Starting phenix.real_space_refine on Wed Sep 17 12:44:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wy0_32883/09_2025/7wy0_32883_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wy0_32883/09_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_32883/09_2025/7wy0_32883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wy0_32883/09_2025/7wy0_32883.map" model { file = "/net/cci-nas-00/data/ceres_data/7wy0_32883/09_2025/7wy0_32883_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wy0_32883/09_2025/7wy0_32883_neut.cif" } resolution = 2.83 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= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.05, per 1000 atoms: 0.24 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: 0.69 Conformation dependent library (CDL) restraints added in 388.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.35 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: 1.42 Time building geometry restraints manager: 0.94 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.970 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.800 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.009 0.001 ARG B 49 TYR 0.028 0.004 TYR R 668 PHE 0.039 0.003 PHE A 282 TRP 0.039 0.003 TRP R 734 HIS 0.009 0.002 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00725 ( 8905) covalent geometry : angle 0.86874 (12061) SS BOND : bond 0.00726 ( 2) SS BOND : angle 1.99549 ( 4) hydrogen bonds : bond 0.14446 ( 441) hydrogen bonds : angle 7.21128 ( 1233) *********************** 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 : 0.349 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: 0.5137 time to fit residues: 101.2703 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 : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 0.0980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.4101 r_free = 0.4101 target = 0.161055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.139551 restraints weight = 12605.895| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 2.04 r_work: 0.3725 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3574 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 8907 Z= 0.176 Angle : 0.656 10.521 12065 Z= 0.342 Chirality : 0.044 0.157 1392 Planarity : 0.004 0.046 1506 Dihedral : 5.236 26.207 1189 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.07 % Allowed : 11.00 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 aren not related in a simple way. whole: -0.36 (0.26), residues: 1090 helix: 1.77 (0.28), residues: 362 sheet: -0.92 (0.28), residues: 270 loop : -1.45 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 314 TYR 0.017 0.002 TYR C 192 PHE 0.021 0.002 PHE A 282 TRP 0.018 0.002 TRP C 178 HIS 0.005 0.001 HIS A 318 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 8905) covalent geometry : angle 0.65591 (12061) SS BOND : bond 0.00612 ( 2) SS BOND : angle 1.28053 ( 4) hydrogen bonds : bond 0.04458 ( 441) hydrogen bonds : angle 5.53976 ( 1233) *********************** 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 205 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 185 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 220 LYS cc_start: 0.8207 (ttmm) cc_final: 0.7899 (ttmm) REVERT: A 376 MET cc_start: 0.7583 (mpp) cc_final: 0.7185 (mpp) REVERT: B 105 TYR cc_start: 0.8376 (t80) cc_final: 0.8095 (t80) REVERT: B 130 GLU cc_start: 0.6968 (mp0) cc_final: 0.6688 (mp0) REVERT: B 145 TYR cc_start: 0.8379 (p90) cc_final: 0.8140 (p90) REVERT: B 150 ARG cc_start: 0.8131 (mmt-90) cc_final: 0.7732 (mpt180) REVERT: B 335 PHE cc_start: 0.8189 (m-10) cc_final: 0.7976 (m-10) REVERT: C 142 MET cc_start: 0.6741 (mmm) cc_final: 0.5276 (mtm) REVERT: C 194 MET cc_start: 0.4549 (tpt) cc_final: 0.4308 (tpp) REVERT: R 627 MET cc_start: 0.7010 (OUTLIER) cc_final: 0.6736 (tpp) REVERT: R 767 THR cc_start: 0.8220 (OUTLIER) cc_final: 0.7878 (m) outliers start: 20 outliers final: 9 residues processed: 192 average time/residue: 0.4789 time to fit residues: 99.1485 Evaluate side-chains 185 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 174 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 ASP 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 228 VAL Chi-restraints excluded: chain R residue 627 MET 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 15 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 71 optimal weight: 0.4980 chunk 55 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 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 = 0.4098 r_free = 0.4098 target = 0.160929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.139495 restraints weight = 12503.112| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 2.03 r_work: 0.3717 