Starting phenix.real_space_refine on Wed Mar 4 09:18:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x2u_32971/03_2026/7x2u_32971_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x2u_32971/03_2026/7x2u_32971.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7x2u_32971/03_2026/7x2u_32971_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x2u_32971/03_2026/7x2u_32971_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7x2u_32971/03_2026/7x2u_32971.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x2u_32971/03_2026/7x2u_32971.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 110 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 36 5.16 5 C 7791 2.51 5 N 1932 2.21 5 O 2100 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11861 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4308 Classifications: {'peptide': 541} Link IDs: {'PTRANS': 13, 'TRANS': 527} Chain breaks: 2 Chain: "B" Number of atoms: 4300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4300 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 13, 'TRANS': 526} Chain breaks: 2 Chain: "C" Number of atoms: 1505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1505 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "D" Number of atoms: 1505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1505 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "A" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 123 Unusual residues: {'85R': 1, 'PGT': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 222 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PGT:plan-1': 5, 'PGT:plan-2': 5} Unresolved non-hydrogen planarities: 34 Chain: "B" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Unusual residues: {'85R': 1, 'PGT': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 190 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 190 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PGT:plan-1': 5, 'PGT:plan-2': 5} Unresolved non-hydrogen planarities: 38 Time building chain proxies: 2.99, per 1000 atoms: 0.25 Number of scatterers: 11861 At special positions: 0 Unit cell: (145, 85, 99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 2 15.00 O 2100 8.00 N 1932 7.00 C 7791 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 528.1 milliseconds 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2718 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 2 sheets defined 77.1% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 53 through 73 Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 83 through 102 Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 111 through 116 Processing helix chain 'A' and resid 119 through 130 removed outlier: 4.182A pdb=" N ILE A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 139 Processing helix chain 'A' and resid 139 through 148 Processing helix chain 'A' and resid 148 through 168 Processing helix chain 'A' and resid 177 through 189 Processing helix chain 'A' and resid 192 through 195 Processing helix chain 'A' and resid 196 through 201 Processing helix chain 'A' and resid 206 through 238 removed outlier: 3.908A pdb=" N ASP A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 276 Processing helix chain 'A' and resid 277 through 279 No H-bonds generated for 'chain 'A' and resid 277 through 279' Processing helix chain 'A' and resid 285 through 304 Processing helix chain 'A' and resid 307 through 318 Processing helix chain 'A' and resid 328 through 360 removed outlier: 3.726A pdb=" N THR A 334 " --> pdb=" O GLN A 330 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 395 removed outlier: 3.623A pdb=" N ARG A 382 " --> pdb=" O ILE A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 411 Processing helix chain 'A' and resid 416 through 425 Processing helix chain 'A' and resid 433 through 464 removed outlier: 5.229A pdb=" N LYS A 457 " --> pdb=" O GLY A 453 " (cutoff:3.500A) Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 475 through 495 removed outlier: 3.661A pdb=" N ASP A 493 " --> pdb=" O SER A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 514 Processing helix chain 'A' and resid 514 through 520 removed outlier: 3.783A pdb=" N VAL A 518 " --> pdb=" O PHE A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 537 removed outlier: 3.647A pdb=" N GLU A 537 " --> pdb=" O ASN A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 624 Processing helix chain 'A' and resid 627 through 631 removed outlier: 3.678A pdb=" N TYR A 631 " --> pdb=" O ARG A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 661 removed outlier: 3.695A pdb=" N ASP A 649 " --> pdb=" O ASP A 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 73 Processing helix chain 'B' and resid 75 through 80 Processing helix chain 'B' and resid 83 through 102 Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 111 through 116 Processing helix chain 'B' and resid 119 through 130 removed outlier: 4.182A pdb=" N ILE B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 139 Processing helix chain 'B' and resid 139 through 148 