26 - 3.80: 8490 3.80 - 4.35: 11391 4.35 - 4.90: 18358 Nonbonded interactions: 43949 Sorted by model distance: nonbonded pdb=" O ARG d 171 " pdb=" NE ARG d 171 " model vdw 2.161 3.120 nonbonded pdb=" O PHE D 19 " pdb=" OG SER D 30 " model vdw 2.342 3.040 nonbonded pdb=" O SER D 30 " pdb=" OG SER D 30 " model vdw 2.345 3.040 nonbonded pdb=" O SER c 34 " pdb=" OG SER c 66 " model vdw 2.355 3.040 nonbonded pdb=" O SER d 34 " pdb=" OG SER d 66 " model vdw 2.356 3.040 ... (remaining 43944 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' and (resid 16 through 140 or resid 149 through 210)) selection = (chain 'D' and (resid 16 through 140 or resid 149 through 210)) } ncs_group { reference = (chain 'c' and (resid 15 through 129 or resid 132 through 192)) selection = chain 'd' } 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 6.990 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.000 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: 0.010 Load rotamer database and sin/cos tables:6.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 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 : 0.012 0.068 5538 Z= 0.917 Angle : 1.436 9.171 7484 Z= 1.101 Chirality : 0.095 0.512 875 Planarity : 0.012 0.128 968 Dihedral : 13.155 83.080 2054 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.57 % Allowed : 9.57 % Favored : 88.87 % 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: -0.35 (0.29), residues: 695 helix: 0.35 (0.24), residues: 396 sheet: -0.24 (0.63), residues: 63 loop : -1.07 (0.36), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG c 28 TYR 0.008 0.001 TYR c 21 PHE 0.015 0.002 PHE c 185 TRP 0.007 0.002 TRP c 174 HIS 0.006 0.001 HIS D 171 Details of bonding type rmsd covalent geometry : bond 0.01244 ( 5538) covalent geometry : angle 1.43640 ( 7484) hydrogen bonds : bond 0.19342 ( 312) hydrogen bonds : angle 6.80175 ( 972) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 173 time to evaluate : 0.187 Fit side-chains revert: symmetry clash REVERT: C 64 GLU cc_start: 0.8372 (tp30) cc_final: 0.7828 (tp30) REVERT: C 193 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8394 (mt-10) REVERT: C 207 ARG cc_start: 0.7749 (mtt180) cc_final: 0.7167 (mtm110) REVERT: C 208 LYS cc_start: 0.3912 (mmtm) cc_final: 0.2670 (mptt) REVERT: D 38 GLU cc_start: 0.8384 (mt-10) cc_final: 0.8064 (mp0) REVERT: D 46 VAL cc_start: 0.8351 (t) cc_final: 0.7972 (p) REVERT: D 83 PHE cc_start: 0.6619 (t80) cc_final: 0.6127 (t80) REVERT: c 55 ASP cc_start: 0.7675 (t70) cc_final: 0.7126 (t0) REVERT: d 192 ARG cc_start: 0.7513 (ttp-170) cc_final: 0.6044 (ppt170) outliers start: 9 outliers final: 3 residues processed: 177 average time/residue: 0.8562 time to fit residues: 155.6171 Evaluate side-chains 105 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 102 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain c residue 44 LEU Chi-restraints excluded: chain d residue 129 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 ASN C 135 HIS c 188 HIS d 142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.077427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.059794 restraints weight = 15576.839| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 3.92 r_work: 0.2793 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5538 Z= 0.134 Angle : 0.598 8.090 7484 Z= 0.303 Chirality : 0.040 0.133 875 Planarity : 0.005 0.035 968 Dihedral : 4.147 41.132 775 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.13 % Allowed : 19.83 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.32), residues: 695 helix: 2.25 (0.26), residues: 400 sheet: 0.18 (0.63), residues: 60 loop : -0.63 (0.39), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 207 TYR 0.008 0.001 TYR d 91 PHE 0.021 0.002 PHE C 19 TRP 0.004 0.001 TRP d 174 HIS 0.009 0.002 HIS d 123 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 5538) covalent geometry : angle 0.59823 ( 7484) hydrogen bonds : bond 0.04142 ( 312) hydrogen bonds : angle 4.25951 ( 972) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 GLU cc_start: 0.8140 (mp0) cc_final: 0.7896 (mp0) REVERT: C 193 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8329 (mt-10) REVERT: C 208 LYS cc_start: 0.4481 (mmtm) cc_final: 0.2987 (mptt) REVERT: D 46 VAL cc_start: 0.9018 (t) cc_final: 0.8782 (p) REVERT: D 47 GLN cc_start: 0.8663 (mm110) cc_final: 0.8304 (mm110) REVERT: D 64 GLU cc_start: 0.8532 (tt0) cc_final: 0.8222 (tt0) REVERT: D 193 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8232 (mt-10) REVERT: D 195 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8480 (tptm) REVERT: c 126 LEU cc_start: 0.8215 (mp) cc_final: 0.7883 (tt) REVERT: c 135 ASP cc_start: 0.8834 (m-30) cc_final: 0.8620 (m-30) REVERT: d 95 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.8320 (ppp) REVERT: d 192 ARG cc_start: 0.7589 (ttp-170) cc_final: 0.5850 (ppt170) outliers start: 18 outliers final: 4 residues processed: 119 average time/residue: 0.7339 time to fit residues: 90.1679 Evaluate side-chains 102 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 195 LYS Chi-restraints excluded: chain d residue 95 MET Chi-restraints excluded: chain d residue 129 VAL Chi-restraints excluded: chain d residue 166 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 56 optimal weight: 7.9990 chunk 35 optimal weight: 0.2980 chunk 42 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 46 optimal weight: 30.0000 chunk 48 optimal weight: 3.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.072523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.055041 restraints weight = 15564.942| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 3.76 r_work: 0.2709 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 5538 Z= 0.161 Angle : 0.579 7.583 7484 Z= 0.294 Chirality : 0.040 0.131 875 Planarity : 0.005 0.038 968 Dihedral : 3.893 24.767 773 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.13 % Allowed : 21.57 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.32), residues: 695 helix: 2.61 (0.26), residues: 399 sheet: 0.55 (0.61), residues: 54 loop : -0.32 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG c 164 TYR 0.008 0.001 TYR d 91 PHE 0.018 0.002 PHE C 19 TRP 0.007 0.001 TRP d 174 HIS 0.003 0.001 HIS d 123 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 5538) covalent geometry : angle 0.57855 ( 7484) hydrogen bonds : bond 0.04670 ( 312) hydrogen bonds : angle 4.00353 ( 972) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 193 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8549 (mt-10) REVERT: C 208 LYS cc_start: 0.5008 (mmtm) cc_final: 0.3029 (mptt) REVERT: D 34 ASN cc_start: 0.8503 (m-40) cc_final: 0.8294 (m110) REVERT: D 47 GLN cc_start: 0.8789 (mm110) cc_final: 0.8410 (mm110) REVERT: D 64 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8278 (tt0) REVERT: D 151 GLU cc_start: 0.9099 (tp30) cc_final: 0.8868 (tp30) REVERT: D 193 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8429 (mt-10) REVERT: c 55 ASP cc_start: 0.8612 (t70) cc_final: 0.7894 (t0) REVERT: d 95 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.8494 (ttp) REVERT: d 166 GLU cc_start: 0.9251 (OUTLIER) cc_final: 0.8925 (pt0) REVERT: d 192 ARG cc_start: 0.7700 (ttp-170) cc_final: 0.5869 (ppt170) outliers start: 18 outliers final: 8 residues processed: 111 average time/residue: 0.7762 time to fit residues: 88.8606 Evaluate side-chains 103 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain d residue 58 LYS Chi-restraints excluded: chain d residue 95 MET Chi-restraints excluded: chain d residue 129 VAL Chi-restraints excluded: chain d residue 166 GLU Chi-restraints excluded: chain d residue 186 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 50 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.071731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.054385 restraints weight = 15876.503| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 3.74 r_work: 0.2672 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.4636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5538 Z= 0.145 Angle : 0.562 7.722 7484 Z= 0.284 Chirality : 0.040 0.137 875 Planarity : 0.004 0.032 968 Dihedral : 3.868 25.334 773 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.13 % Allowed : 22.96 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.33), residues: 695 helix: 2.74 (0.26), residues: 399 sheet: 0.60 (0.60), residues: 54 loop : -0.25 (0.41), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG c 164 TYR 0.006 0.001 TYR C 90 PHE 0.010 0.001 PHE c 185 TRP 0.002 0.001 TRP c 174 HIS 0.003 0.001 HIS D 171 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 5538) covalent geometry : angle 0.56163 ( 7484) hydrogen bonds : bond 0.04090 ( 312) hydrogen bonds : angle 3.81650 ( 972) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 47 GLN cc_start: 0.8843 (mm110) cc_final: 0.8504 (mm-40) REVERT: C 165 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8428 (mp0) REVERT: C 193 GLU cc_start: 0.8986 (mt-10) cc_final: 0.8572 (mt-10) REVERT: D 34 ASN cc_start: 0.8405 (m-40) cc_final: 0.8173 (m110) REVERT: D 47 GLN cc_start: 0.8681 (mm110) cc_final: 0.8384 (mm110) REVERT: D 64 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8250 (tt0) REVERT: D 151 GLU cc_start: 0.9119 (tp30) cc_final: 0.8802 (tp30) REVERT: D 193 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8538 (mt-10) REVERT: d 95 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8371 (ppp) REVERT: d 166 GLU cc_start: 0.9280 (OUTLIER) cc_final: 0.8922 (pt0) REVERT: d 192 ARG cc_start: 0.7676 (ttp-170) cc_final: 0.5825 (ppt170) outliers start: 18 outliers final: 8 residues processed: 110 average time/residue: 0.8200 time to fit residues: 92.9070 Evaluate side-chains 106 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 159 ARG Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain d residue 58 LYS Chi-restraints excluded: chain d residue 95 MET Chi-restraints excluded: chain d residue 129 VAL Chi-restraints excluded: chain d residue 166 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 9 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 47 optimal weight: 7.9990 chunk 46 optimal weight: 30.0000 chunk 49 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.070725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.053046 restraints weight = 16083.933| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 3.87 r_work: 0.2654 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5538 Z= 0.186 Angle : 0.599 8.550 7484 Z= 0.304 Chirality : 0.041 0.131 875 Planarity : 0.004 0.039 968 Dihedral : 3.962 25.679 773 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.65 % Allowed : 23.48 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.40 (0.32), residues: 695 helix: 2.78 (0.26), residues: 397 sheet: 1.63 (0.58), residues: 48 loop : -0.44 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG c 164 TYR 0.007 0.001 TYR D 197 PHE 0.011 0.001 PHE c 175 TRP 0.002 0.001 TRP c 174 HIS 0.003 0.001 HIS D 171 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 5538) covalent geometry : angle 0.59920 ( 7484) hydrogen bonds : bond 0.04648 ( 312) hydrogen bonds : angle 3.86359 ( 972) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 193 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8610 (mt-10) REVERT: D 34 ASN cc_start: 0.8431 (m-40) cc_final: 0.7890 (m110) REVERT: D 47 GLN cc_start: 0.8636 (mm110) cc_final: 0.8314 (mm110) REVERT: D 57 MET cc_start: 0.9146 (mtp) cc_final: 0.8911 (mtm) REVERT: D 64 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8270 (tt0) REVERT: D 151 GLU cc_start: 0.9143 (tp30) cc_final: 0.8802 (tp30) REVERT: D 193 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8583 (mt-10) REVERT: c 55 ASP cc_start: 0.8704 (t70) cc_final: 0.7972 (t0) REVERT: d 95 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8482 (ttp) REVERT: d 166 GLU cc_start: 0.9287 (OUTLIER) cc_final: 0.8914 (pt0) REVERT: d 192 ARG cc_start: 0.7778 (ttp-170) cc_final: 0.5758 (ppt170) outliers start: 21 outliers final: 9 residues processed: 110 average time/residue: 0.7839 time to fit residues: 88.8046 Evaluate side-chains 104 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain d residue 58 LYS Chi-restraints excluded: chain d residue 95 MET Chi-restraints excluded: chain d residue 166 GLU Chi-restraints excluded: chain d residue 186 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 32 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 8 optimal weight: 0.7980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.071110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.053668 restraints