Starting phenix.real_space_refine on Fri Oct 23 09:05:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/27em_81097/10_2026/27em_81097_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/27em_81097/10_2026/27em_81097.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/27em_81097/10_2026/27em_81097_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/27em_81097/10_2026/27em_81097_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/27em_81097/10_2026/27em_81097.map" default_real_map = "/net/cci-nas-00/data/ceres_data/27em_81097/10_2026/27em_81097.map" } resolution = 3.0 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= 0.011 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 50 5.16 5 C 5830 2.51 5 N 1504 2.21 5 O 1706 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9095 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2658 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 310} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1551 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 9, 'TRANS': 195} Chain breaks: 1 Chain: "E" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1587 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 11, 'TRANS': 195} Chain breaks: 1 Chain: "P" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 221 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "R" Number of atoms: 3077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3077 Classifications: {'peptide': 377} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 363} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.05, per 1000 atoms: 0.23 Number of scatterers: 9095 At special positions: 0 Unit cell: (84.68, 98.55, 196.37, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 50 16.00 P 5 15.00 O 1706 8.00 N 1504 7.00 C 5830 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 150 " - pdb=" SG CYS C 206 " distance=2.03 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 195 " distance=2.03 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: 0.86 Conformation dependent library (CDL) restraints added in 316.9 milliseconds 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2164 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 18 sheets defined 29.1% alpha, 28.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'B' and resid 45 through 48 Processing helix chain 'B' and resid 98 through 109 Processing helix chain 'B' and resid 278 through 282 removed outlier: 4.047A pdb=" N ARG B 282 " --> pdb=" O CYS B 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 94 Processing helix chain 'C' and resid 166 through 168 No H-bonds generated for 'chain 'C' and resid 166 through 168' Processing helix chain 'E' and resid 80 through 84 removed outlier: 3.976A pdb=" N PHE E 84 " --> pdb=" O PRO E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 128 Processing helix chain 'E' and resid 184 through 190 Processing helix chain 'P' and resid 2 through 27 Processing helix chain 'R' and resid 25 through 46 Processing helix chain 'R' and resid 78 through 84 removed outlier: 3.523A pdb=" N ARG R 82 " --> pdb=" O PRO R 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 134 Processing helix chain 'R' and resid 141 through 177 removed outlier: 4.232A pdb=" N ASP R 145 " --> pdb=" O SER R 141 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 212 Processing helix chain 'R' and resid 223 through 257 Processing helix chain 'R' and resid 261 through 291 removed outlier: 3.516A pdb=" N TYR R 265 " --> pdb=" O PRO R 261 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N TRP R 268 " --> pdb=" O ARG R 264 " (cutoff:3.500A) Proline residue: R 277 - end of helix Processing helix chain 'R' and resid 302 through 336 removed outlier: 3.997A pdb=" N VAL R 308 " --> pdb=" O ALA R 304 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ILE R 309 " --> pdb=" O LEU R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 342 through 363 removed outlier: 3.891A pdb=" N ILE R 347 " --> pdb=" O ASN R 343 " (cutoff:3.500A) Proline residue: R 360 - end of helix Processing helix chain 'R' and resid 364 through 370 removed outlier: 3.617A pdb=" N ALA R 370 " --> pdb=" O THR R 367 " (cutoff:3.500A) Processing helix chain 'R' and resid 380 through 392 Processing helix chain 'R' and resid 392 through 401 Processing helix chain 'R' and resid 410 through 415 Processing sheet with id=AA1, first strand: chain 'B' and resid 112 through 117 Processing sheet with id=AA2, first strand: chain 'B' and resid 26 through 28 removed outlier: 3.854A pdb=" N TYR B 144 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N LYS B 170 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 9.470A pdb=" N VAL B 142 " --> pdb=" O LYS B 170 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE B 61 " --> pdb=" O ASP B 78 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N ASP B 78 " --> pdb=" O PHE B 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 127 through 129 Processing sheet with id=AA4, first strand: chain 'B' and resid 183 through 188 removed outlier: 4.131A pdb=" N ARG B 188 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU B 197 " --> pdb=" O ARG B 188 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N HIS B 198 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR B 221 " --> pdb=" O HIS B 198 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 207 through 208 removed outlier: 4.135A pdb=" N TYR B 321 " --> pdb=" O PHE B 349 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N LEU B 351 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 9.218A pdb=" N VAL B 319 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL B 328 " --> pdb=" O LYS B 230 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LYS B 230 