Processing helix chain 'B' and resid 148 through 168 Processing helix chain 'B' and resid 177 through 189 Processing helix chain 'B' and resid 192 through 195 Processing helix chain 'B' and resid 196 through 201 Processing helix chain 'B' and resid 206 through 238 removed outlier: 3.908A pdb=" N ASP B 221 " --> pdb=" O SER B 217 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 276 Processing helix chain 'B' and resid 277 through 279 No H-bonds generated for 'chain 'B' and resid 277 through 279' Processing helix chain 'B' and resid 285 through 304 Processing helix chain 'B' and resid 307 through 318 Processing helix chain 'B' and resid 328 through 359 removed outlier: 3.727A pdb=" N THR B 334 " --> pdb=" O GLN B 330 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS B 340 " --> pdb=" O ARG B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 395 removed outlier: 3.622A pdb=" N ARG B 382 " --> pdb=" O ILE B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 411 Processing helix chain 'B' and resid 416 through 425 Processing helix chain 'B' and resid 433 through 464 removed outlier: 5.229A pdb=" N LYS B 457 " --> pdb=" O GLY B 453 " (cutoff:3.500A) Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 475 through 495 removed outlier: 3.661A pdb=" N ASP B 493 " --> pdb=" O SER B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 514 Processing helix chain 'B' and resid 514 through 520 removed outlier: 3.782A pdb=" N VAL B 518 " --> pdb=" O PHE B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 537 removed outlier: 3.648A pdb=" N GLU B 537 " --> pdb=" O ASN B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 631 removed outlier: 3.678A pdb=" N TYR B 631 " --> pdb=" O ARG B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 661 removed outlier: 3.696A pdb=" N ASP B 649 " --> pdb=" O ASP B 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 22 removed outlier: 3.671A pdb=" N ILE C 17 " --> pdb=" O GLU C 13 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 39 Processing helix chain 'C' and resid 47 through 53 Processing helix chain 'C' and resid 62 through 71 removed outlier: 3.694A pdb=" N PHE C 71 " --> pdb=" O ILE C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 88 Processing helix chain 'C' and resid 89 through 91 No H-bonds generated for 'chain 'C' and resid 89 through 91' Processing helix chain 'C' and resid 94 through 99 removed outlier: 3.524A pdb=" N LYS C 98 " --> pdb=" O GLU C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 123 Processing helix chain 'C' and resid 131 through 142 Processing helix chain 'C' and resid 148 through 164 Processing helix chain 'C' and resid 173 through 180 Processing helix chain 'C' and resid 181 through 183 No H-bonds generated for 'chain 'C' and resid 181 through 183' Processing helix chain 'C' and resid 184 through 189 Processing helix chain 'D' and resid 12 through 22 removed outlier: 3.671A pdb=" N ILE D 17 " --> pdb=" O GLU D 13 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS D 18 " --> pdb=" O LEU D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 39 Processing helix chain 'D' and resid 47 through 53 Processing helix chain 'D' and resid 62 through 71 removed outlier: 3.693A pdb=" N PHE D 71 " --> pdb=" O ILE D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 88 Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 94 through 99 removed outlier: 3.523A pdb=" N LYS D 98 " --> pdb=" O GLU D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 123 Processing helix chain 'D' and resid 131 through 142 Processing helix chain 'D' and resid 148 through 164 Processing helix chain 'D' and resid 173 through 180 Processing helix chain 'D' and resid 181 through 183 No H-bonds generated for 'chain 'D' and resid 181 through 183' Processing helix chain 'D' and resid 184 through 189 Processing sheet with id=AA1, first strand: chain 'C' and resid 129 through 130 Processing sheet with id=AA2, first strand: chain 'D' and resid 129 through 130 761 hydrogen bonds defined for protein. 2253 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.62 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1872 1.30 - 1.43: 3251 1.43 - 1.56: 6916 1.56 - 1.68: 4 1.68 - 1.81: 64 Bond restraints: 12107 Sorted by residual: bond pdb=" C ILE A 349 " pdb=" N ILE A 350 " ideal model delta sigma weight residual 1.335 1.444 -0.109 1.26e-02 6.30e+03 7.55e+01 bond pdb=" C ILE A 349 " pdb=" O ILE A 349 " ideal model delta sigma weight residual 1.237 1.177 0.061 1.17e-02 7.31e+03 2.68e+01 bond pdb=" N VAL B 359 " pdb=" CA VAL B 359 " ideal model delta sigma weight residual 1.459 1.493 -0.035 9.10e-03 1.21e+04 1.44e+01 bond pdb=" CA1 85R B 702 " pdb=" OA1 85R B 702 " ideal model delta sigma weight residual 1.333 1.408 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" CA1 85R A 701 " pdb=" OA1 85R A 701 " ideal model delta sigma weight residual 1.333 1.408 -0.075 2.00e-02 2.50e+03 1.40e+01 ... (remaining 12102 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 15975 2.82 - 5.63: 322 5.63 - 8.45: 26 