weight = 15747.103| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 3.80 r_work: 0.2682 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.4916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5538 Z= 0.158 Angle : 0.601 10.021 7484 Z= 0.302 Chirality : 0.040 0.136 875 Planarity : 0.004 0.034 968 Dihedral : 3.874 26.029 772 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.30 % Allowed : 23.65 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.33), residues: 695 helix: 2.84 (0.26), residues: 398 sheet: 0.21 (0.59), residues: 66 loop : -0.20 (0.42), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG c 164 TYR 0.008 0.001 TYR C 90 PHE 0.010 0.001 PHE C 83 TRP 0.002 0.001 TRP c 174 HIS 0.003 0.001 HIS D 171 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 5538) covalent geometry : angle 0.60080 ( 7484) hydrogen bonds : bond 0.04113 ( 312) hydrogen bonds : angle 3.72779 ( 972) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 38 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8189 (mp0) REVERT: C 193 GLU cc_start: 0.8954 (mt-10) cc_final: 0.8599 (mt-10) REVERT: D 47 GLN cc_start: 0.8675 (mm110) cc_final: 0.8378 (mm110) REVERT: D 57 MET cc_start: 0.9144 (mtp) cc_final: 0.8918 (mtm) REVERT: D 64 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8294 (tt0) REVERT: D 151 GLU cc_start: 0.9159 (tp30) cc_final: 0.8822 (tp30) REVERT: D 193 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8590 (mt-10) REVERT: d 95 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8181 (ttp) REVERT: d 166 GLU cc_start: 0.9297 (OUTLIER) cc_final: 0.8934 (pt0) REVERT: d 192 ARG cc_start: 0.7725 (ttp-170) cc_final: 0.5668 (ppt170) outliers start: 19 outliers final: 8 residues processed: 108 average time/residue: 0.7903 time to fit residues: 88.0298 Evaluate side-chains 103 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain d residue 58 LYS Chi-restraints excluded: chain d residue 95 MET Chi-restraints excluded: chain d residue 166 GLU Chi-restraints excluded: chain d residue 186 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 14 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.069959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.052342 restraints weight = 15977.233| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 3.82 r_work: 0.2650 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 5538 Z= 0.217 Angle : 0.647 11.361 7484 Z= 0.327 Chirality : 0.041 0.136 875 Planarity : 0.005 0.041 968 Dihedral : 4.039 28.225 772 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.13 % Allowed : 24.17 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.33), residues: 695 helix: 2.81 (0.26), residues: 397 sheet: 0.57 (0.58), residues: 66 loop : -0.36 (0.41), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG c 171 TYR 0.008 0.001 TYR D 197 PHE 0.012 0.001 PHE c 175 TRP 0.005 0.001 TRP d 174 HIS 0.003 0.001 HIS D 171 Details of bonding type rmsd covalent geometry : bond 0.00514 ( 5538) covalent geometry : angle 0.64726 ( 7484) hydrogen bonds : bond 0.04954 ( 312) hydrogen bonds : angle 3.90595 ( 972) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 181 LYS cc_start: 0.9608 (mtmm) cc_final: 0.9325 (ptpp) REVERT: C 193 GLU cc_start: 0.8969 (mt-10) cc_final: 0.8642 (mt-10) REVERT: D 47 GLN cc_start: 0.8783 (mm110) cc_final: 0.8472 (mm110) REVERT: D 57 MET cc_start: 0.9157 (mtp) cc_final: 0.8935 (mtm) REVERT: D 64 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8357 (tt0) REVERT: D 151 GLU cc_start: 0.9233 (tp30) cc_final: 0.8952 (tp30) REVERT: D 193 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8550 (mt-10) REVERT: c 55 ASP cc_start: 0.8769 (t70) cc_final: 0.8108 (t0) REVERT: c 170 ASP cc_start: 0.7958 (p0) cc_final: 0.7723 (p0) REVERT: d 166 GLU cc_start: 0.9297 (OUTLIER) cc_final: 0.8919 (pt0) REVERT: d 192 ARG cc_start: 0.7798 (ttp-170) cc_final: 0.5665 (ppt170) outliers start: 18 outliers final: 8 residues processed: 104 average time/residue: 0.8002 time to fit residues: 85.7946 Evaluate side-chains 100 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain d residue 58 LYS Chi-restraints excluded: chain d residue 166 GLU Chi-restraints excluded: chain d residue 186 