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE B 231 " --> pdb=" O GLU B 257 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N GLU B 257 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE B 233 " --> pdb=" O MET B 255 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N MET B 255 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL B 235 " --> pdb=" O VAL B 253 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR B 249 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA B 247 " --> pdb=" O ILE B 241 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 6 through 10 removed outlier: 3.964A pdb=" N VAL C 8 " --> pdb=" O ALA C 26 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 14 through 15 removed outlier: 8.626A pdb=" N SER C 35 " --> pdb=" O SER C 55 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N SER C 55 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE C 37 " --> pdb=" O SER C 53 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N SER C 53 " --> pdb=" O ILE C 37 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N TRP C 39 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 14 through 15 removed outlier: 4.049A pdb=" N TYR C 112 " --> pdb=" O ARG C 101 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 130 through 133 removed outlier: 6.219A pdb=" N TYR C 186 " --> pdb=" O ASP C 154 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 161 through 164 Processing sheet with id=AB2, first strand: chain 'E' and resid 5 through 7 Processing sheet with id=AB3, first strand: chain 'E' and resid 11 through 14 removed outlier: 6.608A pdb=" N VAL E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N TYR E 50 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 11 through 14 removed outlier: 3.899A pdb=" N THR E 98 " --> pdb=" O GLN E 91 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 117 through 119 removed outlier: 3.701A pdb=" N VAL E 134 " --> pdb=" O PHE E 119 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N LEU E 176 " --> pdb=" O LEU E 137 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASN E 139 " --> pdb=" O TYR E 174 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N TYR E 174 " --> pdb=" O ASN E 139 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER E 175 " --> pdb=" O THR E 165 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 147 through 151 Processing sheet with id=AB7, first strand: chain 'R' and resid 53 through 54 Processing sheet with id=AB8, first strand: chain 'R' and resid 57 through 58 removed outlier: 3.552A pdb=" N MET R 57 " --> pdb=" O TRP R 64 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TRP R 64 " --> pdb=" O MET R 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'R' and resid 71 through 76 removed outlier: 3.775A pdb=" N GLU R 71 " --> pdb=" O CYS R 118 " (cutoff:3.500A) 448 hydrogen bonds defined for protein. 1227 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: 1.47 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1442 1.32 - 1.44: 2625 1.44 - 1.57: 5164 1.57 - 1.69: 18 1.69 - 1.81: 67 Bond restraints: 9316 Sorted by residual: bond pdb=" OG1 TPO R 434 " pdb=" P TPO R 434 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.92e+01 bond pdb=" OG1 TPO R 433 " pdb=" P TPO R 433 " ideal model delta sigma weight residual 1.717 1.614 0.103 2.00e-02 2.50e+03 2.67e+01 bond pdb=" O2P TPO R 433 " pdb=" P TPO R 433 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" O2P TPO R 434 " pdb=" P TPO R 434 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" O3P TPO R 434 " pdb=" P TPO R 434 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.67e+01 ... (remaining 9311 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 12536 2.71 - 5.42: 112 5.42 - 8.14: 4 8.14 - 10.85: 2 10.85 - 13.56: 3 Bond angle restraints: 12657 Sorted by residual: angle pdb=" O TPO R 434 " pdb=" C TPO R 434 " pdb=" N ALA R 435 " ideal model delta sigma weight residual 123.00 109.44 13.56 1.60e+00 3.91e-01 7.18e+01 angle pdb=" N ARG R 413 " pdb=" CA ARG R 413 " pdb=" C ARG R 413 " ideal model delta sigma weight residual 111.07 106.59 4.48 1.07e+00 8.73e-01 1.76e+01 angle pdb=" CB TPO R 434 " pdb=" OG1 TPO R 434 " pdb=" P TPO R 434 " ideal model delta sigma weight residual 119.31 107.05 12.26 3.00e+00 1.11e-01 1.67e+01 angle pdb=" OG1 TPO R 433 " pdb=" P TPO R 433 " pdb=" O1P TPO R 433 " ideal model delta sigma weight residual 100.43 111.71 -11.28 3.00e+00 1.11e-01 1.41e+01 angle pdb=" N ARG P 14 " pdb=" CA ARG P 14 " pdb=" C ARG P 14 " ideal model delta sigma weight residual 111.11 106.69 4.42 1.20e+00 6.94e-01 1.36e+01 ... (remaining 12652 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 5306 17.67 - 35.34: 152 35.34 - 53.00: 44 53.00 - 70.67: 15 70.67 - 88.34: 4 Dihedral angle restraints: 5521 sinusoidal: 2160 harmonic: 3361 Sorted by residual: dihedral pdb=" CA PHE R 259 " pdb=" C PHE R 259 " pdb=" N PHE R 260 " pdb=" CA PHE R 260 " ideal model delta harmonic sigma weight residual -180.00 -152.78 -27.22 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA THR R 258 " pdb=" C THR R 258 " pdb=" N PHE R 259 " pdb=" CA PHE R 259 " ideal model delta harmonic sigma weight residual -180.00 -157.65 -22.35 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA PHE B 190 " pdb=" C PHE B 190 " pdb=" N LEU B 191 " pdb=" CA LEU B 191 " ideal model delta harmonic sigma weight residual 180.00 162.84 17.16 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 5518 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1106 0.041 - 0.083: 187 0.083 - 0.124: 105 0.124 - 0.166: 15 0.166 - 0.207: 7 Chirality restraints: 1420 Sorted by residual: chirality pdb=" CA ILE P 5 " pdb=" N ILE P 5 " pdb=" C ILE P 5 " pdb=" CB ILE P 5 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA VAL