8.45 - 11.26: 11 11.26 - 14.08: 2 Bond angle restraints: 16336 Sorted by residual: angle pdb=" O ILE A 349 " pdb=" C ILE A 349 " pdb=" N ILE A 350 " ideal model delta sigma weight residual 121.87 111.25 10.62 9.70e-01 1.06e+00 1.20e+02 angle pdb=" CA ILE A 349 " pdb=" C ILE A 349 " pdb=" N ILE A 350 " ideal model delta sigma weight residual 117.15 123.58 -6.43 1.14e+00 7.69e-01 3.18e+01 angle pdb=" O11 85R A 701 " pdb=" P1 85R A 701 " pdb=" O12 85R A 701 " ideal model delta sigma weight residual 122.68 108.60 14.08 3.00e+00 1.11e-01 2.20e+01 angle pdb=" O11 85R B 702 " pdb=" P1 85R B 702 " pdb=" O12 85R B 702 " ideal model delta sigma weight residual 122.68 108.63 14.05 3.00e+00 1.11e-01 2.19e+01 angle pdb=" N VAL B 359 " pdb=" CA VAL B 359 " pdb=" C VAL B 359 " ideal model delta sigma weight residual 113.47 109.27 4.20 1.01e+00 9.80e-01 1.73e+01 ... (remaining 16331 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.06: 6274 18.06 - 36.13: 738 36.13 - 54.19: 163 54.19 - 72.25: 37 72.25 - 90.32: 12 Dihedral angle restraints: 7224 sinusoidal: 3023 harmonic: 4201 Sorted by residual: dihedral pdb=" CA TYR B 322 " pdb=" C TYR B 322 " pdb=" N VAL B 323 " pdb=" CA VAL B 323 " ideal model delta harmonic sigma weight residual 180.00 154.82 25.18 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA TYR A 322 " pdb=" C TYR A 322 " pdb=" N VAL A 323 " pdb=" CA VAL A 323 " ideal model delta harmonic sigma weight residual 180.00 154.84 25.16 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA LYS A 324 " pdb=" C LYS A 324 " pdb=" N ALA A 325 " pdb=" CA ALA A 325 " ideal model delta harmonic sigma weight residual 180.00 157.05 22.95 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 7221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1615 0.074 - 0.147: 246 0.147 - 0.221: 14 0.221 - 0.295: 4 0.295 - 0.368: 2 Chirality restraints: 1881 Sorted by residual: chirality pdb=" CB VAL A 196 " pdb=" CA VAL A 196 " pdb=" CG1 VAL A 196 " pdb=" CG2 VAL A 196 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" CB VAL B 196 " pdb=" CA VAL B 196 " pdb=" CG1 VAL B 196 " pdb=" CG2 VAL B 196 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CB ILE B 327 " pdb=" CA ILE B 327 " pdb=" CG1 ILE B 327 " pdb=" CG2 ILE B 327 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 1878 not shown) Planarity restraints: 2020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 120 " -0.035 5.00e-02 4.00e+02 5.21e-02 4.34e+00 pdb=" N PRO B 121 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 121 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 121 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 120 " 0.034 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO A 121 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 121 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 121 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 349 " 0.011 2.00e-02 2.50e+03 2.03e-02 4.13e+00 pdb=" C ILE A 349 " -0.035 2.00e-02 2.50e+03 pdb=" O ILE A 349 " 0.013 2.00e-02 2.50e+03 pdb=" N ILE A 350 " 0.011 2.00e-02 2.50e+03 ... (remaining 2017 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 303 2.69 - 3.24: 12407 3.24 - 3.79: 19994 3.79 - 4.35: 27084 4.35 - 4.90: 44305 Nonbonded interactions: 104093 Sorted by model distance: nonbonded pdb=" OH TYR A 146 " pdb=" OG1 THR A 390 " model vdw 2.138 3.040 nonbonded pdb=" OH TYR B 146 " pdb=" OG1 THR B 390 " model vdw 2.138 3.040 nonbonded pdb=" NH1 ARG D 65 " pdb=" O LEU D 121 " model vdw 2.175 3.120 nonbonded pdb=" NH1 ARG C 65 " pdb=" O LEU C 121 " model vdw 2.175 3.120 nonbonded pdb=" OH TYR A 625 " pdb=" OE2 GLU A 651 " model vdw 2.210 3.040 ... (remaining 104088 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 40 through 538 or resid 617 through 665 or (resid 703 and \ (name C15 or name C16 or name C17 or name C18 or name C19 or name C20)) or resid \ 706)) selection = (chain 'B' and (resid 40 through 665 or (resid 703 and (name C15 or name C16 or \ name C17 or name C18 or name C19 or name C20)) or resid 706)) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.410 Find NCS groups from input model: 0.140 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 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 : 0.010 0.109 12107 Z= 0.460 Angle : 0.920 14.076 16336 Z= 0.502 Chirality : 0.054 0.368 1881 Planarity : 0.004 0.052 2020 Dihedral : 16.537 90.319 4506 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.94 % Allowed : 1.72 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.22), residues: 1435 helix: -0.22 (0.16), residues: 1036 sheet: None (None), residues: 0 loop : -1.06 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 650 TYR 0.013 0.002 TYR A 322 PHE 0.033 0.002 PHE B 653 TRP 0.009 0.001 TRP B 364 HIS 0.013 0.002 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.01028 (12107) covalent geometry : angle 0.91957 (16336) hydrogen bonds : bond 0.17432 ( 761) hydrogen bonds : angle 7.73515 ( 2253) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 174 time to evaluate : 0.466 Fit side-chains