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3567 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 8907 Z= 0.205 Angle : 0.650 10.805 12065 Z= 0.336 Chirality : 0.045 0.412 1392 Planarity : 0.004 0.042 1506 Dihedral : 5.211 27.479 1189 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.11 % Allowed : 12.97 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 aren not related in a simple way. whole: -0.29 (0.26), residues: 1090 helix: 1.93 (0.28), residues: 357 sheet: -0.92 (0.29), residues: 259 loop : -1.42 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 96 TYR 0.018 0.002 TYR C 192 PHE 0.036 0.002 PHE A 282 TRP 0.015 0.002 TRP C 178 HIS 0.007 0.001 HIS R 820 Details of bonding type rmsd covalent geometry : bond 0.00478 ( 8905) covalent geometry : angle 0.64990 (12061) SS BOND : bond 0.00548 ( 2) SS BOND : angle 1.22836 ( 4) hydrogen bonds : bond 0.04231 ( 441) hydrogen bonds : angle 5.36031 ( 1233) *********************** 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 212 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 182 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 220 LYS cc_start: 0.8167 (ttmm) cc_final: 0.7836 (ttmm) REVERT: A 334 LYS cc_start: 0.6341 (OUTLIER) cc_final: 0.5941 (mptp) REVERT: A 376 MET cc_start: 0.7755 (mpp) cc_final: 0.7458 (mpp) REVERT: B 78 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.6880 (mppt) REVERT: B 130 GLU cc_start: 0.7030 (mp0) cc_final: 0.6694 (mp0) REVERT: B 145 TYR cc_start: 0.8399 (p90) cc_final: 0.8178 (p90) REVERT: B 150 ARG cc_start: 0.8126 (mmt-90) cc_final: 0.7853 (mpt180) REVERT: C 169 HIS cc_start: 0.6940 (t-90) cc_final: 0.6687 (t-90) outliers start: 30 outliers final: 15 residues processed: 193 average time/residue: 0.4817 time to fit residues: 100.0005 Evaluate side-chains 187 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 170 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 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 78 LYS 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 786 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 42 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 15 optimal weight: 0.0010 chunk 85 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.161640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.140166 restraints weight = 12773.161| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 2.05 r_work: 0.3727 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3576 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8907 Z= 0.175 Angle : 0.623 10.222 12065 Z= 0.324 Chirality : 0.044 0.389 1392 Planarity : 0.004 0.044 1506 Dihedral : 5.096 26.368 1189 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.53 % Allowed : 14.32 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 aren not related in a simple way. whole: -0.27 (0.26), residues: 1090 helix: 1.87 (0.27), residues: 366 sheet: -0.96 (0.29), residues: 259 loop : -1.39 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 623 TYR 0.017 0.002 TYR C 192 PHE 0.026 0.002 PHE A 282 TRP 0.017 0.002 TRP C 178 HIS 0.009 0.001 HIS A 318 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 8905) covalent geometry : angle 0.62255 (12061) SS BOND : bond 0.00528 ( 2) SS BOND : angle 1.17012 ( 4) hydrogen bonds : bond 0.03968 ( 441) hydrogen bonds : angle 5.24968 ( 1233) *********************** 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 215 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 181 time to evaluate : 0.340 Fit side-chains REVERT: A 220 LYS cc_start: 0.8174 (ttmm) cc_final: 0.7883 (ttmm) REVERT: B 59 TYR cc_start: 0.5905 (p90) cc_final: 0.5622 (p90) REVERT: B 78 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.6867 (mppt) REVERT: B 130 GLU cc_start: 0.6965 (mp0) cc_final: 0.6609 (mp0) REVERT: B 150 ARG cc_start: 0.8117 (mmt-90) cc_final: 0.7813 (mpt180) REVERT: B 291 ASP cc_start: 0.7009 (p0) cc_final: 0.6721 (p0) REVERT: C 142 MET cc_start: 0.6660 (mmm) cc_final: 0.5293 (mtm) REVERT: C 169 HIS cc_start: 0.6925 (t-90) cc_final: 0.6657 (t-90) REVERT: C 174 THR cc_start: 0.7455 (OUTLIER) cc_final: 0.7136 (t) REVERT: R 767 THR cc_start: 0.8179 (OUTLIER) cc_final: 0.7782 (m) REVERT: R 835 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7388 (tp) outliers start: 34 outliers final: 13 residues processed: 195 average time/residue: 0.4894 time to fit residues: 102.7244 Evaluate side-chains 187 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 170 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 78 LYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 174 THR 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 835 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 16 