Starting phenix.real_space_refine on Sat Jun 7 12:08:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wy0_32883/06_2025/7wy0_32883_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wy0_32883/06_2025/7wy0_32883.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wy0_32883/06_2025/7wy0_32883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wy0_32883/06_2025/7wy0_32883.map" model { file = "/net/cci-nas-00/data/ceres_data/7wy0_32883/06_2025/7wy0_32883_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wy0_32883/06_2025/7wy0_32883_neut.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.001 sd= 0.020 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 56 5.16 5 C 5591 2.51 5 N 1481 2.21 5 O 1595 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8723 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1732 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 3, 'TRANS': 205} Chain breaks: 4 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 1776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1776 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "D" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 2179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2179 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 10, 'TRANS': 266} Chain breaks: 1 Time building chain proxies: 5.58, per 1000 atoms: 0.64 Number of scatterers: 8723 At special positions: 0 Unit cell: (91.8, 119.88, 127.44, 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 56 16.00 O 1595 8.00 N 1481 7.00 C 5591 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 161 " - pdb=" SG CYS C 231 " distance=2.04 Simple disulfide: pdb=" SG CYS R 657 " - pdb=" SG CYS R 733 " 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: 2.33 Conformation dependent library (CDL) restraints added in 1.1 seconds 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2078 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 13 sheets defined 36.8% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 14 through 40 removed outlier: 3.860A pdb=" N THR A 35 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TYR A 36 " --> pdb=" O ARG A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 66 Processing helix chain 'A' and resid 236 through 241 removed outlier: 4.060A pdb=" N SER A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 278 Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.555A pdb=" N SER A 283 " --> pdb=" O ARG A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 320 through 332 removed outlier: 3.764A pdb=" N GLN A 324 " --> pdb=" O LEU A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 375 removed outlier: 3.674A pdb=" N ARG A 361 " --> pdb=" O ARG A 357 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASP A 362 " --> pdb=" O LEU A 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.734A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.624A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'D' and resid 7 through 24 removed outlier: 3.532A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.595A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 568 through 573 Processing helix chain 'R' and resid 581 through 610 removed outlier: 4.319A pdb=" N TRP R 587 " --> pdb=" O PRO R 583 " (cutoff:3.500A) Processing helix chain 'R' and resid 611 through 614 Processing helix chain 'R' and resid 617 through 647 Processing helix chain 'R' and resid 658 through 687 Processing helix chain 'R' and resid 694 through 707 Processing helix chain 'R' and resid 707 through 722 Processing helix chain 'R' and resid 723 through 725 No H-bonds generated for 'chain 'R' and resid 723 through 725' Processing helix chain 'R' and resid 742 through 746 removed outlier: 3.501A pdb=" N LEU R 745 " --> pdb=" O LYS R 742 " (cutoff:3.500A) Processing helix chain 'R' and resid 747 through 770 Processing helix chain 'R' and resid 785 through 800 Proline residue: R 798 - end of helix Processing helix chain 'R' and resid 802 through 805 Processing helix chain 'R' and resid 806 through 813 Processing helix chain 'R' and resid 819 through 828 Processing helix chain 'R' and resid 829 through 838 Processing helix chain 'R' and resid 842 through 854 Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 213 removed outlier: 6.277A pdb=" N VAL A 41 " --> pdb=" O LYS A 220 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LYS A 42 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU A 245 " --> pdb=" O LYS A 42 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU A 44 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N LEU A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU A 46 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N SER A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE A 287 " --> pdb=" O TYR A 344 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N HIS A 346 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU A 289 " --> pdb=" O HIS A 346 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 4.116A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.717A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.621A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.656A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 6.610A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.416A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 5.948A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 3 through 7 removed outlier: 5.974A pdb=" N GLY C 16 " --> pdb=" O SER C 85 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.322A pdb=" N GLY C 10 " --> pdb=" O THR C 118 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N MET C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TYR C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.322A pdb=" N GLY C 10 " --> pdb=" O THR C 118 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE C 110 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 142 through 143 Processing sheet with id=AB4, first strand: chain 'C' and resid 148 through 150 removed outlier: 3.679A pdb=" N GLU C 248 " --> pdb=" O VAL C 149 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU C 176 " --> pdb=" O TYR C 192 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N TYR C 192 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP C 178 " --> pdb=" O LEU C 190 " (cutoff:3.500A) 445 hydrogen bonds defined for protein. 1233 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: 2.62 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2779 1.34 - 1.46: 2061 1.46 - 1.58: 3983 1.58 - 1.70: 0 1.70 - 1.82: 82 Bond restraints: 8905 Sorted by residual: bond pdb=" C ARG R 624 " pdb=" N ILE R 625 " ideal model delta sigma weight residual 1.334 1.287 0.047 1.25e-02 6.40e+03 1.42e+01 bond pdb=" N ASP C 139 " pdb=" CA ASP C 139 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.23e-02 6.61e+03 6.95e+00 bond pdb=" N ASN R 816 " pdb=" CA ASN R 816 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.57e+00 bond pdb=" C TYR C 192 " pdb=" N ARG C 193 " ideal model delta sigma weight residual 1.333 1.299 0.034 1.45e-02 4.76e+03 5.47e+00 bond pdb=" CA SER R 814 " pdb=" CB SER R 814 " ideal model delta sigma weight residual 1.530 1.496 0.034 1.57e-02 4.06e+03 4.70e+00 ... (remaining 8900 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 11665 2.09 - 4.19: 310 4.19 - 6.28: 67 6.28 - 8.37: 14 8.37 - 10.47: 5 Bond angle restraints: 12061 Sorted by residual: angle pdb=" N GLY C 56 " pdb=" CA GLY C 56 " pdb=" C GLY C 56 " ideal model delta sigma weight residual 110.21 116.71 -6.50 9.10e-01 1.21e+00 5.11e+01 angle pdb=" N ALA B 203 " pdb=" CA ALA B 203 " pdb=" C ALA B 203 " ideal model delta sigma weight residual 110.41 117.45 -7.04 1.18e+00 7.18e-01 3.56e+01 angle pdb=" N GLU A 236 " pdb=" CA GLU A 236 " pdb=" C GLU A 236 " ideal model delta sigma weight residual 114.75 108.66 6.09 1.26e+00 6.30e-01 2.34e+01 angle pdb=" N LYS A 232 " pdb=" CA LYS A 232 " pdb=" C LYS A 232 " ideal model delta sigma weight residual 112.72 118.75 -6.03 1.28e+00 6.10e-01 2.22e+01 angle pdb=" C ASP B 290 " pdb=" CA ASP B 290 " pdb=" CB ASP B 290 " ideal model delta sigma weight residual 110.56 102.61 7.95 1.69e+00 3.50e-01 2.22e+01 ... (remaining 12056 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 4891 17.62 - 35.24: 328 35.24 - 52.86: 41 52.86 - 70.49: 3 70.49 - 88.11: 5 Dihedral angle restraints: 5268 sinusoidal: 2057 harmonic: 3211 Sorted by residual: dihedral pdb=" CA ILE A 351 " pdb=" C ILE A 351 " pdb=" N ASN A 352 " pdb=" CA ASN A 352 " ideal model delta harmonic sigma weight residual 180.00 160.02 19.98 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA GLU A 15 " pdb=" C GLU A 15 " pdb=" N ASP A 16 " pdb=" CA ASP A 16 " ideal model delta harmonic sigma weight residual 180.00 160.05 19.95 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 160.32 19.68 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 5265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 1372 0.146 - 0.292: 17 0.292 - 0.438: 2 0.438 - 0.583: 0 0.583 - 0.729: 1 Chirality restraints: 1392 Sorted by residual: chirality pdb=" CG LEU C 176 " pdb=" CB LEU C 176 " pdb=" CD1 LEU C 176 " pdb=" CD2 LEU C 176 " both_signs ideal model delta sigma weight residual False -2.59 -1.86 -0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" CA CYS R 657 " pdb=" N CYS R 657 " pdb=" C CYS R 657 " pdb=" CB CYS R 657 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CA CYS B 204 " pdb=" N CYS B 204 " pdb=" C CYS B 204 " pdb=" CB CYS B 204 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.66e+00 ... (remaining 1389 not shown) Planarity restraints: 1506 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 14 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C ALA A 14 " 0.055 2.00e-02 2.50e+03 pdb=" O ALA A 14 " -0.021 2.00e-02 