P 19 " pdb=" N VAL P 19 " pdb=" C VAL P 19 " pdb=" CB VAL P 19 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.62e-01 chirality pdb=" CA GLN P 16 " pdb=" N GLN P 16 " pdb=" C GLN P 16 " pdb=" CB GLN P 16 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.91e-01 ... (remaining 1417 not shown) Planarity restraints: 1587 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TPO R 434 " -0.071 2.00e-02 2.50e+03 1.33e-01 1.78e+02 pdb=" C TPO R 434 " 0.231 2.00e-02 2.50e+03 pdb=" O TPO R 434 " -0.085 2.00e-02 2.50e+03 pdb=" N ALA R 435 " -0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 79 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.37e+00 pdb=" C LEU B 79 " 0.032 2.00e-02 2.50e+03 pdb=" O LEU B 79 " -0.012 2.00e-02 2.50e+03 pdb=" N PHE B 80 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 14 " -0.008 2.00e-02 2.50e+03 1.77e-02 3.13e+00 pdb=" C PRO B 14 " 0.031 2.00e-02 2.50e+03 pdb=" O PRO B 14 " -0.012 2.00e-02 2.50e+03 pdb=" N ASN B 15 " -0.010 2.00e-02 2.50e+03 ... (remaining 1584 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 102 2.60 - 3.17: 7852 3.17 - 3.75: 13568 3.75 - 4.32: 18924 4.32 - 4.90: 32066 Nonbonded interactions: 72512 Sorted by model distance: nonbonded pdb=" OE1 GLN C 181 " pdb=" OG SER C 187 " model vdw 2.019 3.040 nonbonded pdb=" O LEU R 357 " pdb=" OH TYR R 400 " model vdw 2.113 3.040 nonbonded pdb=" NZ LYS B 95 " pdb=" OE2 GLU B 118 " model vdw 2.165 3.120 nonbonded pdb=" O PRO B 121 " pdb=" ND2 ASN B 122 " model vdw 2.177 3.120 nonbonded pdb=" OG SER R 164 " pdb=" O SER R 390 " model vdw 2.180 3.040 ... (remaining 72507 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 8.760 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: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.690 Find NCS groups from input model: 0.050 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:6.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 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 : 0.004 0.108 9319 Z= 0.222 Angle : 0.595 13.559 12663 Z= 0.361 Chirality : 0.044 0.207 1420 Planarity : 0.004 0.133 1587 Dihedral : 10.139 88.339 3348 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.31 % Favored : 96.51 % Rotamer: Outliers : 2.78 % Allowed : 5.05 % Favored : 92.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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 (0.27), residues: 1119 helix: 3.21 (0.31), residues: 279 sheet: 2.07 (0.30), residues: 351 loop : -0.03 (0.30), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 70 TYR 0.020 0.001 TYR R 157 PHE 0.007 0.001 PHE R 196 TRP 0.005 0.001 TRP R 243 HIS 0.004 0.001 HIS P 1 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.22 ( 9316) covalent geometry : angle 0.59525 / 0.36 (12657) SS BOND : bond 0.00207 / 0.10 ( 3) SS BOND : angle 0.28619 / 0.13 ( 6) hydrogen bonds : bond 0.15710 / 10.55 ( 438) hydrogen bonds : angle 6.24669 / 4.25 ( 1227) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 222 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 138 LYS cc_start: 0.7644 (mmmm) cc_final: 0.7329 (pttm) REVERT: B 249 TYR cc_start: 0.7671 (OUTLIER) cc_final: 0.6943 (m-80) REVERT: C 92 GLU cc_start: 0.7535 (pm20) cc_final: 0.7076 (tm-30) REVERT: E 93 LYS cc_start: 0.7822 (tttt) cc_final: 0.6975 (tmmt) REVERT: E 174 TYR cc_start: 0.6964 (m-10) cc_final: 0.6503 (m-10) REVERT: R 185 ARG cc_start: 0.6964 (tmm160) cc_final: 0.6527 (ttt-90) REVERT: R 266 PHE cc_start: 0.4777 (t80) cc_final: 0.3798 (t80) REVERT: R 340 MET cc_start: -0.0316 (tpp) cc_final: -0.1402 (tmm) REVERT: R 348 TYR cc_start: 0.5612 (m-80) cc_final: 0.5351 (m-80) REVERT: R 415 TRP cc_start: 0.6346 (t60) cc_final: 0.5912 (t-100) outliers start: 28 outliers final: 9 residues processed: 245 average time/residue: 0.4559 time to fit residues: 120.2110 Evaluate side-chains 142 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 23 LEU Chi-restraints excluded: chain R residue 260 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: [108, 49, 97, 53, 5, 33, 65, 62, 51, 100, 106] chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.0000 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.0570 chunk 65 optimal weight: 30.0000 chunk 62 optimal weight: 0.0770 chunk 51 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 chunk 106 optimal weight: 0.6980 overall best weight: 0.3260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 248 GLN C 6 GLN C 16 GLN E 28 GLN P 16 GLN ** R 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 240 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.157472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.118243 restraints weight = 18833.100| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.92 r_work: 0.3580 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9319 Z= 0.135 Angle : 0.628 9.588 12663 Z= 0.317 Chirality : 0.044 0.340 1420 Planarity : 0.004 0.039 1587 Dihedral : 6.769 74.265 1275 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.57 % Favored : 96.34 % Rotamer: Outliers : 4.76 % Allowed : 13.48 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: 1.86 (0.26), residues: 1119 helix: 2.57 (0.30), residues: 281 sheet: 2.04 (0.29), residues: 346 loop : -0.17 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 103 TYR 0.018 0.002 TYR R 157 PHE 0.015 0.002 PHE R 127 TRP 0.023 0.001 TRP C 106 HIS 0.005 0.001 HIS C 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 9316) covalent geometry : angle 0.62734 / 0.32 (12657) SS BOND : bond 0.00445 / 0.18 ( 3) SS BOND : angle 1.07233 / 0.58 ( 6) hydrogen bonds : bond 0.03893 / 2.58 ( 438) hydrogen bonds : angle 4.97903 / 3.42 ( 1227) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 141 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 249 TYR