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.160795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.139153 restraints weight = 12702.734| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.04 r_work: 0.3712 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3559 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 8907 Z= 0.219 Angle : 0.654 11.155 12065 Z= 0.338 Chirality : 0.046 0.428 1392 Planarity : 0.004 0.043 1506 Dihedral : 5.147 27.908 1189 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 4.15 % Allowed : 15.04 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 aren not related in a simple way. whole: -0.26 (0.26), residues: 1090 helix: 1.89 (0.27), residues: 367 sheet: -0.94 (0.29), residues: 257 loop : -1.41 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 96 TYR 0.018 0.002 TYR C 192 PHE 0.026 0.002 PHE B 151 TRP 0.015 0.002 TRP C 178 HIS 0.007 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00511 ( 8905) covalent geometry : angle 0.65330 (12061) SS BOND : bond 0.00549 ( 2) SS BOND : angle 1.60867 ( 4) hydrogen bonds : bond 0.04092 ( 441) hydrogen bonds : angle 5.30746 ( 1233) *********************** 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 215 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 175 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 LYS cc_start: 0.8187 (ttmm) cc_final: 0.7909 (ttmm) REVERT: A 334 LYS cc_start: 0.6499 (OUTLIER) cc_final: 0.6069 (mptp) REVERT: B 78 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.6891 (mppt) REVERT: B 129 ARG cc_start: 0.7606 (mtp85) cc_final: 0.7331 (mtp85) REVERT: B 130 GLU cc_start: 0.7057 (mp0) cc_final: 0.6713 (mp0) REVERT: C 4 LEU cc_start: 0.8290 (mm) cc_final: 0.8022 (mt) REVERT: C 169 HIS cc_start: 0.6904 (t-90) cc_final: 0.6680 (t-90) REVERT: C 174 THR cc_start: 0.7503 (OUTLIER) cc_final: 0.7189 (t) outliers start: 40 outliers final: 21 residues processed: 195 average time/residue: 0.4942 time to fit residues: 103.6409 Evaluate side-chains 200 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 176 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 236 GLU 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 78 LYS Chi-restraints excluded: chain B residue 120 ILE 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 190 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 786 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 63 optimal weight: 0.0970 chunk 90 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 50 optimal weight: 0.3980 chunk 71 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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** ** 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 = 0.4115 r_free = 0.4115 target = 0.162689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.140912 restraints weight = 12594.652| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 2.05 r_work: 0.3737 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3586 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.2065 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 : 0.609 7.565 12065 Z= 0.316 Chirality : 0.045 0.449 1392 Planarity : 0.004 0.042 1506 Dihedral : 4.995 25.726 1189 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.63 % Allowed : 16.39 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 aren not related in a simple way. whole: -0.14 (0.26), residues: 1090 helix: 2.10 (0.27), residues: 364 sheet: -0.90 (0.29), residues: 258 loop : -1.39 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 134 TYR 0.016 0.002 TYR B 289 PHE 0.017 0.002 PHE B 151 TRP 0.014 0.002 TRP C 178 HIS 0.005 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 8905) covalent geometry : angle 0.60800 (12061) SS BOND : bond 0.00640 ( 2) SS BOND : angle 1.57785 ( 4) hydrogen bonds : bond 0.03811 ( 441) hydrogen bonds : angle 5.18655 ( 1233) *********************** 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 213 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: B 59 TYR cc_start: 0.5921 (p90) cc_final: 0.5604 (p90) REVERT: B 78 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.6857 (mppt) REVERT: B 88 ASN cc_start: 0.8513 (OUTLIER) cc_final: 0.8003 (m110) REVERT: B 101 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.7888 (ptp) REVERT: B 130 GLU cc_start: 0.6957 (mp0) cc_final: 0.6595 (mp0) REVERT: B 150 ARG cc_start: 0.8105 (mmt-90) cc_final: 0.7776 (mpt180) REVERT: C 4 LEU cc_start: 0.8294 (mm) cc_final: 0.8022 (mt) REVERT: C 169 HIS cc_start: 0.6872 (t-90) cc_final: 0.6656 (t-90) REVERT: C 174 THR cc_start: 0.7438 (OUTLIER) cc_final: 0.7212 (t) outliers start: 35 outliers final: 15 residues processed: 197 average time/residue: 0.4577 time to fit residues: 97.4899 Evaluate side-chains 