2.50e+03 pdb=" N GLU A 15 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 214 " -0.029 2.00e-02 2.50e+03 1.90e-02 6.33e+00 pdb=" CG PHE C 214 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE C 214 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE C 214 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE C 214 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE C 214 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 214 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.040 5.00e-02 4.00e+02 6.10e-02 5.96e+00 pdb=" N PRO B 236 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.034 5.00e-02 4.00e+02 ... (remaining 1503 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.33: 15 2.33 - 2.97: 4498 2.97 - 3.62: 13150 3.62 - 4.26: 20622 4.26 - 4.90: 34950 Nonbonded interactions: 73235 Sorted by model distance: nonbonded pdb=" CB LEU C 176 " pdb=" SD MET C 194 " model vdw 1.690 3.800 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.089 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.147 3.040 nonbonded pdb=" OE2 GLU A 236 " pdb=" NH1 ARG B 314 " model vdw 2.157 3.120 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP D 48 " model vdw 2.201 3.040 ... (remaining 73230 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.740 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:12.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 8907 Z= 0.324 Angle : 0.869 10.467 12065 Z= 0.501 Chirality : 0.058 0.729 1392 Planarity : 0.005 0.061 1506 Dihedral : 11.976 88.107 3184 Min Nonbonded Distance : 1.690 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.25), residues: 1090 helix: 0.90 (0.28), residues: 368 sheet: -1.03 (0.29), residues: 276 loop : -1.71 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP R 734 HIS 0.009 0.002 HIS C 35 PHE 0.039 0.003 PHE A 282 TYR 0.028 0.004 TYR R 668 ARG 0.009 0.001 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.14446 ( 441) hydrogen bonds : angle 7.21128 ( 1233) SS BOND : bond 0.00726 ( 2) SS BOND : angle 1.99549 ( 4) covalent geometry : bond 0.00725 ( 8905) covalent geometry : angle 0.86874 (12061) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.892 Fit side-chains revert: symmetry clash REVERT: A 249 SER cc_start: 0.8228 (m) cc_final: 0.7924 (p) REVERT: B 97 SER cc_start: 0.8172 (p) cc_final: 0.7902 (p) REVERT: B 146 LEU cc_start: 0.8094 (tp) cc_final: 0.7864 (tp) REVERT: B 150 ARG cc_start: 0.7886 (mmt-90) cc_final: 0.7556 (mpt180) REVERT: D 38 MET cc_start: 0.6206 (mtt) cc_final: 0.6005 (mtt) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 1.2322 time to fit residues: 243.1297 Evaluate side-chains 162 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.5980 chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 0.0980 chunk 27 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 43 optimal weight: 0.4980 chunk 84 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 220 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.161192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.139719 restraints weight = 12472.929| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 2.03 r_work: 0.3728 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3578 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 8907 Z= 0.167 Angle : 0.653 10.277 12065 Z= 0.341 Chirality : 0.044 0.173 1392 Planarity : 0.004 0.045 1506 Dihedral : 5.252 25.834 1189 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.97 % Allowed : 10.89 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.26), residues: 1090 helix: 1.74 (0.28), residues: 362 sheet: -0.95 (0.28), residues: 275 loop : -1.44 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 178 HIS 0.004 0.001 HIS C 35 PHE 0.021 0.002 PHE A 282 TYR 0.017 0.002 TYR C 192 ARG 0.007 0.001 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.04551 ( 441) hydrogen bonds : angle 5.58637 ( 1233) SS BOND : bond 0.00601 ( 2) SS BOND : angle 1.19298 ( 4) covalent geometry : bond 0.00380 ( 8905) covalent geometry : angle 0.65315 (12061) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 178 time to evaluate : 1.041 Fit side-chains REVERT: A 17 LYS cc_start: 0.8313 (mtmm) cc_final: 0.8068 (mttm) REVERT: A 33 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7539 (mt-10) REVERT: A 220 LYS cc_start: 0.8207 (ttmm) cc_final: 0.7966 (ttmm) REVERT: A 376 MET cc_start: 0.7593 (mpp) cc_final: 0.7198 (mpp) REVERT: B 105 TYR cc_start: 0.8355 (t80) cc_final: 0.8112 (t80) REVERT: B 130 GLU cc_start: 0.6960 (mp0) cc_final: 0.6685 (mp0) REVERT: B 150 ARG cc_start: 0.8134 (mmt-90) cc_final: 0.7730 (mpt180) REVERT: B 335 PHE cc_start: 0.8152 (m-10) cc_final: 0.7952 (m-10) REVERT: C 142 MET cc_start: 0.6738 (mmm) cc_final: 0.5242 (mtm) REVERT: C 194 MET cc_start: 0.4549 (tpt) cc_final: 0.4295 (tpp) REVERT: R 627 MET cc_start: 0.7011 (OUTLIER) cc_final: 0.6730 (tpp) REVERT: R 767 THR cc_start: 0.8221 (m) cc_final: 0.7890 (m) outliers start: 19 outliers final: 8 residues processed: 185 average time/residue: 1.0583 time to fit residues: 210.4995 Evaluate side-chains 182 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 173 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain R residue 627 MET Chi-restraints excluded: chain R residue 705 LEU Chi-restraints excluded: chain R residue 786 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 7 optimal weight: 0.4980 chunk 92 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 220 GLN B 293 ASN ** B 340 ASN ** 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 = 0.4092 r_free = 0.4092 target = 0.160343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.138679 restraints weight = 12645.440| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.06 r_work: 0.3713 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3561 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 8907 Z= 0.204 Angle : 0.644 11.521 12065 Z= 0.334 Chirality : 0.045 0.400 1392 Planarity : 0.004 0.041 1506 Dihedral : 5.191 27.744 1189 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.42 % Allowed : 12.34 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.26), residues: 1090 helix: 1.92 (0.27), residues: 356 sheet: -0.86 (0.29), residues: 259 loop : -1.44 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 178 HIS 0.011 0.001 HIS A 318 PHE 0.033 0.002 PHE A 282 TYR 0.018 0.002 TYR C 192 ARG 0.007 0.001 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.04245 ( 441) hydrogen bonds : angle 5.38755 ( 1233) SS BOND : bond 0.00540 ( 2) SS BOND : angle 1.20982 ( 4) covalent geometry : bond 0.00473 ( 8905) covalent geometry : angle 0.64364 (12061) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 181 time to evaluate : 0.913 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8287 (mtmm) cc_final: 0.8056 (mttm) REVERT: A 220 LYS cc_start: 0.8168 (ttmm) cc_final: 0.7828 (ttmm) REVERT: A 334 LYS cc_start: 0.6396 (OUTLIER) cc_final: 0.6054 (mptp) REVERT: A 376 MET cc_start: 0.7762 (mpp) cc_final: 0.7432 (mpp) REVERT: B 130 GLU cc_start: 0.7058 (mp0) cc_final: 0.6719 (mp0) REVERT: B 150 ARG cc_start: 0.8136 (mmt-90) cc_final: 0.7861 (mpt180) REVERT: C 169 HIS cc_start: 0.6954 (t-90) cc_final: 0.6746 (t-90) REVERT: R 767 THR cc_start: 0.8231 (OUTLIER) cc_final: 0.7858 (m) outliers start: 33 outliers final: 16 residues processed: 193 average time/residue: 0.9874 time to fit residues: 205.9668 Evaluate side-chains 189 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 171 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain R residue 600 LEU Chi-restraints excluded: chain R residue 635 LEU Chi-restraints excluded: chain R residue 705 LEU Chi-restraints excluded: chain R residue 767 THR Chi-restraints excluded: chain R residue 786 ILE Chi-restraints excluded: chain R residue 794 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 7 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 79 optimal weight: 0.0060 chunk 89 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 chunk 85 optimal weight: 0.0970 chunk 25 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 293 ASN ** B 340 ASN ** 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 = 0.4103 r_free = 0.4103 target = 0.161446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.139920 restraints weight = 12638.509| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 2.05 r_work: 0.3734 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3585 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8907 Z= 0.159 Angle : 0.614 10.698 12065 Z= 0.318 Chirality : 0.044 0.394 1392 Planarity : 0.004 0.043 1506 Dihedral : 5.018 25.676 1189 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.63 % Allowed : 14.32 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.26), residues: 1090 helix: 1.90 (0.28), residues: 366 sheet: -0.86 (0.29), residues: 259 loop : -1.35 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 178 HIS 0.010 0.001 HIS A 318 PHE 0.019 0.002 PHE B 151 TYR 0.016 0.002 TYR C 192 ARG 0.010 0.001 ARG R 623 Details of bonding type rmsd hydrogen bonds : bond 0.03850 ( 441) hydrogen bonds : angle 5.20107 ( 1233) SS BOND : bond 0.00512 ( 2) SS BOND : angle 1.15028 ( 4) covalent geometry : bond 0.00368 ( 8905) covalent geometry : angle 0.61325 (12061) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 177 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8151 (mtmm) cc_final: 0.7867 (mttm) REVERT: A 220 LYS cc_start: 0.8169 (ttmm) cc_final: 0.7892 (ttmm) REVERT: B 59 TYR cc_start: 0.7931 (OUTLIER) cc_final: 0.7083 (t80) REVERT: B 130 GLU cc_start: 0.6959 (mp0) cc_final: 0.6610 (mp0) REVERT: B 150 ARG cc_start: 0.8093 (mmt-90) cc_final: 0.7788 (mpt180) REVERT: B 291 ASP cc_start: 0.6999 (p0) cc_final: 0.6671 (p0) REVERT: B 293 ASN cc_start: 0.7745 (m-40) cc_final: 0.7543 (p0) REVERT: C 142 MET