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 66 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 chunk 10 optimal weight: 0.1980 chunk 8 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.072375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.054933 restraints weight = 15483.260| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 3.77 r_work: 0.2703 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.5121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5538 Z= 0.134 Angle : 0.657 13.432 7484 Z= 0.329 Chirality : 0.040 0.132 875 Planarity : 0.004 0.038 968 Dihedral : 3.816 28.622 772 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.09 % Allowed : 25.39 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.47 (0.33), residues: 695 helix: 2.86 (0.26), residues: 398 sheet: 0.58 (0.60), residues: 60 loop : -0.23 (0.41), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 185 TYR 0.012 0.001 TYR C 197 PHE 0.009 0.001 PHE c 185 TRP 0.005 0.001 TRP c 174 HIS 0.002 0.001 HIS D 171 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 5538) covalent geometry : angle 0.65731 ( 7484) hydrogen bonds : bond 0.03492 ( 312) hydrogen bonds : angle 3.65713 ( 972) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 181 LYS cc_start: 0.9612 (mtmm) cc_final: 0.9354 (ptpp) REVERT: C 193 GLU cc_start: 0.8954 (mt-10) cc_final: 0.8618 (mt-10) REVERT: D 47 GLN cc_start: 0.8670 (mm110) cc_final: 0.8360 (mm110) REVERT: D 64 GLU cc_start: 0.8601 (tt0) cc_final: 0.8317 (tp30) REVERT: D 151 GLU cc_start: 0.9251 (tp30) cc_final: 0.8975 (tp30) REVERT: D 165 GLU cc_start: 0.8513 (mp0) cc_final: 0.8277 (mp0) REVERT: D 193 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8561 (mt-10) REVERT: d 95 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.8279 (ppp) REVERT: d 121 LEU cc_start: 0.8856 (tp) cc_final: 0.8145 (mt) REVERT: d 166 GLU cc_start: 0.9266 (OUTLIER) cc_final: 0.8920 (pt0) REVERT: d 192 ARG cc_start: 0.7730 (ttp-170) cc_final: 0.5684 (ppt170) outliers start: 12 outliers final: 5 residues processed: 105 average time/residue: 0.8039 time to fit residues: 87.0242 Evaluate side-chains 102 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain d residue 58 LYS Chi-restraints excluded: chain d residue 95 MET Chi-restraints excluded: chain d residue 166 GLU Chi-restraints excluded: chain d residue 186 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 28 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 22 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.070298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.052700 restraints weight = 15869.638| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 3.80 r_work: 0.2643 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.5108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5538 Z= 0.213 Angle : 0.685 13.584 7484 Z= 0.345 Chirality : 0.041 0.142 875 Planarity : 0.005 0.043 968 Dihedral : 4.009 29.450 772 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.26 % Allowed : 25.57 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.33), residues: 695 helix: 2.76 (0.26), residues: 398 sheet: 0.58 (0.59), residues: 66 loop : -0.40 (0.41), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 185 TYR 0.006 0.001 TYR C 197 PHE 0.012 0.001 PHE c 175 TRP 0.006 0.001 TRP d 174 HIS 0.003 0.001 HIS D 171 Details of bonding type rmsd covalent geometry : bond 0.00508 ( 5538) covalent geometry : angle 0.68522 ( 7484) hydrogen bonds : bond 0.04762 ( 312) hydrogen bonds : angle 3.88893 ( 972) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 193 GLU cc_start: 0.8965 (mt-10) cc_final: 0.8632 (mt-10) REVERT: D 38 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8581 (mt-10) REVERT: D 47 GLN cc_start: 0.8771 (mm110) cc_final: 0.8456 (mm110) REVERT: D 57 MET cc_start: 0.9159 (mtp) cc_final: 0.8908 (mtm) REVERT: D 64 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8397 (tt0) REVERT: D 151 GLU cc_start: 0.9227 (tp30) cc_final: 0.8970 (tp30) REVERT: D 193 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8552 (mt-10) REVERT: c 55 ASP cc_start: 0.8800 (t70) cc_final: 0.8163 (t0) REVERT: c 170 ASP cc_start: 0.8083 (p0) cc_final: 0.7816 (p0) REVERT: d 95 