Starting phenix.real_space_refine on Thu Feb 13 05:46:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wy0_32883/02_2025/7wy0_32883_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wy0_32883/02_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_32883/02_2025/7wy0_32883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wy0_32883/02_2025/7wy0_32883.map" model { file = "/net/cci-nas-00/data/ceres_data/7wy0_32883/02_2025/7wy0_32883_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wy0_32883/02_2025/7wy0_32883_neut.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 5591 2.51 5 N 1481 2.21 5 O 1595 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 4.89, per 1000 atoms: 0.56 Number of scatterers: 8723 At special positions: 0 Unit cell: (91.8, 119.88, 127.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1595 8.00 N 1481 7.00 C 5591 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 161 " - pdb=" SG CYS C 231 " distance=2.04 Simple disulfide: pdb=" SG CYS R 657 " - pdb=" SG CYS R 733 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 946.8 milliseconds 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: 0.98 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: 2.86 Time building geometry restraints manager: 2.54 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: 0.970 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: 0.290 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.180 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:12.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.590 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.963 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: 1.1077 time to fit residues: 219.2682 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 : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.5980 chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 0.0980 chunk 27 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 43 optimal weight: 0.4980 chunk 84 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 220 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.161192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.139719 restraints weight = 12472.928| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 2.03 r_work: 0.3728 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3578 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 8905 Z= 0.245 Angle : 0.653 10.277 12061 Z= 0.341 Chirality : 0.044 0.173 1392 Planarity : 0.004 0.045 1506 Dihedral : 5.252 25.834 1189 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.97 % Allowed : 10.89 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.26), residues: 1090 helix: 1.74 (0.28), residues: 362 sheet: -0.95 (0.28), residues: 275 loop : -1.44 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 178 HIS 0.004 0.001 HIS C 35 PHE 0.021 0.002 PHE A 282 TYR 0.017 0.002 TYR C 192 ARG 0.007 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 178 time to evaluate : 0.899 Fit side-chains REVERT: A 17 LYS cc_start: 0.8311 (mtmm) cc_final: 0.8066 (mttm) REVERT: A 33 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7544 (mt-10) REVERT: A 220 LYS cc_start: 0.8207 (ttmm) cc_final: 0.7966 (ttmm) REVERT: A 376 MET cc_start: 0.7587 (mpp) cc_final: 0.7190 (mpp) REVERT: B 105 TYR cc_start: 0.8356 (t80) cc_final: 0.8110 (t80) REVERT: B 130 GLU cc_start: 0.6963 (mp0) cc_final: 0.6689 (mp0) REVERT: B 150 ARG cc_start: 0.8136 (mmt-90) cc_final: 0.7731 (mpt180) REVERT: B 335 PHE cc_start: 0.8151 (m-10) cc_final: 0.7951 (m-10) REVERT: C 142 MET cc_start: 0.6738 (mmm) cc_final: 0.5245 (mtm) REVERT: C 194 MET cc_start: 0.4547 (tpt) cc_final: 0.4294 (tpp) REVERT: R 627 MET cc_start: 0.7014 (OUTLIER) cc_final: 0.6733 (tpp) REVERT: R 767 THR cc_start: 0.8219 (m) cc_final: 0.7888 (m) outliers start: 19 outliers final: 8 residues processed: 185 average time/residue: 1.0466 time to fit residues: 208.2003 Evaluate side-chains 182 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 173 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain R residue 627 MET Chi-restraints excluded: chain R residue 705 LEU Chi-restraints excluded: chain R residue 786 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 7 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 58 optimal weight: 0.1980 chunk 54 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 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 