190 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 171 time to evaluate : 0.327 ------------------------------------------------------------------------------- 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 78 LYS Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 101 MET 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 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 600 LEU Chi-restraints excluded: chain R residue 635 LEU Chi-restraints excluded: chain R residue 786 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 25 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 24 optimal weight: 0.0030 chunk 7 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 104 optimal weight: 0.2980 overall best weight: 0.5390 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.162625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.140912 restraints weight = 12671.021| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.05 r_work: 0.3740 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3588 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.2178 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= 0.164 Angle : 0.611 10.591 12065 Z= 0.317 Chirality : 0.045 0.471 1392 Planarity : 0.004 0.044 1506 Dihedral : 4.930 26.079 1189 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.84 % Allowed : 17.53 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 aren not related in a simple way. whole: -0.15 (0.26), residues: 1090 helix: 2.03 (0.27), residues: 370 sheet: -0.89 (0.29), residues: 257 loop : -1.40 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 96 TYR 0.018 0.002 TYR B 289 PHE 0.019 0.002 PHE B 151 TRP 0.016 0.002 TRP B 332 HIS 0.005 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 8905) covalent geometry : angle 0.61032 (12061) SS BOND : bond 0.00575 ( 2) SS BOND : angle 1.50969 ( 4) hydrogen bonds : bond 0.03777 ( 441) hydrogen bonds : angle 5.14895 ( 1233) *********************** 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 209 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 172 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 LYS cc_start: 0.8120 (ttmm) cc_final: 0.7891 (tttp) REVERT: A 334 LYS cc_start: 0.6477 (OUTLIER) cc_final: 0.6010 (mptp) REVERT: B 33 ILE cc_start: 0.7069 (mp) cc_final: 0.6559 (mp) REVERT: B 59 TYR cc_start: 0.5884 (p90) cc_final: 0.5586 (p90) REVERT: B 78 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.6839 (mppt) REVERT: B 88 ASN cc_start: 0.8510 (OUTLIER) cc_final: 0.8016 (m110) REVERT: B 101 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.7874 (ptp) REVERT: B 130 GLU cc_start: 0.6935 (mp0) cc_final: 0.6559 (mp0) REVERT: B 150 ARG cc_start: 0.8120 (mmt-90) cc_final: 0.7781 (mpt180) REVERT: C 4 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8027 (mt) REVERT: C 43 LYS cc_start: 0.7399 (OUTLIER) cc_final: 0.7193 (mmtm) REVERT: C 169 HIS cc_start: 0.6883 (t-90) cc_final: 0.6674 (t-90) REVERT: C 174 THR cc_start: 0.7515 (OUTLIER) cc_final: 0.7147 (t) REVERT: C 194 MET cc_start: 0.4086 (tpt) cc_final: 0.3811 (tpt) REVERT: R 701 VAL cc_start: 0.8421 (p) cc_final: 0.8146 (t) outliers start: 37 outliers final: 20 residues processed: 189 average time/residue: 0.4893 time to fit residues: 99.6111 Evaluate side-chains 199 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 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 78 LYS Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 101 MET 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 12 VAL Chi-restraints excluded: chain C residue 43 LYS 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 600 LEU Chi-restraints excluded: chain R residue 627 MET Chi-restraints excluded: chain R residue 786 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 67 optimal weight: 4.9990 chunk 47 optimal weight: 0.2980 chunk 48 optimal weight: 0.9990 chunk 85 optimal weight: 0.0770 chunk 93 optimal weight: 0.4980 chunk 106 optimal weight: 0.6980 chunk 33 optimal weight: 0.0570 chunk 0 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.3256 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.164090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.142527 restraints weight = 12525.627| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 2.03 r_work: 0.3759 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3610 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8907 Z= 0.130 Angle : 0.583 7.795 12065 Z= 0.304 Chirality : 0.043 0.298 1392 Planarity : 0.004 0.040 1506 Dihedral : 4.736 24.157 1189 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.22 % Allowed : 17.84 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 aren not related in a simple way. whole: -0.03 (0.26), residues: 