Starting phenix.real_space_refine on Mon Mar 11 17:13:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wy0_32883/03_2024/7wy0_32883_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wy0_32883/03_2024/7wy0_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wy0_32883/03_2024/7wy0_32883.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wy0_32883/03_2024/7wy0_32883.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wy0_32883/03_2024/7wy0_32883_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wy0_32883/03_2024/7wy0_32883_neut.pdb" } 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 Residue "A TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.04, per 1000 atoms: 0.58 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 - 3.50 Amino acid : False - 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: 3.09 Conformation dependent library (CDL) restraints added in 1.6 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: 0.89 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: 2.74 Time building geometry restraints manager: 3.39 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: 98.32 - 105.48: 138 105.48 - 112.64: 4759 112.64 - 119.80: 2864 119.80 - 126.95: 4188 126.95 - 134.11: 112 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 2.440 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.147 2.440 nonbonded pdb=" OE2 GLU A 236 " pdb=" NH1 ARG B 314 " model vdw 2.157 2.520 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP D 48 " model vdw 2.201 2.440 ... (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 ========== 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: 0.960 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: 3.960 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 25.700 Find NCS groups from input model: 0.230 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: 0.000 Load rotamer database and sin/cos tables:10.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.730 ------------------------------------------------------------------------------- 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 8905 Z= 0.478 Angle : 0.869 10.467 12061 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.037 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: 1.0906 time to fit residues: 215.8551 Evaluate side-chains 162 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.008 ------------------------------------------------------------------------------- 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: 0.3980 chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 0.0770 chunk 27 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 43 optimal weight: 0.0970 chunk 84 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 overall best weight: 0.3536 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN C 173 ASN C 181 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 8905 Z= 0.210 Angle : 0.624 10.117 12061 Z= 0.324 Chirality : 0.043 0.148 1392 Planarity : 0.004 0.043 1506 Dihedral : 5.082 23.985 1189 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.76 % Allowed : 10.68 % Favored : 87.55 % 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: 1.87 (0.28), residues: 362 sheet: -0.93 (0.28), residues: 281 loop : -1.39 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 178 HIS 0.003 0.001 HIS C 35 PHE 0.019 0.002 PHE A 282 TYR 0.017 0.002 TYR R 668 ARG 0.008 0.001 ARG B 134 *********************** 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 196 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 179 time to evaluate : 0.998 Fit side-chains REVERT: A 220 LYS cc_start: 0.7457 (ttmm) cc_final: 0.7202 (ttmm) REVERT: A 376 MET cc_start: 0.6730 (mpp) cc_final: 0.6324 (mpp) REVERT: B 130 GLU cc_start: 0.6398 (mp0) cc_final: 0.6171 (mp0) REVERT: B 150 ARG cc_start: 0.7819 (mmt-90) cc_final: 0.7428 (mpt180) REVERT: C 142 MET cc_start: 0.6566 (mmm) cc_final: 0.4753 (mtm) REVERT: R 627 MET cc_start: 0.6358 (OUTLIER) cc_final: 0.6145 (tpp) REVERT: R 767 THR cc_start: 0.7713 (m) cc_final: 0.7406 (m) outliers start: 17 outliers final: 9 residues processed: 185 average time/residue: 1.0383 time to fit residues: 206.8317 Evaluate side-chains 181 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 171 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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 128 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain R residue 599 SER Chi-restraints excluded: chain R residue 627 MET Chi-restraints excluded: chain R residue 705 LEU Chi-restraints excluded: chain R residue 786 ILE Chi-restraints excluded: chain R residue 811 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 81 optimal weight: 0.4980 chunk 66 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 0.4980 chunk 106 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 8905 Z= 0.283 Angle : 0.621 11.188 12061 Z= 0.320 Chirality : 0.044 0.407 1392 Planarity : 0.004 0.037 1506 Dihedral : 5.043 25.996 1189 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.63 % Allowed : 12.55 % Favored : 83.82 % 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: -0.16 (0.26), residues: 1090 helix: 2.06 (0.28), residues: 358 sheet: -0.84 (0.29), residues: 265 loop : -1.39 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 178 HIS 0.011 0.001 HIS A 318 PHE 0.033 0.002 PHE A 282 TYR 0.017 0.002 TYR C 192 ARG 0.006 0.000 ARG B 251 *********************** 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 217 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 182 time to evaluate : 0.970 Fit side-chains REVERT: A 220 LYS cc_start: 0.7428 (ttmm) cc_final: 0.7157 (ttmm) REVERT: A 334 LYS cc_start: 0.6092 (OUTLIER) cc_final: 0.5718 (mptp) REVERT: B 78 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.6867 (mppt) REVERT: B 130 GLU cc_start: 0.6451 (mp0) cc_final: 0.6188 (mp0) REVERT: B 150 ARG cc_start: 0.7823 (mmt-90) cc_final: 0.7534 (mpt180) REVERT: R 767 THR cc_start: 0.7748 (OUTLIER) cc_final: 0.7371 (m) outliers start: 35 outliers final: 18 residues processed: 194 average time/residue: 1.0370 time to fit residues: 216.7676 Evaluate side-chains 198 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 177 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 59 TYR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL 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 203 ASP Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain R residue 599 SER 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.2980 chunk 73 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 0.0060 chunk 98 optimal weight: 0.9990 chunk 104 optimal weight: 0.0060 chunk 51 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.4012 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8905 Z= 0.204 Angle : 0.576 10.261 12061 Z= 0.297 Chirality : 0.043 0.378 1392 Planarity : 0.004 0.048 1506 Dihedral : 4.792 24.584 1189 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.32 % Allowed : 15.25 % Favored : 81.43 % 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: -0.01 (0.26), residues: 1090 helix: 2.25 (0.27), residues: 359 sheet: -0.83 (0.29), residues: 270 loop : -1.32 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 178 HIS 0.012 0.001 HIS A 318 PHE 0.029 0.002 PHE A 282 TYR 0.016 0.002 TYR B 289 ARG 0.007 0.000 ARG R 623 *********************** 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 fitting. rotamer outliers: 32 poor density : 180 time to evaluate : 1.108 Fit side-chains REVERT: A 38 LYS cc_start: 0.7913 (mttp) cc_final: 0.7662 (mttp) REVERT: B 59 TYR cc_start: 0.7346 (OUTLIER) cc_final: 0.6661 (t80) REVERT: B 78 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.6907 (mppt) REVERT: B 130 GLU cc_start: 0.6338 (mp0) cc_final: 0.6063 (mp0) REVERT: B 150 ARG cc_start: 0.7799 (mmt-90) cc_final: 0.7474 (mpt180) REVERT: B 186 ASP cc_start: 0.6854 (m-30) cc_final: 0.6615 (m-30) REVERT: B 239 ASN cc_start: 0.7965 (p0) cc_final: 0.7557 (p0) REVERT: B 291 ASP cc_start: 0.6127 (p0) cc_final: 0.5229 (p0) REVERT: R 767 THR cc_start: 0.7647 (OUTLIER) cc_final: 0.7320 (m) outliers start: 32 outliers final: 9 residues processed: 194 average time/residue: 1.0360 time to fit residues: 216.2356 Evaluate side-chains 180 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 168 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 59 TYR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain R residue 599 SER Chi-restraints excluded: chain R residue 635 LEU Chi-restraints excluded: chain R residue 767 THR Chi-restraints excluded: chain R residue 786 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.8980 chunk 59 optimal weight: 0.4980 chunk 1 optimal weight: 0.1980 chunk 77 optimal weight: 0.8980 chunk 43 optimal weight: 0.1980 chunk 89 optimal weight: 0.0970 chunk 72 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.3378 ------------------------------------------------------------------------------- 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 125 ASN ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8905 Z= 0.192 Angle : 0.565 9.758 12061 Z= 0.290 Chirality : 0.043 0.387 1392 Planarity : 0.003 0.038 1506 Dihedral : 4.665 23.616 1189 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.22 % Allowed : 15.87 % Favored : 80.91 % 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: 0.10 (0.26), residues: 1090 helix: 2.25 (0.27), residues: 366 sheet: -0.71 (0.29), residues: 265 loop : -1.26 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 178 HIS 0.012 0.001 HIS A 318 PHE 0.028 0.002 PHE A 282 TYR 0.016 0.001 TYR B 289 ARG 0.008 0.000 ARG B 134 *********************** 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 200 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 169 time to evaluate : 0.938 Fit side-chains revert: symmetry clash REVERT: A 38 LYS cc_start: 0.7920 (mttp) cc_final: 0.7699 (mttp) REVERT: A 334 LYS cc_start: 0.6103 (OUTLIER) cc_final: 0.5675 (mptp) REVERT: A 376 MET cc_start: 0.6708 (mpp) cc_final: 0.6384 (mtp) REVERT: B 78 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.6896 (mppt) REVERT: B 129 ARG cc_start: 0.7051 (mtp85) cc_final: 0.6733 (mtp85) REVERT: B 130 GLU cc_start: 0.6302 (mp0) cc_final: 0.6035 (mp0) REVERT: B 186 ASP cc_start: 0.6845 (m-30) cc_final: 0.6563 (m-30) REVERT: B 318 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7505 (pt) REVERT: R 701 VAL cc_start: 0.8233 (p) cc_final: 0.7970 (t) outliers start: 31 outliers final: 13 residues processed: 183 average time/residue: 0.9700 time to fit residues: 192.4027 Evaluate side-chains 188 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 172 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 334 LYS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain R residue 599 SER Chi-restraints excluded: chain R residue 627 MET 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 35 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 25 optimal weight: 0.4980 chunk 104 optimal weight: 0.0870 chunk 86 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 8 optimal weight: 0.0970 chunk 34 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 overall best weight: 0.4556 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8905 Z= 0.216 Angle : 0.570 9.743 12061 Z= 0.294 Chirality : 0.043 0.340 1392 Planarity : 0.003 0.037 1506 Dihedral : 4.664 29.474 1189 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.80 % Allowed : 16.49 % Favored : 80.71 % 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: 2.31 (0.27), residues: 366 sheet: -0.69 (0.29), residues: 265 loop : -1.27 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 178 HIS 0.005 0.001 HIS C 35 PHE 0.031 0.002 PHE A 282 TYR 0.016 0.001 TYR C 192 ARG 0.006 0.000 ARG B 96 *********************** 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 205 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 178 time to evaluate : 1.036 Fit side-chains revert: symmetry clash REVERT: A 38 LYS cc_start: 0.7938 (mttp) cc_final: 0.7733 (mttp) REVERT: A 376 MET cc_start: 0.6713 (mpp) cc_final: 0.6371 (mtp) REVERT: B 33 ILE cc_start: 0.7173 (mp) cc_final: 0.6920 (mp) REVERT: B 78 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.6935 (mppt) REVERT: B 130 GLU cc_start: 0.6367 (mp0) cc_final: 0.6092 (mp0) REVERT: B 150 ARG cc_start: 0.7850 (mmt-90) cc_final: 0.7502 (mpt180) REVERT: B 186 ASP cc_start: 0.6954 (m-30) cc_final: 0.6616 (m-30) REVERT: B 289 TYR cc_start: 0.7567 (m-80) cc_final: 0.7114 (m-80) REVERT: R 701 VAL cc_start: 0.8229 (p) cc_final: 0.7998 (t) outliers start: 27 outliers final: 15 residues processed: 190 average time/residue: 1.0111 time to fit residues: 207.1584 Evaluate side-chains 189 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 173 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 59 TYR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain R residue 599 SER Chi-restraints excluded: chain R residue 627 MET Chi-restraints excluded: chain R residue 786 ILE Chi-restraints excluded: chain R residue 810 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.6980 chunk 11 optimal weight: 0.0370 chunk 59 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 104 optimal weight: 0.1980 chunk 65 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.4858 ------------------------------------------------------------------------------- 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 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8905 Z= 0.225 Angle : 0.592 11.216 12061 Z= 0.302 Chirality : 0.044 0.477 1392 Planarity : 0.003 0.044 1506 Dihedral : 4.659 28.503 1189 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.32 % Allowed : 17.22 % Favored : 79.46 % 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: 0.12 (0.26), residues: 1090 helix: 2.29 (0.27), residues: 367 sheet: -0.76 (0.29), residues: 