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 = 0.4097 r_free = 0.4097 target = 0.160607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.139014 restraints weight = 12654.063| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 2.05 r_work: 0.3720 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3568 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 8905 Z= 0.286 Angle : 0.633 11.195 12061 Z= 0.328 Chirality : 0.045 0.386 1392 Planarity : 0.004 0.041 1506 Dihedral : 5.141 27.220 1189 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.42 % Allowed : 12.24 % Favored : 84.34 % 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: -0.24 (0.26), residues: 1090 helix: 1.97 (0.28), residues: 356 sheet: -0.85 (0.29), residues: 259 loop : -1.42 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 178 HIS 0.011 0.001 HIS A 318 PHE 0.030 0.002 PHE A 282 TYR 0.017 0.002 TYR C 192 ARG 0.008 0.001 ARG B 96 *********************** 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 216 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 183 time to evaluate : 0.960 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8260 (mtmm) cc_final: 0.7946 (mttm) REVERT: A 220 LYS cc_start: 0.8163 (ttmm) cc_final: 0.7821 (ttmm) REVERT: A 334 LYS cc_start: 0.6327 (OUTLIER) cc_final: 0.5934 (mptp) REVERT: A 376 MET cc_start: 0.7748 (mpp) cc_final: 0.7419 (mpp) REVERT: B 130 GLU cc_start: 0.7031 (mp0) cc_final: 0.6700 (mp0) REVERT: B 150 ARG cc_start: 0.8126 (mmt-90) cc_final: 0.7843 (mpt180) REVERT: B 335 PHE cc_start: 0.8201 (m-10) cc_final: 0.7983 (m-10) REVERT: C 169 HIS cc_start: 0.6942 (t-90) cc_final: 0.6729 (t-90) REVERT: R 767 THR cc_start: 0.8217 (OUTLIER) cc_final: 0.7849 (m) outliers start: 33 outliers final: 15 residues processed: 195 average time/residue: 1.0260 time to fit residues: 215.7712 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 : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain R residue 600 LEU Chi-restraints excluded: chain R residue 635 LEU Chi-restraints excluded: chain R residue 705 LEU Chi-restraints excluded: chain R residue 767 THR Chi-restraints excluded: chain R residue 786 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 7 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 79 optimal weight: 0.0980 chunk 89 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 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 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 293 ASN 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 = 0.160957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.139408 restraints weight = 12618.225| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 2.05 r_work: 0.3728 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3580 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8905 Z= 0.266 Angle : 0.620 10.944 12061 Z= 0.321 Chirality : 0.044 0.364 1392 Planarity : 0.004 0.043 1506 Dihedral : 5.052 26.319 1189 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.73 % Allowed : 14.11 % 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 (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: -0.22 (0.26), residues: 1090 helix: 1.87 (0.27), residues: 366 sheet: -0.85 (0.29), residues: 259 loop : -1.36 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 178 HIS 0.010 0.001 HIS A 318 PHE 0.032 0.002 PHE A 282 TYR 0.017 0.002 TYR C 192 ARG 0.009 0.001 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 211 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 175 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8193 (mtmm) cc_final: 0.7880 (mttm) REVERT: A 220 LYS cc_start: 0.8164 (ttmm) cc_final: 0.7878 (ttmm) REVERT: B 59 TYR cc_start: 0.7945 (OUTLIER) cc_final: 0.7084 (t80) REVERT: B 130 GLU cc_start: 0.6968 (mp0) cc_final: 0.6613 (mp0) REVERT: B 150 ARG cc_start: 0.8104 (mmt-90) cc_final: 0.7800 (mpt180) REVERT: B 291 ASP cc_start: 0.7004 (p0) cc_final: 0.6653 (p0) REVERT: B 293 ASN cc_start: 0.7750 (m-40) cc_final: 0.7534 (p0) REVERT: C 142 MET cc_start: 0.6637 (mmm) cc_final: 0.5282 (mtm) REVERT: C 174 THR cc_start: 0.7484 (OUTLIER) cc_final: 0.7122 (t) REVERT: R 767 THR cc_start: 0.8171 (OUTLIER) cc_final: 0.7782 (m) REVERT: R 810 THR cc_start: 0.7440 (OUTLIER) cc_final: 0.6946 (t) REVERT: R 835 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7376 (tp) outliers start: 36 outliers final: 15 residues processed: 190 average time/residue: 1.0639 time to fit residues: 