cc_start: 0.6587 (mmm) cc_final: 0.5211 (mtm) REVERT: C 169 HIS cc_start: 0.6897 (t-90) cc_final: 0.6669 (t-90) REVERT: C 174 THR cc_start: 0.7467 (OUTLIER) cc_final: 0.7114 (t) REVERT: R 810 THR cc_start: 0.7384 (OUTLIER) cc_final: 0.6925 (t) REVERT: R 835 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7368 (tp) outliers start: 35 outliers final: 15 residues processed: 192 average time/residue: 1.1058 time to fit residues: 228.0939 Evaluate side-chains 189 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain R residue 590 TYR Chi-restraints excluded: chain R residue 600 LEU Chi-restraints excluded: chain R residue 635 LEU Chi-restraints excluded: chain R residue 786 ILE Chi-restraints excluded: chain R residue 810 THR Chi-restraints excluded: chain R residue 835 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 55 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 81 optimal weight: 0.0370 chunk 95 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 overall best weight: 0.7062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.160876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.139325 restraints weight = 12649.448| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 2.04 r_work: 0.3721 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3568 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 8907 Z= 0.190 Angle : 0.631 11.541 12065 Z= 0.325 Chirality : 0.045 0.406 1392 Planarity : 0.004 0.041 1506 Dihedral : 5.022 27.106 1189 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.15 % Allowed : 15.25 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.26), residues: 1090 helix: 1.96 (0.27), residues: 366 sheet: -0.93 (0.29), residues: 264 loop : -1.37 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 178 HIS 0.010 0.001 HIS A 318 PHE 0.023 0.002 PHE B 151 TYR 0.017 0.002 TYR C 192 ARG 0.009 0.001 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03925 ( 441) hydrogen bonds : angle 5.22351 ( 1233) SS BOND : bond 0.00528 ( 2) SS BOND : angle 1.17178 ( 4) covalent geometry : bond 0.00444 ( 8905) covalent geometry : angle 0.63028 (12061) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 177 time to evaluate : 0.906 Fit side-chains REVERT: A 17 LYS cc_start: 0.8192 (mtmm) cc_final: 0.7907 (mttm) REVERT: A 334 LYS cc_start: 0.6479 (OUTLIER) cc_final: 0.6057 (mptp) REVERT: B 59 TYR cc_start: 0.7962 (OUTLIER) cc_final: 0.7081 (t80) REVERT: B 78 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7070 (mppt) REVERT: B 88 ASN cc_start: 0.8504 (OUTLIER) cc_final: 0.8021 (m110) REVERT: B 130 GLU cc_start: 0.7057 (mp0) cc_final: 0.6709 (mp0) REVERT: B 145 TYR cc_start: 0.8463 (p90) cc_final: 0.8226 (p90) REVERT: B 150 ARG cc_start: 0.8111 (mmt-90) cc_final: 0.7795 (mpt180) REVERT: B 291 ASP cc_start: 0.7048 (p0) cc_final: 0.6549 (p0) REVERT: B 293 ASN cc_start: 0.7697 (m-40) cc_final: 0.7495 (p0) REVERT: C 4 LEU cc_start: 0.8293 (mm) cc_final: 0.8026 (mt) REVERT: C 174 THR cc_start: 0.7510 (OUTLIER) cc_final: 0.7145 (t) REVERT: R 767 THR cc_start: 0.8156 (OUTLIER) cc_final: 0.7767 (m) REVERT: R 810 THR cc_start: 0.7419 (OUTLIER) cc_final: 0.6869 (t) REVERT: R 835 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7382 (tp) outliers start: 40 outliers final: 19 residues processed: 197 average time/residue: 1.0141 time to fit residues: 215.4994 Evaluate side-chains 192 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain R residue 590 TYR Chi-restraints excluded: chain R residue 600 LEU Chi-restraints excluded: chain R residue 635 LEU Chi-restraints excluded: chain R residue 705 LEU Chi-restraints excluded: chain R residue 767 THR Chi-restraints excluded: chain R residue 786 ILE Chi-restraints excluded: chain R residue 810 THR Chi-restraints excluded: chain R residue 835 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 63 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 26 optimal weight: 0.0970 chunk 45 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.161275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.139800 restraints weight = 12507.519| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 2.02 r_work: 0.3726 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3574 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8907 Z= 0.182 Angle : 0.621 10.820 12065 Z= 0.323 Chirality : 0.045 0.448 1392 Planarity : 0.004 0.042 1506 Dihedral : 5.002 26.658 1189 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 4.15 % Allowed : 16.60 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.26), residues: 1090 helix: 2.07 (0.27), residues: 364 sheet: -0.88 (0.29), residues: 263 loop : -1.38 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 178 HIS 0.006 0.001 HIS C 35 PHE 0.034 0.002 PHE A 282 TYR 0.018 0.002 TYR C 175 ARG 0.009 0.001 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03906 ( 441) hydrogen bonds : angle 5.21142 ( 1233) SS BOND : bond 0.00646 ( 2) SS BOND : angle 1.38067 ( 4) covalent geometry : bond 0.00425 ( 8905) covalent geometry : angle 0.62025 (12061) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 174 time to evaluate : 1.725 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8184 (mtmm) cc_final: 0.7891 (mttm) REVERT: A 209 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6895 (mt-10) REVERT: A 220 LYS cc_start: 0.8121 (ttmm) cc_final: 0.7759 (tttp) REVERT: B 33 ILE cc_start: 0.7184 (mp) cc_final: 0.6770 (mp) REVERT: B 59 TYR cc_start: 0.7980 (OUTLIER) cc_final: 0.7127 (t80) REVERT: B 78 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7064 (mppt) REVERT: B 88 ASN cc_start: 0.8526 (OUTLIER) cc_final: 0.8028 (m110) REVERT: B 129 ARG cc_start: 0.7563 (mtp85) cc_final: 0.7234 (mtp85) REVERT: B 130 GLU cc_start: 0.7028 (mp0) cc_final: 0.6668 (mp0) REVERT: B 145 TYR cc_start: 0.8566 (p90) cc_final: 0.8273 (p90) REVERT: B 291 ASP cc_start: 0.7032 (p0) cc_final: 0.6816 (p0) REVERT: C 4 LEU cc_start: 0.8275 (mm) cc_final: 0.8016 (mt) REVERT: C 174 THR cc_start: 0.7467 (OUTLIER) cc_final: 0.7149 (t) REVERT: C 194 MET cc_start: 0.3914 (tpt) cc_final: 0.3606 (tpt) REVERT: D 38 MET cc_start: 0.6712 (mtt) cc_final: 0.6512 (mtt) REVERT: R 767 THR cc_start: 0.8137 (OUTLIER) cc_final: 0.7762 (m) REVERT: R 835 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7354 (tp) outliers start: 40 outliers final: 23 residues processed: 194 average time/residue: 1.1315 time to fit residues: 238.1803 Evaluate side-chains 200 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain R residue 590 TYR Chi-restraints excluded: chain R residue 600 LEU Chi-restraints excluded: chain R residue 627 MET Chi-restraints excluded: chain R residue 635 LEU Chi-restraints excluded: chain R residue 698 MET Chi-restraints excluded: chain R residue 767 THR Chi-restraints excluded: chain R residue 786 ILE Chi-restraints excluded: chain R residue 810 THR Chi-restraints excluded: chain R residue 835 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 40 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 14 optimal weight: 0.0470 chunk 84 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 97 optimal weight: 0.0470 chunk 19 optimal weight: 0.4980 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.162441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.140806 restraints weight = 12650.696| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 2.05 r_work: 0.3741 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3592 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8907 Z= 0.143 Angle : 0.599 10.336 12065 Z= 0.308 Chirality : 0.044 0.476 1392 Planarity : 0.004 0.041 1506 Dihedral : 4.834 24.971 1189 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.05 % Allowed : 17.74 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.26), residues: 1090 helix: 2.09 (0.27), residues: 370 sheet: -0.81 (0.29), residues: 270 loop : -1.36 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 332 HIS 0.004 0.001 HIS C 35 PHE 0.030 0.002 PHE A 282 TYR 0.016 0.002 TYR B 289 ARG 0.010 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03670 ( 441) hydrogen bonds : angle 5.09817 ( 1233) SS BOND : bond 0.00542 ( 2) SS BOND : angle 1.30451 ( 4) covalent geometry : bond 0.00331 ( 8905) covalent geometry : angle 0.59840 (12061) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 182 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8067 (mtmm) cc_final: 0.7840 (mttm) REVERT: A 220 LYS cc_start: 0.8099 (ttmm) cc_final: 0.7843 (tttp) REVERT: B 33 ILE cc_start: 0.7136 (mp) cc_final: 0.6687 (mp) REVERT: B 59 TYR cc_start: 0.7950 (OUTLIER) cc_final: 0.7148 (t80) REVERT: B 78 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7046 (mppt) REVERT: B 130 GLU cc_start: 0.6900 (mp0) cc_final: 0.6583 (mp0) REVERT: B 145 TYR cc_start: 0.8512 (p90) cc_final: 0.8237 (p90) REVERT: B 150 ARG cc_start: 0.8108 (mmt-90) cc_final: 0.7778 (mpt180) REVERT: C 4 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8033 (mt) REVERT: C 43 LYS cc_start: 0.7361 (OUTLIER) cc_final: 0.7152 (mmtm) REVERT: C 174 THR cc_start: 0.7422 (OUTLIER) cc_final: 0.7124 (t) REVERT: C 194 MET cc_start: 0.4226 (tpt) cc_final: 0.3935 (tpt) REVERT: D 38 MET cc_start: 0.6857 (mtt) cc_final: 0.6630 (mtt) REVERT: R 701 VAL cc_start: 0.8404 (p) cc_final: 0.8126 (t) REVERT: R 835 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7367 (tp) outliers start: 39 outliers final: 20 residues processed: 201 average time/residue: 1.0486 time to fit residues: 227.4335 Evaluate side-chains 203 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 177 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain R residue 590 TYR Chi-restraints excluded: chain R residue 600 LEU Chi-restraints excluded: chain R residue 786 ILE Chi-restraints excluded: chain R residue 810 THR Chi-restraints excluded: chain R residue 