1090 helix: 2.16 (0.27), residues: 370 sheet: -0.82 (0.28), residues: 261 loop : -1.36 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 134 TYR 0.021 0.002 TYR C 175 PHE 0.014 0.001 PHE B 151 TRP 0.018 0.002 TRP B 332 HIS 0.003 0.001 HIS R 621 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 8905) covalent geometry : angle 0.58230 (12061) SS BOND : bond 0.00473 ( 2) SS BOND : angle 1.24920 ( 4) hydrogen bonds : bond 0.03563 ( 441) hydrogen bonds : angle 5.01323 ( 1233) *********************** 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 209 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 178 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 LYS cc_start: 0.8075 (ttmm) cc_final: 0.7821 (tttp) REVERT: B 33 ILE cc_start: 0.6830 (mp) cc_final: 0.6287 (mp) REVERT: B 59 TYR cc_start: 0.5865 (p90) cc_final: 0.5552 (p90) REVERT: B 78 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.6834 (mppt) REVERT: B 101 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.7852 (ptp) REVERT: B 130 GLU cc_start: 0.6844 (mp0) cc_final: 0.6522 (mp0) REVERT: B 150 ARG cc_start: 0.8092 (mmt-90) cc_final: 0.7737 (mpt180) REVERT: B 170 ASP cc_start: 0.7843 (t70) cc_final: 0.7641 (t0) REVERT: C 4 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8048 (mt) REVERT: C 169 HIS cc_start: 0.6863 (t-90) cc_final: 0.6577 (t-90) REVERT: C 174 THR cc_start: 0.7576 (OUTLIER) cc_final: 0.7107 (t) REVERT: R 701 VAL cc_start: 0.8326 (p) cc_final: 0.8080 (t) REVERT: R 734 TRP cc_start: 0.7963 (t-100) cc_final: 0.7676 (t-100) outliers start: 31 outliers final: 15 residues processed: 194 average time/residue: 0.4738 time to fit residues: 99.1812 Evaluate side-chains 191 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 172 time to evaluate : 0.239 ------------------------------------------------------------------------------- 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 311 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 101 MET 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 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 600 LEU Chi-restraints excluded: chain R residue 625 ILE Chi-restraints excluded: chain R residue 786 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 101 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 103 optimal weight: 0.0670 chunk 72 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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 = 0.4112 r_free = 0.4112 target = 0.162670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.140909 restraints weight = 12505.521| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.03 r_work: 0.3738 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3587 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.2389 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= 0.181 Angle : 0.637 8.469 12065 Z= 0.329 Chirality : 0.046 0.489 1392 Planarity : 0.004 0.040 1506 Dihedral : 4.868 26.768 1189 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.49 % Allowed : 18.88 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 aren not related in a simple way. whole: -0.04 (0.26), residues: 1090 helix: 2.20 (0.27), residues: 364 sheet: -0.86 (0.28), residues: 266 loop : -1.34 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 251 TYR 0.022 0.002 TYR C 175 PHE 0.022 0.002 PHE B 151 TRP 0.022 0.002 TRP B 332 HIS 0.006 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 8905) covalent geometry : angle 0.63623 (12061) SS BOND : bond 0.00601 ( 2) SS BOND : angle 1.33462 ( 4) hydrogen bonds : bond 0.03788 ( 441) hydrogen bonds : angle 5.12324 ( 1233) *********************** 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 198 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 174 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 LYS cc_start: 0.8090 (ttmm) cc_final: 0.7816 (tttp) REVERT: B 33 ILE cc_start: 0.6768 (mp) cc_final: 0.6254 (mp) REVERT: B 59 TYR cc_start: 0.5865 (p90) cc_final: 0.5559 (p90) REVERT: B 78 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.6863 (mppt) REVERT: B 101 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.7844 (ptp) REVERT: B 130 GLU cc_start: 0.7013 (mp0) cc_final: 0.6631 (mp0) REVERT: B 150 ARG cc_start: 0.8115 (mmt-90) cc_final: 0.7757 (mpt180) REVERT: C 4 LEU cc_start: 0.8274 (mm) cc_final: 0.8004 (mt) REVERT: C 169 HIS cc_start: 0.6875 (t-90) cc_final: 0.6637 (t-90) REVERT: C 174 THR cc_start: 0.7572 (OUTLIER) cc_final: 0.7158 (t) REVERT: R 701 VAL cc_start: 0.8343 (p) cc_final: 0.8088 (t) outliers start: 24 outliers final: 19 residues processed: 186 average time/residue: 0.4940 time to fit residues: 98.9128 Evaluate side-chains 189 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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 78 LYS Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 217 MET 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 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 600 LEU Chi-restraints excluded: chain R residue 786 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 87 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 chunk 81 optimal weight: 0.0470 chunk 98 optimal weight: 1.