217.2420 Evaluate side-chains 186 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain R residue 590 TYR Chi-restraints excluded: chain R residue 600 LEU Chi-restraints excluded: chain R residue 635 LEU Chi-restraints excluded: chain R residue 767 THR Chi-restraints excluded: chain R residue 786 ILE Chi-restraints excluded: chain R residue 810 THR Chi-restraints excluded: chain R residue 835 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 55 optimal weight: 0.9980 chunk 49 optimal weight: 0.0870 chunk 106 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 81 optimal weight: 0.0000 chunk 95 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 overall best weight: 0.4962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.161553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.140105 restraints weight = 12673.237| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 2.05 r_work: 0.3733 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8905 Z= 0.235 Angle : 0.611 10.732 12061 Z= 0.315 Chirality : 0.044 0.372 1392 Planarity : 0.004 0.041 1506 Dihedral : 4.938 25.840 1189 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.84 % Allowed : 15.35 % 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 (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: -0.15 (0.26), residues: 1090 helix: 1.99 (0.27), residues: 367 sheet: -0.92 (0.29), residues: 264 loop : -1.31 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 178 HIS 0.004 0.001 HIS C 35 PHE 0.027 0.002 PHE A 282 TYR 0.016 0.002 TYR C 192 ARG 0.009 0.001 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 212 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 175 time to evaluate : 0.932 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8134 (mtmm) cc_final: 0.7850 (mttm) REVERT: A 220 LYS cc_start: 0.8155 (ttmm) cc_final: 0.7858 (ttmm) REVERT: B 78 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7051 (mppt) REVERT: B 129 ARG cc_start: 0.7560 (mtp85) cc_final: 0.7244 (mtp85) REVERT: B 130 GLU cc_start: 0.6946 (mp0) cc_final: 0.6595 (mp0) REVERT: B 145 TYR cc_start: 0.8449 (p90) cc_final: 0.8231 (p90) REVERT: B 291 ASP cc_start: 0.7025 (p0) cc_final: 0.6804 (p0) REVERT: B 318 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7725 (pt) REVERT: C 4 LEU cc_start: 0.8289 (mm) cc_final: 0.8024 (mt) REVERT: C 157 VAL cc_start: 0.8342 (t) cc_final: 0.8134 (p) REVERT: C 174 THR cc_start: 0.7464 (OUTLIER) cc_final: 0.7133 (t) REVERT: R 810 THR cc_start: 0.7346 (OUTLIER) cc_final: 0.6842 (t) REVERT: R 835 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7385 (tp) outliers start: 37 outliers final: 17 residues processed: 195 average time/residue: 0.9582 time to fit residues: 202.2755 Evaluate side-chains 192 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 170 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain R residue 590 TYR Chi-restraints excluded: chain R residue 600 LEU Chi-restraints excluded: chain R residue 627 MET Chi-restraints excluded: chain R residue 635 LEU Chi-restraints excluded: chain R residue 786 ILE Chi-restraints excluded: chain R residue 810 THR Chi-restraints excluded: chain R residue 835 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 63 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 82 optimal weight: 0.3980 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 0.2980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.161662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.140210 restraints weight = 12517.746| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 2.03 r_work: 0.3740 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3590 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.2184 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= 0.234 Angle : 0.602 9.774 12061 Z= 0.312 Chirality : 0.045 0.425 1392 Planarity : 0.004 0.041 1506 Dihedral : 4.909 25.447 1189 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.22 % Allowed : 17.01 % Favored : 79.77 % 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: 2.13 (0.27), residues: 365 sheet: -0.86 (0.28), residues: 269 loop : -1.34 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 178 HIS 0.005 0.001 HIS C 35 PHE 0.018 0.002 PHE B 151 TYR 0.017 0.002 TYR C 175 ARG 0.009 0.001 ARG B 134 *********************** 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 200 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 169 time to evaluate : 0.803 