cc_start: 0.7571 (OUTLIER) cc_final: 0.7070 (m-80) REVERT: B 315 LEU cc_start: 0.6543 (OUTLIER) cc_final: 0.6087 (pp) REVERT: C 6 GLN cc_start: 0.8459 (mt0) cc_final: 0.8254 (mt0) REVERT: C 92 GLU cc_start: 0.7749 (pm20) cc_final: 0.7178 (tm-30) REVERT: E 82 GLU cc_start: 0.8023 (pm20) cc_final: 0.7803 (pm20) REVERT: E 93 LYS cc_start: 0.8099 (tttt) cc_final: 0.7095 (tmmt) REVERT: R 170 THR cc_start: 0.8491 (m) cc_final: 0.8280 (p) REVERT: R 185 ARG cc_start: 0.7315 (tmm160) cc_final: 0.6365 (mpt-90) REVERT: R 266 PHE cc_start: 0.5162 (t80) cc_final: 0.4282 (t80) REVERT: R 276 THR cc_start: 0.9122 (m) cc_final: 0.8893 (p) REVERT: R 340 MET cc_start: -0.0692 (tpp) cc_final: -0.1568 (tmm) REVERT: R 357 LEU cc_start: 0.8207 (tp) cc_final: 0.7896 (tt) outliers start: 48 outliers final: 19 residues processed: 179 average time/residue: 0.4675 time to fit residues: 90.0107 Evaluate side-chains 134 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 20 LYS Chi-restraints excluded: chain P residue 23 LEU Chi-restraints excluded: chain R residue 127 PHE Chi-restraints excluded: chain R residue 149 TYR Chi-restraints excluded: chain R residue 303 THR Chi-restraints excluded: chain R residue 351 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: [60, 2, 30, 103, 14, 42, 54, 18, 38, 5, 13] chunk 60 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 248 GLN E 7 GLN ** R 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.158302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.118545 restraints weight = 18901.249| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 3.20 r_work: 0.3507 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9319 Z= 0.179 Angle : 0.634 9.297 12663 Z= 0.319 Chirality : 0.045 0.330 1420 Planarity : 0.004 0.041 1587 Dihedral : 6.604 75.681 1271 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.38 % Favored : 95.53 % Rotamer: Outliers : 4.06 % Allowed : 16.06 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: 1.46 (0.26), residues: 1119 helix: 2.01 (0.29), residues: 282 sheet: 1.87 (0.29), residues: 344 loop : -0.34 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 285 TYR 0.025 0.002 TYR R 148 PHE 0.033 0.002 PHE R 260 TRP 0.008 0.001 TRP R 306 HIS 0.006 0.001 HIS B 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 ( 9316) covalent geometry : angle 0.63297 / 0.32 (12657) SS BOND : bond 0.00597 / 0.26 ( 3) SS BOND : angle 1.50757 / 0.91 ( 6) hydrogen bonds : bond 0.03795 / 2.54 ( 438) hydrogen bonds : angle 4.90898 / 3.35 ( 1227) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 122 time to evaluate : 0.288 Fit side-chains REVERT: B 198 HIS cc_start: 0.6887 (OUTLIER) cc_final: 0.6277 (p-80) REVERT: B 315 LEU cc_start: 0.6634 (OUTLIER) cc_final: 0.6168 (pp) REVERT: E 82 GLU cc_start: 0.8006 (pm20) cc_final: 0.7679 (pm20) REVERT: E 93 LYS cc_start: 0.8320 (tttt) cc_final: 0.7230 (tmmt) REVERT: P 23 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7432 (tm) REVERT: R 45 MET cc_start: 0.5593 (tmm) cc_final: 0.5369 (mtt) REVERT: R 170 THR cc_start: 0.8455 (m) cc_final: 0.8124 (p) REVERT: R 185 ARG cc_start: 0.7265 (tmm160) cc_final: 0.6331 (mpt-90) REVERT: R 197 MET cc_start: 0.6888 (OUTLIER) cc_final: 0.6644 (mpt) REVERT: R 266 PHE cc_start: 0.5495 (t80) cc_final: 0.4479 (t80) REVERT: R 276 THR cc_start: 0.9203 (m) cc_final: 0.8907 (p) REVERT: R 300 ASN cc_start: 0.6058 (m-40) cc_final: 0.5564 (p0) REVERT: R 340 MET cc_start: -0.0862 (tpp) cc_final: -0.1638 (tmm) REVERT: R 357 LEU cc_start: 0.8288 (tp) cc_final: 0.7980 (tt) REVERT: R 413 ARG cc_start: 0.7404 (OUTLIER) cc_final: 0.6495 (ppt-90) REVERT: R 415 TRP cc_start: 0.6393 (t60) cc_final: 0.5703 (t-100) outliers start: 41 outliers final: 20 residues processed: 151 average time/residue: 0.4631 time to fit residues: 75.6676 Evaluate side-chains 138 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 198 HIS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 20 LYS Chi-restraints excluded: chain P residue 23 LEU Chi-restraints excluded: chain P residue 27 LEU Chi-restraints excluded: chain R residue 117 ASN Chi-restraints excluded: chain R residue 197 MET Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 303 THR Chi-restraints excluded: chain R residue 351 LEU Chi-restraints excluded: chain R residue 413 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: [42, 35, 57, 93, 84, 18, 85, 98, 104, 37, 88] chunk 42 optimal weight: 0.5980 chunk 35 optimal weight: 0.0970 chunk 57 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 84 optimal weight: 9.9990 chunk 18 optimal weight: 0.0570 chunk 85 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 104 optimal weight: 0.0050 chunk 37 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 overall best weight: 0.3310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 248 GLN C 6 GLN R 117 ASN ** R 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.154705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.114587 restraints weight = 18907.380| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.94 r_work: 0.3510 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9319 Z= 0.120 Angle : 0.597 10.316 12663 Z= 0.297 Chirality : 0.043 0.317 1420 Planarity : 0.004 0.039 1587 Dihedral : 6.331 75.927 1269 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.57 % Favored : 96.34 % Rotamer: Outliers : 3.47 % Allowed : 17.24 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: 1.39 (0.26), residues: 1119 helix: 1.95 (0.29), residues: 281 sheet: 1.83 (0.28), residues: 342 loop : -0.36 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 285 TYR 0.020 0.002 TYR P 22 PHE 0.025 0.002 PHE R 127 TRP 0.008 0.001 TRP C 106 HIS 0.004 0.001 HIS P 1 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 