270 loop : -1.24 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 178 HIS 0.005 0.001 HIS C 35 PHE 0.031 0.002 PHE A 282 TYR 0.014 0.001 TYR C 192 ARG 0.010 0.000 ARG B 96 *********************** 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 215 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 183 time to evaluate : 1.060 Fit side-chains revert: symmetry clash REVERT: A 38 LYS cc_start: 0.7928 (mttp) cc_final: 0.7716 (mttp) REVERT: B 33 ILE cc_start: 0.6926 (mp) cc_final: 0.6474 (mp) REVERT: B 59 TYR cc_start: 0.7387 (OUTLIER) cc_final: 0.6669 (t80) REVERT: B 78 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.6944 (mppt) REVERT: B 130 GLU cc_start: 0.6378 (mp0) cc_final: 0.6100 (mp0) REVERT: B 150 ARG cc_start: 0.7861 (mmt-90) cc_final: 0.7507 (mpt180) REVERT: B 186 ASP cc_start: 0.6968 (m-30) cc_final: 0.6751 (m-30) REVERT: B 289 TYR cc_start: 0.7544 (m-80) cc_final: 0.7245 (m-80) REVERT: C 4 LEU cc_start: 0.7879 (mm) cc_final: 0.7609 (mt) REVERT: R 701 VAL cc_start: 0.8289 (p) cc_final: 0.8011 (t) outliers start: 32 outliers final: 21 residues processed: 198 average time/residue: 1.0151 time to fit residues: 216.7159 Evaluate side-chains 203 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 180 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 253 PHE 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 59 TYR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain R residue 567 THR Chi-restraints excluded: chain R residue 599 SER Chi-restraints excluded: chain R residue 627 MET Chi-restraints excluded: chain R residue 786 ILE Chi-restraints excluded: chain R residue 810 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 81 optimal weight: 0.1980 chunk 94 optimal weight: 0.9990 chunk 99 optimal weight: 0.0970 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** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8905 Z= 0.229 Angle : 0.594 9.881 12061 Z= 0.304 Chirality : 0.045 0.491 1392 Planarity : 0.004 0.050 1506 Dihedral : 4.685 27.965 1189 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.42 % Allowed : 17.43 % Favored : 79.15 % 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: 0.13 (0.26), residues: 1090 helix: 2.31 (0.27), residues: 367 sheet: -0.74 (0.29), residues: 270 loop : -1.26 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 332 HIS 0.005 0.001 HIS C 35 PHE 0.037 0.002 PHE A 282 TYR 0.014 0.001 TYR C 192 ARG 0.011 0.000 ARG B 96 *********************** 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 214 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 181 time to evaluate : 1.037 Fit side-chains revert: symmetry clash REVERT: B 33 ILE cc_start: 0.6778 (mp) cc_final: 0.6322 (mp) REVERT: B 78 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.6957 (mppt) REVERT: B 130 GLU cc_start: 0.6436 (mp0) cc_final: 0.6125 (mp0) REVERT: B 150 ARG cc_start: 0.7859 (mmt-90) cc_final: 0.7494 (mpt180) REVERT: B 186 ASP cc_start: 0.6993 (m-30) cc_final: 0.6765 (m-30) REVERT: B 289 TYR cc_start: 0.7530 (m-80) cc_final: 0.7232 (m-80) REVERT: B 318 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7456 (pt) REVERT: R 701 VAL cc_start: 0.8260 (p) cc_final: 0.8043 (t) outliers start: 33 outliers final: 26 residues processed: 195 average time/residue: 0.9863 time to fit residues: 207.8492 Evaluate side-chains 206 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 178 time to evaluate : 0.989 ------------------------------------------------------------------------------- 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 253 PHE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 195 ASP 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 C residue 79 LEU Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain R residue 567 THR Chi-restraints excluded: chain R residue 599 SER Chi-restraints excluded: chain R residue 627 MET Chi-restraints excluded: chain R residue 786 ILE Chi-restraints excluded: chain R residue 810 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.9990 chunk 97 optimal weight: 0.2980 chunk 99 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 91 optimal weight: 0.2980 chunk 96 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8905 Z= 0.261 Angle : 0.627 11.880 12061 Z= 0.318 Chirality : 0.045 0.421 1392 Planarity : 0.004 0.088 1506 Dihedral : 4.745 27.043 1189 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.22 % Allowed : 18.26 % Favored : 78.53 % 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: 2.24 (0.27), residues: 367 sheet: -0.80 (0.29), residues: 270 loop : -1.27 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 