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8101 (mtmm) cc_final: 0.7877 (mttm) REVERT: A 220 LYS cc_start: 0.8161 (ttmm) cc_final: 0.7859 (ttmm) REVERT: B 59 TYR cc_start: 0.7973 (OUTLIER) cc_final: 0.7122 (t80) REVERT: B 78 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7054 (mppt) REVERT: B 130 GLU cc_start: 0.6909 (mp0) cc_final: 0.6548 (mp0) REVERT: B 150 ARG cc_start: 0.8114 (mmt-90) cc_final: 0.7785 (mpt180) REVERT: C 4 LEU cc_start: 0.8293 (mm) cc_final: 0.8028 (mt) REVERT: C 157 VAL cc_start: 0.8339 (t) cc_final: 0.8129 (p) REVERT: C 174 THR cc_start: 0.7401 (OUTLIER) cc_final: 0.7116 (t) REVERT: C 194 MET cc_start: 0.3817 (tpt) cc_final: 0.3551 (tpt) REVERT: R 835 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7344 (tp) outliers start: 31 outliers final: 19 residues processed: 185 average time/residue: 1.0649 time to fit residues: 212.4340 Evaluate side-chains 190 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 167 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain R residue 590 TYR Chi-restraints excluded: chain R residue 600 LEU Chi-restraints excluded: chain R residue 627 MET Chi-restraints excluded: chain R residue 786 ILE Chi-restraints excluded: chain R residue 810 THR Chi-restraints excluded: chain R residue 835 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 40 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 97 optimal weight: 0.5980 chunk 19 optimal weight: 0.0980 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** ** A 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN ** R 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.161708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.140011 restraints weight = 12621.112| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.04 r_work: 0.3736 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3585 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8905 Z= 0.253 Angle : 0.606 10.515 12061 Z= 0.314 Chirality : 0.044 0.281 1392 Planarity : 0.004 0.043 1506 Dihedral : 4.889 25.944 1189 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 4.46 % Allowed : 17.01 % 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: -0.05 (0.26), residues: 1090 helix: 2.18 (0.27), residues: 364 sheet: -0.85 (0.28), residues: 267 loop : -1.35 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 332 HIS 0.005 0.001 HIS C 35 PHE 0.034 0.002 PHE A 282 TYR 0.019 0.002 TYR B 289 ARG 0.011 0.001 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 216 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 173 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 LYS cc_start: 0.8176 (ttmm) cc_final: 0.7875 (ttmm) REVERT: B 78 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7020 (mppt) REVERT: B 130 GLU cc_start: 0.6983 (mp0) cc_final: 0.6607 (mp0) REVERT: B 145 TYR cc_start: 0.8545 (p90) cc_final: 0.8312 (p90) REVERT: B 150 ARG cc_start: 0.8128 (mmt-90) cc_final: 0.7792 (mpt180) REVERT: C 4 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8020 (mt) REVERT: C 174 THR cc_start: 0.7460 (OUTLIER) cc_final: 0.7075 (t) REVERT: C 194 MET cc_start: 0.4251 (tpt) cc_final: 0.3957 (tpt) REVERT: R 835 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7352 (tp) outliers start: 43 outliers final: 26 residues processed: 199 average time/residue: 0.9999 time to fit residues: 215.0223 Evaluate side-chains 196 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 0.881 ------------------------------------------------------------------------------- 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 43 ILE Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 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 79 LEU Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain R residue 590 TYR Chi-restraints excluded: chain R residue 600 LEU Chi-restraints excluded: chain R residue 627 MET Chi-restraints excluded: chain R residue 786 ILE Chi-restraints excluded: chain R residue 810 THR Chi-restraints excluded: chain R residue 835 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 31 optimal weight: 0.3980 chunk 97 optimal weight: 0.9980 chunk 106 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 69 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN C 234 HIS R 736 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.162636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.140861 restraints weight = 12684.073| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 