835 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 31 optimal weight: 0.6980 chunk 97 optimal weight: 0.2980 chunk 106 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 70 optimal weight: 0.0170 chunk 42 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 69 optimal weight: 0.1980 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN C 234 HIS R 736 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.163368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.141624 restraints weight = 12695.938| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 2.07 r_work: 0.3749 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3599 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8907 Z= 0.140 Angle : 0.595 9.659 12065 Z= 0.307 Chirality : 0.044 0.304 1392 Planarity : 0.003 0.040 1506 Dihedral : 4.767 24.622 1189 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.84 % Allowed : 17.84 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.26), residues: 1090 helix: 2.10 (0.27), residues: 371 sheet: -0.75 (0.29), residues: 264 loop : -1.35 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 332 HIS 0.004 0.001 HIS C 35 PHE 0.035 0.002 PHE A 282 TYR 0.015 0.002 TYR B 289 ARG 0.004 0.000 ARG B 48 Details of bonding type rmsd hydrogen bonds : bond 0.03628 ( 441) hydrogen bonds : angle 5.03351 ( 1233) SS BOND : bond 0.00477 ( 2) SS BOND : angle 1.42313 ( 4) covalent geometry : bond 0.00324 ( 8905) covalent geometry : angle 0.59446 (12061) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 176 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 LYS cc_start: 0.8096 (ttmm) cc_final: 0.7834 (tttp) REVERT: B 33 ILE cc_start: 0.7053 (mp) cc_final: 0.6585 (mp) REVERT: B 59 TYR cc_start: 0.7957 (OUTLIER) cc_final: 0.7115 (t80) REVERT: B 78 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7011 (mppt) REVERT: B 130 GLU cc_start: 0.6881 (mp0) cc_final: 0.6622 (mp0) REVERT: B 145 TYR cc_start: 0.8568 (p90) cc_final: 0.8273 (p90) REVERT: B 150 ARG cc_start: 0.8118 (mmt-90) cc_final: 0.7775 (mpt180) REVERT: B 336 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8111 (mt) REVERT: C 4 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8050 (mt) REVERT: D 38 MET cc_start: 0.6818 (mtt) cc_final: 0.6587 (mtt) REVERT: R 701 VAL cc_start: 0.8356 (p) cc_final: 0.8090 (t) REVERT: R 835 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7360 (tp) outliers start: 37 outliers final: 22 residues processed: 194 average time/residue: 1.0352 time to fit residues: 216.3486 Evaluate side-chains 202 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 175 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain R residue 590 TYR Chi-restraints excluded: chain R residue 600 LEU Chi-restraints excluded: chain R residue 786 ILE Chi-restraints excluded: chain R residue 810 THR Chi-restraints excluded: chain R residue 835 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 45 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 34 optimal weight: 0.0970 chunk 12 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 69 optimal weight: 0.0270 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.163202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.141397 restraints weight = 12688.545| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 2.05 r_work: 0.3750 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3599 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8907 Z= 0.145 Angle : 0.625 11.323 12065 Z= 0.319 Chirality : 0.044 0.432 1392 Planarity : 0.003 0.040 1506 Dihedral : 4.766 24.626 1189 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.22 % Allowed : 18.78 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.26), residues: 1090 helix: 2.30 (0.27), residues: 365 sheet: -0.76 (0.29), residues: 265 loop : -1.30 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 332 HIS 0.005 0.001 HIS C 35 PHE 0.033 0.002 PHE A 282 TYR 0.014 0.001 TYR B 289 ARG 0.003 0.000 ARG B 48 Details of bonding type rmsd hydrogen bonds : bond 0.03619 ( 441) hydrogen bonds : angle 5.05324 ( 1233) SS BOND : bond 0.00532 ( 2) SS BOND : angle 1.40335 ( 4) covalent geometry : bond 0.00338 ( 8905) covalent geometry : angle 0.62443 (12061) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 171 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 LYS cc_start: 0.8083 (ttmm) cc_final: 0.7819 (tttp) REVERT: B 59 TYR cc_start: 0.7954 (OUTLIER) cc_final: 0.7154 (t80) REVERT: B 129 ARG cc_start: 0.7537 (mtp85) cc_final: 0.7245 (mtp85) REVERT: B 130 GLU cc_start: 0.6911 (mp0) cc_final: 0.6645 (mp0) REVERT: B 150 ARG cc_start: 0.8104 (mmt-90) cc_final: 0.7756 (mpt180) REVERT: B 336 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8141 (mt) REVERT: C 4 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8048 (mt) REVERT: C 174 THR cc_start: 0.7475 (OUTLIER) cc_final: 0.7161 (t) REVERT: R 701 VAL cc_start: 0.8344 (p) cc_final: 