9316) covalent geometry : angle 0.59632 / 0.30 (12657) SS BOND : bond 0.00493 / 0.20 ( 3) SS BOND : angle 1.14676 / 0.63 ( 6) hydrogen bonds : bond 0.03388 / 2.23 ( 438) hydrogen bonds : angle 4.67823 / 3.19 ( 1227) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 122 time to evaluate : 0.303 Fit side-chains REVERT: B 198 HIS cc_start: 0.6817 (OUTLIER) cc_final: 0.6163 (p-80) REVERT: B 249 TYR cc_start: 0.7681 (OUTLIER) cc_final: 0.7132 (m-80) REVERT: B 315 LEU cc_start: 0.6612 (OUTLIER) cc_final: 0.6141 (pp) REVERT: E 82 GLU cc_start: 0.8019 (pm20) cc_final: 0.7671 (pm20) REVERT: E 93 LYS cc_start: 0.8315 (tttt) cc_final: 0.7253 (tmmt) REVERT: E 104 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.7839 (ttpp) REVERT: P 20 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8042 (tptm) REVERT: P 23 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7461 (tm) REVERT: R 185 ARG cc_start: 0.7219 (OUTLIER) cc_final: 0.6343 (mpt-90) REVERT: R 197 MET cc_start: 0.6751 (OUTLIER) cc_final: 0.6492 (mpt) REVERT: R 259 PHE cc_start: 0.4473 (m-80) cc_final: 0.3455 (t80) REVERT: R 266 PHE cc_start: 0.5494 (t80) cc_final: 0.4522 (t80) REVERT: R 276 THR cc_start: 0.9174 (m) cc_final: 0.8919 (p) REVERT: R 300 ASN cc_start: 0.6051 (m-40) cc_final: 0.5605 (p0) REVERT: R 340 MET cc_start: -0.0822 (tpp) cc_final: -0.1608 (tmm) REVERT: R 357 LEU cc_start: 0.8182 (tp) cc_final: 0.7826 (tt) REVERT: R 413 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.6506 (ppt-90) outliers start: 35 outliers final: 14 residues processed: 148 average time/residue: 0.4794 time to fit residues: 76.5829 Evaluate side-chains 134 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 198 HIS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 104 LYS Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 20 LYS Chi-restraints excluded: chain P residue 23 LEU Chi-restraints excluded: chain R residue 117 ASN Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 185 ARG Chi-restraints excluded: chain R residue 197 MET Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 413 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: [83, 74, 85, 105, 86, 38, 14, 35, 34, 40, 63] chunk 83 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 chunk 105 optimal weight: 0.0670 chunk 86 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 6 GLN P 16 GLN ** R 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.152337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.112377 restraints weight = 18889.661| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.81 r_work: 0.3488 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9319 Z= 0.151 Angle : 0.614 9.556 12663 Z= 0.306 Chirality : 0.044 0.316 1420 Planarity : 0.004 0.041 1587 Dihedral : 6.333 75.918 1268 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.11 % Favored : 95.80 % Rotamer: Outliers : 3.47 % Allowed : 18.14 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: 1.24 (0.25), residues: 1119 helix: 1.83 (0.29), residues: 280 sheet: 1.69 (0.28), residues: 342 loop : -0.40 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 285 TYR 0.022 0.002 TYR R 250 PHE 0.033 0.002 PHE R 260 TRP 0.015 0.001 TRP R 415 HIS 0.005 0.001 HIS P 1 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 9316) covalent geometry : angle 0.61317 / 0.31 (12657) SS BOND : bond 0.00421 / 0.17 ( 3) SS BOND : angle 1.56546 / 0.88 ( 6) hydrogen bonds : bond 0.03446 / 2.27 ( 438) hydrogen bonds : angle 4.67200 / 3.18 ( 1227) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 118 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: B 152 GLU cc_start: 0.8240 (mp0) cc_final: 0.7982 (mp0) REVERT: B 198 HIS cc_start: 0.7227 (OUTLIER) cc_final: 0.6575 (p-80) REVERT: B 249 TYR cc_start: 0.7850 (OUTLIER) cc_final: 0.7281 (m-80) REVERT: B 315 LEU cc_start: 0.6790 (OUTLIER) cc_final: 0.6318 (pp) REVERT: E 82 GLU cc_start: 0.8167 (pm20) cc_final: 0.7846 (pm20) REVERT: E 104 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8024 (ttpp) REVERT: P 20 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8025 (tptm) REVERT: P 23 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7472 (tm) REVERT: R 45 MET cc_start: 0.5514 (tmm) cc_final: 0.5048 (mtt) REVERT: R 72 MET cc_start: 0.5006 (OUTLIER) cc_final: 0.4648 (tpp) REVERT: R 185 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.6431 (mpt-90) REVERT: R 197 MET cc_start: 0.6840 (OUTLIER) cc_final: 0.6623 (mpt) REVERT: R 259 PHE cc_start: 0.4592 (m-80) cc_final: 0.3408 (t80) REVERT: R 266 PHE cc_start: 0.5591 (t80) cc_final: 0.4624 (t80) REVERT: R 276 THR cc_start: 0.9210 (m) cc_final: 0.8934 (p) REVERT: R 300 ASN cc_start: 0.6160 (m-40) cc_final: 0.5656 (p0) REVERT: R 340 MET cc_start: -0.0777 (tpp) cc_final: -0.1585 (tmm) REVERT: R 357 LEU cc_start: 0.8233 (tp) cc_final: 0.7939 (tt) REVERT: R 413 ARG cc_start: 0.7526 (OUTLIER) cc_final: 0.6568 (ppt-90) outliers start: 35 outliers final: 20 residues processed: 146 average time/residue: 0.4537 time to fit residues: 71.7962 Evaluate side-chains 135 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 198 HIS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain E residue 104 LYS Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 13 TYR Chi-restraints excluded: chain P residue 20 LYS Chi-restraints excluded: chain P residue 23 LEU Chi-restraints excluded: chain R residue 72 MET Chi-restraints excluded: chain R residue 117 ASN Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 185 ARG Chi-restraints excluded: chain R residue 197 MET Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 351 LEU Chi-restraints excluded: chain R residue 413 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: [12, 68, 85, 47, 33, 35, 98, 15, 52, 4, 0] chunk 12 