2.05 r_work: 0.3742 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8905 Z= 0.238 Angle : 0.610 9.268 12061 Z= 0.317 Chirality : 0.044 0.388 1392 Planarity : 0.004 0.040 1506 Dihedral : 4.843 25.590 1189 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.63 % Allowed : 18.05 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.26), residues: 1090 helix: 2.10 (0.27), residues: 371 sheet: -0.77 (0.29), residues: 264 loop : -1.37 (0.30), residues: 455 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 0.033 0.002 PHE A 282 TYR 0.019 0.002 TYR B 289 ARG 0.009 0.001 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 210 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 175 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: A 220 LYS cc_start: 0.8125 (ttmm) cc_final: 0.7806 (tttp) REVERT: B 33 ILE cc_start: 0.6989 (mp) cc_final: 0.6648 (mp) REVERT: B 59 TYR cc_start: 0.7958 (OUTLIER) cc_final: 0.7097 (t80) REVERT: B 78 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7034 (mppt) REVERT: B 130 GLU cc_start: 0.6943 (mp0) cc_final: 0.6572 (mp0) REVERT: B 145 TYR cc_start: 0.8594 (p90) cc_final: 0.8372 (p90) REVERT: B 150 ARG cc_start: 0.8120 (mmt-90) cc_final: 0.7773 (mpt180) REVERT: B 336 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8187 (mt) REVERT: C 4 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8018 (mt) REVERT: R 701 VAL cc_start: 0.8405 (p) cc_final: 0.8132 (t) REVERT: R 835 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7350 (tp) outliers start: 35 outliers final: 22 residues processed: 192 average time/residue: 1.0415 time to fit residues: 215.7916 Evaluate side-chains 197 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 170 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain R residue 590 TYR Chi-restraints excluded: chain R residue 600 LEU Chi-restraints excluded: chain R residue 627 MET Chi-restraints excluded: chain R residue 786 ILE Chi-restraints excluded: chain R residue 810 THR Chi-restraints excluded: chain R residue 835 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 45 optimal weight: 1.9990 chunk 38 optimal weight: 0.1980 chunk 59 optimal weight: 1.9990 chunk 34 optimal weight: 0.3980 chunk 12 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 29 optimal weight: 0.0670 chunk 58 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 69 optimal weight: 0.0670 overall best weight: 0.2856 ------------------------------------------------------------------------------- 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 = 0.4133 r_free = 0.4133 target = 0.164216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.141609 restraints weight = 12665.402| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 2.16 r_work: 0.3752 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3597 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8905 Z= 0.192 Angle : 0.606 11.485 12061 Z= 0.311 Chirality : 0.043 0.302 1392 Planarity : 0.004 0.040 1506 Dihedral : 4.732 23.727 1189 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.01 % Allowed : 19.29 % Favored : 77.70 % 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: 2.35 (0.27), residues: 365 sheet: -0.78 (0.29), residues: 264 loop : -1.26 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 332 HIS 0.003 0.001 HIS C 35 PHE 0.029 0.002 PHE A 282 TYR 0.019 0.001 TYR B 289 ARG 0.010 0.000 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 205 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 LYS cc_start: 0.8162 (ttmm) cc_final: 0.7906 (ttmm) REVERT: B 33 ILE cc_start: 0.6708 (mp) cc_final: 0.6357 (mp) REVERT: B 59 TYR cc_start: 0.7994 (OUTLIER) cc_final: 0.7104 (t80) REVERT: B 78 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.6872 (mppt) REVERT: B 130 GLU cc_start: 0.6850 (mp0) cc_final: 0.6511 (mp0) REVERT: B 150 ARG cc_start: 0.8133 (mmt-90) cc_final: 0.7788 (mpt180) REVERT: B 170 ASP cc_start: 0.7882 (t70) cc_final: 0.7649 (t0) REVERT: C 174 THR cc_start: 0.7421 (OUTLIER) cc_final: 0.7114 (t) REVERT: R 701 VAL cc_start: 0.8236 (p) cc_final: 0.7957 (t) REVERT: R 835 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7297 (tp) outliers start: 29 outliers final: 20 residues processed: 189 average time/residue: 1.0345 time to fit residues: 211.0362 Evaluate side-chains 192 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 168 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain R residue 