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8302 (ppp) REVERT: d 166 GLU cc_start: 0.9300 (OUTLIER) cc_final: 0.8928 (pt0) REVERT: d 192 ARG cc_start: 0.7818 (ttp-170) cc_final: 0.5667 (ppt170) outliers start: 13 outliers final: 8 residues processed: 100 average time/residue: 0.8159 time to fit residues: 84.1159 Evaluate side-chains 101 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain d residue 44 LEU Chi-restraints excluded: chain d residue 58 LYS Chi-restraints excluded: chain d residue 95 MET Chi-restraints excluded: chain d residue 166 GLU Chi-restraints excluded: chain d residue 186 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 6 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.071511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.054010 restraints weight = 15678.730| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 3.79 r_work: 0.2682 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.5204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5538 Z= 0.164 Angle : 0.711 13.735 7484 Z= 0.360 Chirality : 0.041 0.133 875 Planarity : 0.005 0.038 968 Dihedral : 3.943 29.813 772 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.74 % Allowed : 25.91 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.32), residues: 695 helix: 2.66 (0.26), residues: 398 sheet: 1.01 (0.59), residues: 60 loop : -0.40 (0.41), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 185 TYR 0.006 0.001 TYR c 91 PHE 0.009 0.001 PHE C 83 TRP 0.006 0.001 TRP d 174 HIS 0.002 0.001 HIS D 171 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 5538) covalent geometry : angle 0.71095 ( 7484) hydrogen bonds : bond 0.04086 ( 312) hydrogen bonds : angle 3.81203 ( 972) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 156 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8463 (pp20) REVERT: C 193 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8644 (mt-10) REVERT: D 38 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8613 (mt-10) REVERT: D 47 GLN cc_start: 0.8720 (mm110) cc_final: 0.8410 (mm110) REVERT: D 57 MET cc_start: 0.9148 (mtp) cc_final: 0.8897 (mtm) REVERT: D 64 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8474 (tt0) REVERT: D 151 GLU cc_start: 0.9218 (tp30) cc_final: 0.8982 (tp30) REVERT: D 193 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8546 (mt-10) REVERT: c 170 ASP cc_start: 0.8170 (p0) cc_final: 0.7878 (p0) REVERT: d 95 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8317 (ppp) REVERT: d 166 GLU cc_start: 0.9299 (OUTLIER) cc_final: 0.8962 (pt0) REVERT: d 192 ARG cc_start: 0.7779 (ttp-170) cc_final: 0.5631 (ppt170) outliers start: 10 outliers final: 5 residues processed: 96 average time/residue: 0.8229 time to fit residues: 81.4944 Evaluate side-chains 99 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain d residue 58 LYS Chi-restraints excluded: chain d residue 95 MET Chi-restraints excluded: chain d residue 166 GLU Chi-restraints excluded: chain d residue 186 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 48 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.070434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.052901 restraints weight = 15628.967| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 3.78 r_work: 0.2653 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.5191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 5538 Z= 0.206 Angle : 0.683 10.839 7484 Z= 0.350 Chirality : 0.041 0.146 875 Planarity : 0.005 0.042 968 Dihedral : 3.900 15.734 770 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.74 % Allowed : 26.09 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.33), residues: 695 helix: 2.66 (0.26), residues: 398 sheet: 0.98 (0.59), residues: 60 loop : -0.48 (0.41), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 185 TYR 0.006 0.001 TYR c 91 PHE 0.012 0.001 PHE c 175 TRP 0.008 0.002 TRP d 174 HIS 0.003 0.001 HIS C 171 Details of bonding type rmsd covalent geometry : bond 0.00489 ( 5538) covalent geometry : angle 0.68285 ( 7484) hydrogen bonds : bond 0.04742 ( 312) hydrogen bonds : angle 3.92213 ( 972) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2309.84 seconds wall clock time: 39 minutes 56.49 seconds (2396.49 seconds total)