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 = 0.4115 r_free = 0.4115 target = 0.162947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.141220 restraints weight = 12496.754| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 2.04 r_work: 0.3742 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3594 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 8907 Z= 0.168 Angle : 0.637 8.783 12065 Z= 0.328 Chirality : 0.044 0.337 1392 Planarity : 0.004 0.040 1506 Dihedral : 4.867 26.167 1189 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.49 % Allowed : 20.23 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 aren not related in a simple way. whole: -0.06 (0.26), residues: 1090 helix: 2.21 (0.27), residues: 364 sheet: -0.88 (0.28), residues: 269 loop : -1.38 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 134 TYR 0.017 0.002 TYR B 145 PHE 0.020 0.002 PHE B 151 TRP 0.025 0.002 TRP B 332 HIS 0.007 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 8905) covalent geometry : angle 0.63636 (12061) SS BOND : bond 0.00630 ( 2) SS BOND : angle 1.36468 ( 4) hydrogen bonds : bond 0.03729 ( 441) hydrogen bonds : angle 5.11368 ( 1233) ********************** 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 199 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 175 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 220 LYS cc_start: 0.8095 (ttmm) cc_final: 0.7798 (tttp) REVERT: B 33 ILE cc_start: 0.6697 (mp) cc_final: 0.6214 (mp) REVERT: B 59 TYR cc_start: 0.5875 (p90) cc_final: 0.5580 (p90) REVERT: B 78 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.6902 (mppt) REVERT: B 101 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.7853 (ptp) REVERT: B 130 GLU cc_start: 0.6971 (mp0) cc_final: 0.6581 (mp0) REVERT: B 150 ARG cc_start: 0.8109 (mmt-90) cc_final: 0.7756 (mpt180) REVERT: C 4 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7967 (mt) REVERT: C 169 HIS cc_start: 0.6884 (t-90) cc_final: 0.6624 (t-90) REVERT: C 174 THR cc_start: 0.7593 (OUTLIER) cc_final: 0.7203 (t) REVERT: R 701 VAL cc_start: 0.8330 (p) cc_final: 0.8069 (t) outliers start: 24 outliers final: 19 residues processed: 186 average time/residue: 0.4718 time to fit residues: 94.6942 Evaluate side-chains 196 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 173 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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 78 LYS Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 217 MET 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 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 600 LEU Chi-restraints excluded: chain R residue 786 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 71 optimal weight: 0.0060 chunk 24 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 93 optimal weight: 0.1980 chunk 45 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 16 optimal weight: 0.3980 overall best weight: 0.3996 ------------------------------------------------------------------------------- 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 = 0.4125 r_free = 0.4125 target = 0.163890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.142243 restraints weight = 12438.259| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 2.02 r_work: 0.3762 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3615 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8907 Z= 0.143 Angle : 0.618 8.279 12065 Z= 0.318 Chirality : 0.044 0.305 1392 Planarity : 0.004 0.040 1506 Dihedral : 4.786 25.305 1189 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.49 % Allowed : 20.44 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.26), residues: 1090 helix: 2.30 (0.27), residues: 364 sheet: -0.89 (0.28), residues: 270 loop : -1.36 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 134 TYR 0.022 0.002 TYR C 175 PHE 0.016 0.002 PHE B 151 TRP 0.027 0.002 TRP B 332 HIS 0.005 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 8905) covalent geometry : angle 0.61797 (12061) SS BOND : bond 0.00571 ( 2) SS BOND : angle 1.15112 ( 4) hydrogen bonds : bond 0.03575 ( 441) hydrogen bonds : angle 5.04761 ( 1233) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3657.71 seconds wall clock time: 63 minutes 7.74 seconds (3787.74 seconds total)