178 HIS 0.006 0.001 HIS C 35 PHE 0.039 0.002 PHE A 282 TYR 0.015 0.002 TYR C 192 ARG 0.020 0.001 ARG B 96 *********************** 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 211 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 180 time to evaluate : 0.978 Fit side-chains REVERT: B 33 ILE cc_start: 0.6698 (mp) cc_final: 0.6233 (mp) REVERT: B 59 TYR cc_start: 0.7422 (OUTLIER) cc_final: 0.6685 (t80) REVERT: B 78 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.6928 (mppt) REVERT: B 150 ARG cc_start: 0.7865 (mmt-90) cc_final: 0.7491 (mpt180) REVERT: B 289 TYR cc_start: 0.7532 (m-80) cc_final: 0.7270 (m-80) REVERT: R 701 VAL cc_start: 0.8323 (p) cc_final: 0.8052 (t) outliers start: 31 outliers final: 25 residues processed: 192 average time/residue: 0.9894 time to fit residues: 205.9901 Evaluate side-chains 201 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 174 time to evaluate : 1.190 ------------------------------------------------------------------------------- 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 253 PHE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain R residue 567 THR Chi-restraints excluded: chain R residue 599 SER Chi-restraints excluded: chain R residue 627 MET Chi-restraints excluded: chain R residue 786 ILE Chi-restraints excluded: chain R residue 810 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.1980 chunk 62 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 71 optimal weight: 0.0980 chunk 107 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 chunk 66 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8905 Z= 0.209 Angle : 0.608 9.642 12061 Z= 0.307 Chirality : 0.044 0.420 1392 Planarity : 0.004 0.089 1506 Dihedral : 4.671 26.389 1189 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.49 % Allowed : 19.29 % 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: 0.07 (0.26), residues: 1090 helix: 2.27 (0.27), residues: 367 sheet: -0.81 (0.29), residues: 270 loop : -1.27 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 332 HIS 0.005 0.001 HIS C 35 PHE 0.032 0.002 PHE A 282 TYR 0.014 0.001 TYR B 145 ARG 0.020 0.001 ARG B 96 ********************** 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 196 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 172 time to evaluate : 1.054 Fit side-chains REVERT: B 33 ILE cc_start: 0.6618 (mp) cc_final: 0.6144 (mp) REVERT: B 59 TYR cc_start: 0.7429 (OUTLIER) cc_final: 0.6693 (t80) REVERT: B 78 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.6933 (mppt) REVERT: B 150 ARG cc_start: 0.7864 (mmt-90) cc_final: 0.7486 (mpt180) REVERT: B 289 TYR cc_start: 0.7492 (m-80) cc_final: 0.7224 (m-80) REVERT: R 701 VAL cc_start: 0.8279 (p) cc_final: 0.8020 (t) outliers start: 24 outliers final: 20 residues processed: 181 average time/residue: 0.9712 time to fit residues: 190.7982 Evaluate side-chains 192 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 170 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 311 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR 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 195 ASP Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain R residue 567 THR Chi-restraints excluded: chain R residue 599 SER Chi-restraints excluded: chain R residue 627 MET Chi-restraints excluded: chain R residue 786 ILE Chi-restraints excluded: chain R residue 810 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 79 optimal weight: 0.2980 chunk 12 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 0.3980 chunk 75 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 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 = 0.4118 r_free = 0.4118 target = 0.162963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.141041 restraints weight = 12524.538| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 2.02 r_work: 0.3742 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3594 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8905 Z= 0.251 Angle : 0.629 10.895 12061 Z= 0.317 Chirality : 0.044 0.337 1392 Planarity : 0.004 0.087 1506 Dihedral : 4.739 26.259 1189 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.01 % Allowed : 18.88 % Favored : 78.11 % 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: 2.28 (0.27), residues: 367 sheet: -0.84 (0.29), residues: 270 loop : -1.29 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 332 HIS 0.006 0.001 HIS C 35 PHE 0.035 0.002 PHE A 282 TYR 0.015 0.001 TYR C 192 ARG 0.020 0.001 ARG B 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3895.72 seconds wall clock time: 70 minutes 2.93 seconds (4202.93 seconds total)