0.8076 (t) REVERT: R 835 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7368 (tp) outliers start: 31 outliers final: 22 residues processed: 187 average time/residue: 1.0472 time to fit residues: 210.9607 Evaluate side-chains 194 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 167 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain R residue 590 TYR Chi-restraints excluded: chain R residue 600 LEU Chi-restraints excluded: chain R residue 625 ILE Chi-restraints excluded: chain R residue 627 MET Chi-restraints excluded: chain R residue 635 LEU Chi-restraints excluded: chain R residue 786 ILE Chi-restraints excluded: chain R residue 810 THR Chi-restraints excluded: chain R residue 835 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 45 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 106 optimal weight: 0.6980 chunk 57 optimal weight: 0.2980 chunk 63 optimal weight: 0.3980 chunk 46 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN ** R 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.162869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.141024 restraints weight = 12559.026| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 2.04 r_work: 0.3745 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3595 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8907 Z= 0.172 Angle : 0.636 9.655 12065 Z= 0.327 Chirality : 0.045 0.329 1392 Planarity : 0.004 0.055 1506 Dihedral : 4.837 26.171 1189 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.90 % Allowed : 20.02 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.26), residues: 1090 helix: 2.29 (0.27), residues: 364 sheet: -0.80 (0.29), residues: 263 loop : -1.30 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 332 HIS 0.005 0.001 HIS C 35 PHE 0.035 0.002 PHE A 282 TYR 0.024 0.002 TYR C 175 ARG 0.013 0.001 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03767 ( 441) hydrogen bonds : angle 5.10898 ( 1233) SS BOND : bond 0.00658 ( 2) SS BOND : angle 1.45926 ( 4) covalent geometry : bond 0.00404 ( 8905) covalent geometry : angle 0.63565 (12061) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8040 (mtmm) cc_final: 0.7824 (mttm) REVERT: A 220 LYS cc_start: 0.8078 (ttmm) cc_final: 0.7794 (tttp) REVERT: B 59 TYR cc_start: 0.7981 (OUTLIER) cc_final: 0.7119 (t80) REVERT: B 129 ARG cc_start: 0.7533 (mtp85) cc_final: 0.7245 (mtp85) REVERT: B 130 GLU cc_start: 0.6957 (mp0) cc_final: 0.6651 (mp0) REVERT: B 150 ARG cc_start: 0.8101 (mmt-90) cc_final: 0.7757 (mpt180) REVERT: B 336 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8169 (mt) REVERT: C 4 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8047 (mt) REVERT: C 174 THR cc_start: 0.7502 (OUTLIER) cc_final: 0.7088 (t) REVERT: R 701 VAL cc_start: 0.8370 (p) cc_final: 0.8107 (t) REVERT: R 835 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7351 (tp) outliers start: 28 outliers final: 20 residues processed: 191 average time/residue: 1.2463 time to fit residues: 257.7479 Evaluate side-chains 194 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 169 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain R residue 590 TYR Chi-restraints excluded: chain R residue 600 LEU Chi-restraints excluded: chain R residue 625 ILE Chi-restraints excluded: chain R residue 635 LEU Chi-restraints excluded: chain R residue 786 ILE Chi-restraints excluded: chain R residue 810 THR Chi-restraints excluded: chain R residue 835 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 107 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 97 optimal weight: 0.0470 chunk 49 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 80 optimal weight: 0.4980 chunk 34 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.163180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.141221 restraints weight = 12599.014| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 2.06 r_work: 0.3747 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3597 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8907 Z= 0.161 Angle : 0.634 11.425 12065 Z= 0.326 Chirality : 0.044 0.298 1392 Planarity : 0.004 0.041 1506 Dihedral : 4.835 25.690 1189 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.90 % Allowed : 20.23 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.26), residues: 1090 helix: 2.30 (0.27), residues: 364 sheet: -0.84 (0.28), residues: 268 loop : -1.29 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 332 HIS 0.007 0.001 HIS C 35 PHE 0.033 0.002 PHE A 282 TYR 0.013 0.002 TYR C 192 ARG 0.010 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03703 ( 441) hydrogen bonds : angle 5.09255 ( 1233) SS BOND : bond 0.00601 ( 2) SS BOND : angle 1.47685 ( 4) covalent geometry : bond 0.00378 ( 8905) covalent geometry : angle 0.63355 (12061) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8192.79 seconds wall clock time: 143 minutes 51.79 seconds (8631.79 seconds total)