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 4 optimal weight: 0.8980 chunk 0 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 222 ASN B 223 ASN C 6 GLN C 38 HIS E 39 GLN R 117 ASN ** R 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.155149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.114045 restraints weight = 18080.211| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.94 r_work: 0.3433 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9319 Z= 0.218 Angle : 0.659 9.465 12663 Z= 0.334 Chirality : 0.046 0.262 1420 Planarity : 0.004 0.044 1587 Dihedral : 6.643 75.333 1268 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.56 % Favored : 95.35 % Rotamer: Outliers : 3.96 % Allowed : 18.24 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.25), residues: 1119 helix: 1.64 (0.29), residues: 279 sheet: 1.46 (0.28), residues: 347 loop : -0.60 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 285 TYR 0.019 0.002 TYR R 250 PHE 0.023 0.002 PHE C 105 TRP 0.011 0.002 TRP R 64 HIS 0.007 0.001 HIS P 1 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.22 ( 9316) covalent geometry : angle 0.65788 / 0.33 (12657) SS BOND : bond 0.00508 / 0.22 ( 3) SS BOND : angle 1.48123 / 0.83 ( 6) hydrogen bonds : bond 0.03701 / 2.44 ( 438) hydrogen bonds : angle 4.76189 / 3.25 ( 1227) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 113 time to evaluate : 0.292 Fit side-chains REVERT: B 152 GLU cc_start: 0.8253 (mp0) cc_final: 0.7925 (mp0) REVERT: B 198 HIS cc_start: 0.7268 (OUTLIER) cc_final: 0.6607 (p-80) REVERT: B 249 TYR cc_start: 0.7901 (OUTLIER) cc_final: 0.7308 (m-80) REVERT: B 315 LEU cc_start: 0.6972 (OUTLIER) cc_final: 0.6472 (pp) REVERT: C 179 VAL cc_start: 0.8387 (t) cc_final: 0.7907 (p) REVERT: E 82 GLU cc_start: 0.8193 (pm20) cc_final: 0.7890 (pm20) REVERT: E 94 TYR cc_start: 0.7797 (m-10) cc_final: 0.7487 (m-10) REVERT: E 104 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8089 (ttpp) REVERT: P 20 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8045 (tptm) REVERT: P 23 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7502 (tm) REVERT: R 185 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.6435 (mpt-90) REVERT: R 190 MET cc_start: 0.7995 (mtp) cc_final: 0.7412 (tpp) REVERT: R 259 PHE cc_start: 0.4791 (m-80) cc_final: 0.3489 (t80) REVERT: R 266 PHE cc_start: 0.5809 (t80) cc_final: 0.4846 (t80) REVERT: R 276 THR cc_start: 0.9210 (m) cc_final: 0.8934 (p) REVERT: R 299 MET cc_start: 0.6346 (pp-130) cc_final: 0.5217 (mmt) REVERT: R 300 ASN cc_start: 0.6200 (m-40) cc_final: 0.5468 (p0) REVERT: R 340 MET cc_start: -0.0880 (tpp) cc_final: -0.1480 (pp-130) REVERT: R 357 LEU cc_start: 0.8472 (tp) cc_final: 0.8190 (tt) REVERT: R 413 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.6645 (ppt-90) outliers start: 40 outliers final: 22 residues processed: 147 average time/residue: 0.4591 time to fit residues: 73.1074 Evaluate side-chains 132 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 102 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 198 HIS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 104 LYS Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 20 LYS Chi-restraints excluded: chain P residue 23 LEU Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 185 ARG Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 351 LEU Chi-restraints excluded: chain R residue 413 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: [27, 82, 71, 7, 109, 111, 10, 4, 32, 68, 94] chunk 27 optimal weight: 0.1980 chunk 82 optimal weight: 7.9990 chunk 71 optimal weight: 9.9990 chunk 7 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 111 optimal weight: 0.0470 chunk 10 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 85 GLN B 159 HIS C 6 GLN C 115 GLN R 182 HIS ** R 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.152360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.111906 restraints weight = 18651.211| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.83 r_work: 0.3471 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9319 Z= 0.136 Angle : 0.626 11.255 12663 Z= 0.310 Chirality : 0.043 0.301 1420 Planarity : 0.004 0.054 1587 Dihedral : 6.477 74.708 1268 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.11 % Favored : 95.80 % Rotamer: Outliers : 3.27 % Allowed : 19.72 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.25), residues: 1119 helix: 1.63 (0.28), residues: 284 sheet: 1.42 (0.28), residues: 342 loop : -0.62 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 285 TYR 0.018 0.001 TYR R 157 PHE 0.027 0.002 PHE R 260 TRP 0.008 0.001 TRP C 113 HIS 0.004 0.001 HIS P 1 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 9316) covalent geometry : angle 0.62589 / 0.31 (12657) SS BOND : bond 0.00431 / 0.18 ( 3) SS BOND : angle 1.19064 / 0.67 ( 6) hydrogen bonds : bond 0.03431 / 2.26 ( 438) hydrogen bonds : angle 4.59808 / 3.13 ( 1227) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 104 time to evaluate : 0.368 Fit side-chains REVERT: B 152 GLU cc_start: 0.8240 (mp0) cc_final: 0.7977 (mp0) REVERT: B 198 HIS cc_start: 0.7270 (OUTLIER) cc_final: 0.6639 (p-80) REVERT: B 315 LEU cc_start: 0.6848 (OUTLIER) cc_final: 0.6366 (pp) REVERT: C 179 VAL cc_start: 0.8377 (t) cc_final: 0.7907 (p) REVERT: E 94 TYR cc_start: 0.7768 (m-10) cc_final: 0.7473 (m-10) REVERT: P 20 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.8009 (tptm) REVERT: P 22 TYR cc_start: 0.7121 (t80) cc_final: 0.6833 (t80) REVERT: P 23 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7436 (tm) REVERT: R 45 MET cc_start: 0.5415 (tmm) cc_final: 0.5046 (mtt) REVERT: R 185 ARG cc_start: 0.7288 (OUTLIER) cc_final: 0.6382 (mpt-90) REVERT: R 190 MET cc_start: 0.7943 (mtp) cc_final: 0.7465 (tpp) REVERT: R 259 PHE cc_start: 0.4943 (m-80) cc_final: 0.3436 (t80) REVERT: R 266 PHE cc_start: 0.5851 (t80) cc_final: 0.4851 (t80) REVERT: R 276 THR cc_start: 0.9202 (m) cc_final: 0.8936 (p) REVERT: R 299 MET cc_start: 0.6387 (pp-130) cc_final: 0.5175 (mmt) REVERT: R 300 ASN cc_start: 0.6178 (m-40) cc_final: 0.5551 (p0) REVERT: R 340 MET cc_start: -0.0908 (tpp) cc_final: -0.2103 (ttp) REVERT: R 357 LEU cc_start: 0.8535 (tp) cc_final: 0.8250 (tt) REVERT: R 413 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.6614 (ppt-90) outliers start: 33 outliers final: 18 residues processed: 131 average time/residue: 0.4859 time to fit residues: 68.5108 Evaluate side-chains 128 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 198 HIS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 20 LYS Chi-restraints excluded: chain P residue 23 LEU Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 185 ARG Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 413 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: [64, 23, 77, 54, 52, 94, 2, 14, 78, 26, 13] chunk 64 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 77 optimal weight: 0.0060 chunk 54 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 overall best weight: 0.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 115 GLN R 234 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.153631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.112480 restraints weight = 18225.052| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.97 r_work: 0.3440 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9319 Z= 0.180 Angle : 0.636 10.822 12663 Z= 0.317 Chirality : 0.044 0.284 1420 Planarity : 0.004 0.069 1587 Dihedral : 6.571 74.429 1268 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.47 % Allowed : 19.52 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: 0.93 (0.25), residues: 1119 helix: 1.74 (0.29), residues: 280 sheet: 1.35 (0.28), residues: 347 loop : -0.59 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 285 TYR 0.019 0.002 TYR R 157 PHE 0.019 0.002 PHE C 105 TRP 0.010 0.001 TRP R 243 HIS 0.008 0.001 HIS R 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 ( 9316) covalent geometry : angle 0.63524 / 0.32 (12657) SS BOND : bond 0.00468 / 0.20 ( 3) SS BOND : angle 1.18263 / 0.66 ( 6) hydrogen bonds : bond 0.03513 / 2.32 ( 438) hydrogen bonds : angle 4.64696 / 3.18 ( 1227) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 105 time to evaluate : 0.412 Fit side-chains REVERT: B 152 GLU cc_start: 0.8112 (mp0) cc_final: 0.7884 (mp0) REVERT: B 198 HIS cc_start: 0.6931 (OUTLIER) cc_final: 0.6275 (p-80) REVERT: B 315 LEU cc_start: 0.6823 (OUTLIER) cc_final: 0.6347 (pp) REVERT: C 158 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6678 (pp20) REVERT: C 179 VAL cc_start: 0.8331 (t) cc_final: 0.7859 (p) REVERT: P 20 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.8069 (tmtm) REVERT: P 23 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7469 (tm) REVERT: R 30 GLU cc_start: 0.6823 (tt0) cc_final: 0.6583 (tt0) REVERT: R 45 MET cc_start: 0.5502 (tmm) cc_final: 0.5131 (mtp) REVERT: R 72 MET cc_start: 0.5256 (tpt) cc_final: 0.4654 (tpt) REVERT: R 185 ARG cc_start: 0.7093 (tmm160) cc_final: 0.6237 (mpt-90) REVERT: R 259 PHE cc_start: 0.5050 (m-80) cc_final: 0.3496 (t80) REVERT: R 266 PHE cc_start: 0.5726 (t80) cc_final: 0.4736 (t80) REVERT: R 276 THR cc_start: 0.9167 (m) cc_final: 0.8906 (p) REVERT: R 299 MET cc_start: 0.6301 (pp-130) cc_final: 0.5141 (mmt) REVERT: R 300 ASN cc_start: 0.6146 (m-40) cc_final: 0.5433 (p0) REVERT: R 340 MET cc_start: -0.0665 (tpp) cc_final: -0.1980 (ttp) REVERT: R 413 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.6748 (ppt-90) outliers start: 35 outliers final: 17 residues processed: 132 average time/residue: 0.4984 time to fit residues: 71.1288 Evaluate side-chains 124 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 198 HIS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 20 LYS Chi-restraints excluded: chain P residue 23 LEU Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 413 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: [92, 95, 88, 55, 61, 58, 40, 84, 41, 78, 15] chunk 92 optimal weight: 0.0970 chunk 95 optimal weight: 0.7980 chunk 88 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 115 GLN E 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.156889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.121756 restraints weight = 18352.007| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 4.08 r_work: 0.3392 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9319 Z= 0.147 Angle : 0.640 11.648 12663 Z= 0.316 Chirality : 0.044 0.311 1420 Planarity : 0.004 0.073 1587 Dihedral : 6.529 73.894 1268 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.27 % Allowed : 20.12 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.25), residues: 1119 helix: 1.59 (0.29), residues: 280 sheet: 1.34 (0.28), residues: 347 loop : -0.57 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 285 TYR 0.018 0.001 TYR R 157 PHE 0.029 0.002 PHE R 260 TRP 0.009 0.001 TRP R 243 HIS 0.011 0.001 HIS R 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 9316) covalent geometry : angle 0.63977 / 0.32 (12657) SS BOND : bond 0.00434 / 0.18 ( 3) SS BOND : angle 1.07135 / 0.60 ( 6) hydrogen bonds : bond 0.03405 / 2.24 ( 438) hydrogen bonds : angle 4.66298 / 3.18 ( 1227) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 104 time to evaluate : 0.298 Fit side-chains REVERT: B 198 HIS cc_start: 0.7067 (OUTLIER) cc_final: 0.6470 (p-80) REVERT: B 315 LEU cc_start: 0.6822 (OUTLIER) cc_final: 0.6361 (pp) REVERT: C 158 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6652 (pp20) REVERT: P 20 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.8069 (tmtm) REVERT: P 23 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7487 (tm) REVERT: R 45 MET cc_start: 0.5511 (tmm) cc_final: 0.5161 (mtt) REVERT: R 72 MET cc_start: 0.5251 (tpt) cc_final: 0.4652 (tpt) REVERT: R 185 ARG cc_start: 0.6974 (OUTLIER) cc_final: 0.6084 (mpt-90) REVERT: R 190 MET cc_start: 0.7915 (mtp) cc_final: 0.7579 (mmm) REVERT: R 266 PHE cc_start: 0.5691 (t80) cc_final: 0.4722 (t80) REVERT: R 276 THR cc_start: 0.9177 (m) cc_final: 0.8929 (p) REVERT: R 299 MET cc_start: 0.6444 (pp-130) cc_final: 0.5206 (mmt) REVERT: R 300 ASN cc_start: 0.6127 (m-40) cc_final: 0.5510 (p0) REVERT: R 340 MET cc_start: -0.0931 (tpp) cc_final: -0.2116 (ttp) REVERT: R 413 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.6768 (ppt-90) outliers start: 33 outliers final: 21 residues processed: 129 average time/residue: 0.4753 time to fit residues: 66.2075 Evaluate side-chains 130 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 198 HIS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 20 LYS Chi-restraints excluded: chain P residue 23 LEU Chi-restraints excluded: chain R residue 174 ILE Chi-restraints excluded: chain R residue 185 ARG Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 413 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: [99, 52, 108, 98, 11, 12, 78, 101, 56, 103, 65] chunk 99 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 108 optimal weight: 0.0000 chunk 98 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 12 optimal weight: 0.4980 chunk 78 optimal weight: 7.9990 chunk 101 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 103 optimal weight: 0.1980 chunk 65 optimal weight: 8.9990 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.156832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.120337 restraints weight = 18117.580| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 3.84 r_work: 0.3428 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.4641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9319 Z= 0.124 Angle : 0.637 11.953 12663 Z= 0.312 Chirality : 0.043 0.318 1420 Planarity : 0.004 0.076 1587 Dihedral : 6.444 73.474 1268 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.58 % Allowed : 21.01 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: 0.93 (0.25), residues: 1119 helix: 1.72 (0.29), residues: 278 sheet: 1.40 (0.28), residues: 342 loop : -0.58 (0.29), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 285 TYR 0.018 0.001 TYR R 157 PHE 0.017 0.001 PHE R 260 TRP 0.009 0.001 TRP R 243 HIS 0.008 0.001 HIS R 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 9316) covalent geometry : angle 0.63723 / 0.31 (12657) SS BOND : bond 0.00399 / 0.16 ( 3) SS BOND : angle 0.93857 / 0.53 ( 6) hydrogen bonds : bond 0.03308 / 2.16 ( 438) hydrogen bonds : angle 4.54275 / 3.10 ( 1227) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.358 Fit side-chains REVERT: B 138 LYS cc_start: 0.7956 (ttpt) cc_final: 0.7634 (ttpp) REVERT: B 198 HIS cc_start: 0.6982 (OUTLIER) cc_final: 0.6381 (p-80) REVERT: B 315 LEU cc_start: 0.6759 (OUTLIER) cc_final: 0.6308 (pp) REVERT: C 158 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6609 (pp20) REVERT: P 8 ASP cc_start: 0.7351 (OUTLIER) cc_final: 0.7126 (t0) REVERT: P 23 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7472 (tm) REVERT: R 45 MET cc_start: 0.5468 (tmm) cc_final: 0.5133 (mtt) REVERT: R 72 MET cc_start: 0.5253 (tpt) cc_final: 0.4674 (tpt) REVERT: R 185 ARG cc_start: 0.6864 (OUTLIER) cc_final: 0.5977 (mpt-90) REVERT: R 190 MET cc_start: 0.7896 (mtp) cc_final: 0.7592 (mmm) REVERT: R 266 PHE cc_start: 0.5743 (t80) cc_final: 0.4775 (t80) REVERT: R 276 THR cc_start: 0.9166 (m) cc_final: 0.8930 (p) REVERT: R 299 MET cc_start: 0.6453 (pp-130) cc_final: 0.5306 (mmt) REVERT: R 340 MET cc_start: -0.0957 (tpp) cc_final: -0.2117 (ttp) REVERT: R 413 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.6746 (ppt-90) outliers start: 26 outliers final: 15 residues processed: 126 average time/residue: 0.5034 time to fit residues: 68.2191 Evaluate side-chains 123 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 198 HIS Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 23 LEU Chi-restraints excluded: chain R residue 185 ARG Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 413 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: [87, 80, 52, 84, 70, 85, 45, 50, 86, 41, 13] chunk 87 optimal weight: 0.9980 chunk 80 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.150367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.109978 restraints weight = 18596.021| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.81 r_work: 0.3431 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.4827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9319 Z= 0.195 Angle : 0.678 10.804 12663 Z= 0.336 Chirality : 0.045 0.307 1420 Planarity : 0.005 0.078 1587 Dihedral : 6.578 72.890 1268 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.11 % Favored : 95.80 % Rotamer: Outliers : 2.97 % Allowed : 21.01 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.25), residues: 1119 helix: 1.68 (0.29), residues: 277 sheet: 1.30 (0.28), residues: 347 loop : -0.58 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 285 TYR 0.018 0.002 TYR R 157 PHE 0.028 0.002 PHE R 260 TRP 0.011 0.002 TRP R 243 HIS 0.009 0.001 HIS R 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.20 ( 9316) covalent geometry : angle 0.67793 / 0.34 (12657) SS BOND : bond 0.00449 / 0.20 ( 3) SS BOND : angle 1.14694 / 0.64 ( 6) hydrogen bonds : bond 0.03552 / 2.36 ( 438) hydrogen bonds : angle 4.71739 / 3.22 ( 1227) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3728.77 seconds wall clock time: 64 minutes 18.96 seconds (3858.96 seconds total)