590 TYR Chi-restraints excluded: chain R residue 600 LEU Chi-restraints excluded: chain R residue 627 MET Chi-restraints excluded: chain R residue 705 LEU Chi-restraints excluded: chain R residue 786 ILE Chi-restraints excluded: chain R residue 810 THR Chi-restraints excluded: chain R residue 835 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 45 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 chunk 57 optimal weight: 0.0370 chunk 63 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 0.0010 chunk 76 optimal weight: 2.9990 overall best weight: 0.5066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN ** R 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.163529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.141731 restraints weight = 12560.457| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 2.04 r_work: 0.3749 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3599 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8905 Z= 0.238 Angle : 0.612 8.794 12061 Z= 0.318 Chirality : 0.044 0.304 1392 Planarity : 0.004 0.043 1506 Dihedral : 4.796 25.726 1189 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.11 % Allowed : 19.40 % Favored : 77.49 % 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: 2.34 (0.27), residues: 365 sheet: -0.78 (0.28), residues: 265 loop : -1.26 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 332 HIS 0.006 0.001 HIS C 35 PHE 0.035 0.002 PHE A 282 TYR 0.013 0.001 TYR C 192 ARG 0.010 0.000 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 203 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 173 time to evaluate : 1.038 Fit side-chains revert: symmetry clash REVERT: A 299 GLU cc_start: 0.6947 (mt-10) cc_final: 0.6686 (mt-10) REVERT: B 59 TYR cc_start: 0.7947 (OUTLIER) cc_final: 0.7106 (t80) REVERT: B 78 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.6982 (mppt) REVERT: B 130 GLU cc_start: 0.6904 (mp0) cc_final: 0.6554 (mp0) REVERT: B 150 ARG cc_start: 0.8140 (mmt-90) cc_final: 0.7793 (mpt180) REVERT: B 331 SER cc_start: 0.8042 (t) cc_final: 0.7789 (t) REVERT: C 4 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8044 (mt) REVERT: C 174 THR cc_start: 0.7514 (OUTLIER) cc_final: 0.7176 (t) REVERT: R 701 VAL cc_start: 0.8260 (p) cc_final: 0.8019 (t) REVERT: R 835 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7350 (tp) outliers start: 30 outliers final: 20 residues processed: 187 average time/residue: 1.0252 time to fit residues: 208.5985 Evaluate side-chains 199 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 174 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain 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 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 212 ASP 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 115 THR Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain R residue 590 TYR Chi-restraints excluded: chain R residue 600 LEU Chi-restraints excluded: chain R residue 627 MET Chi-restraints excluded: chain R residue 786 ILE Chi-restraints excluded: chain R residue 835 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 107 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 97 optimal weight: 0.0170 chunk 49 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 79 optimal weight: 0.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- 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 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.162192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.140356 restraints weight = 12554.003| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 2.03 r_work: 0.3740 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3590 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.2583 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= 0.275 Angle : 0.637 8.943 12061 Z= 0.329 Chirality : 0.045 0.370 1392 Planarity : 0.004 0.043 1506 Dihedral : 4.876 26.346 1189 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.49 % Allowed : 20.54 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.26), residues: 1090 helix: 2.27 (0.27), residues: 364 sheet: -0.88 (0.28), residues: 271 loop : -1.29 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 332 HIS 0.007 0.001 HIS C 35 PHE 0.038 0.002 PHE A 282 TYR 0.023 0.002 TYR C 175 ARG 0.010 0.001 ARG B 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7151.62 seconds wall clock time: 126 minutes 54.82 seconds (7614.82 seconds total)