REVERT: B 348 THR cc_start: 0.8634 (OUTLIER) cc_final: 0.8404 (m) REVERT: C 56 GLU cc_start: 0.7906 (pm20) cc_final: 0.7467 (pm20) REVERT: D 56 GLU cc_start: 0.7819 (pm20) cc_final: 0.7550 (pm20) REVERT: D 135 LEU cc_start: 0.7905 (tp) cc_final: 0.7644 (tp) REVERT: D 188 LYS cc_start: 0.8537 (ptmt) cc_final: 0.8098 (ptmt) outliers start: 12 outliers final: 4 residues processed: 183 average time/residue: 0.1219 time to fit residues: 30.8889 Evaluate side-chains 155 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 150 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 408 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS B 76 HIS C 109 ASN C 195 HIS D 195 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.136609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.092929 restraints weight = 13447.065| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 1.56 r_work: 0.2707 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2577 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12107 Z= 0.167 Angle : 0.580 7.025 16336 Z= 0.306 Chirality : 0.042 0.195 1881 Planarity : 0.004 0.050 2020 Dihedral : 9.341 59.139 1815 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.47 % Allowed : 8.93 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.22), residues: 1435 helix: 0.61 (0.16), residues: 1021 sheet: None (None), residues: 0 loop : -0.98 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 637 TYR 0.013 0.001 TYR A 322 PHE 0.022 0.002 PHE B 200 TRP 0.007 0.001 TRP B 507 HIS 0.010 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00391 (12107) covalent geometry : angle 0.57952 (16336) hydrogen bonds : bond 0.04799 ( 761) hydrogen bonds : angle 5.09339 ( 2253) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 169 time to evaluate : 0.373 Fit side-chains REVERT: C 56 GLU cc_start: 0.7945 (pm20) cc_final: 0.7437 (pm20) REVERT: C 188 LYS cc_start: 0.8409 (ptmt) cc_final: 0.8039 (ptmt) REVERT: D 56 GLU cc_start: 0.8169 (pm20) cc_final: 0.7705 (pm20) REVERT: D 135 LEU cc_start: 0.7639 (tp) cc_final: 0.7297 (tp) outliers start: 6 outliers final: 0 residues processed: 171 average time/residue: 0.1199 time to fit residues: 28.3451 Evaluate side-chains 156 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 17 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS B 76 HIS C 109 ASN C 195 HIS D 195 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.137387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.093618 restraints weight = 13410.403| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 1.55 r_work: 0.2710 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2583 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12107 Z= 0.168 Angle : 0.548 6.633 16336 Z= 0.288 Chirality : 0.042 0.156 1881 Planarity : 0.004 0.049 2020 Dihedral : 8.513 59.435 1808 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.25 % Allowed : 11.75 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.22), residues: 1435 helix: 0.71 (0.16), residues: 1046 sheet: None (None), residues: 0 loop : -0.84 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 637 TYR 0.012 0.001 TYR B 322 PHE 0.020 0.002 PHE B 200 TRP 0.007 0.001 TRP B 507 HIS 0.006 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00401 (12107) covalent geometry : angle 0.54806 (16336) hydrogen bonds : bond 0.04575 ( 761) hydrogen bonds : angle 4.80160 ( 2253) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 176 time to evaluate : 0.411 Fit side-chains REVERT: A 381 TYR cc_start: 0.9284 (m-80) cc_final: 0.9004 (m-10) REVERT: B 339 MET cc_start: 0.9023 (mtt) cc_final: 0.8786 (mtt) REVERT: B 381 TYR cc_start: 0.9262 (m-80) cc_final: 0.8974 (m-10) REVERT: C 56 GLU cc_start: 0.8162 (pm20) cc_final: 0.7690 (pm20) REVERT: C 135 LEU cc_start: 0.7792 (tp) cc_final: 0.7530 (tp) REVERT: C 188 LYS cc_start: 0.8430 (ptmt) cc_final: 0.8135 (ptmt) REVERT: D 56 GLU cc_start: 0.8212 (pm20) cc_final: 0.7767 (pm20) REVERT: D 123 ASP cc_start: 0.6198 (t0) cc_final: 0.5632 (t0) REVERT: D 135 LEU cc_start: 0.7711 (tp) cc_final: 0.7365 (tp) outliers start: 16 outliers final: 14 residues processed: 181 average time/residue: 0.1168 time to fit residues: 29.5601 Evaluate side-chains 181 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 167 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 GLN Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 136 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 43 optimal weight: 0.6980 chunk 51 optimal weight: 0.3980 chunk 41 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 0.0670 chunk 93 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 54 optimal weight: 0.0570 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS B 76 HIS C 109 ASN C 195 HIS D 195 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.142762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.099960 restraints weight = 13305.301| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.51 r_work: 0.2809 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12107 Z= 0.117 Angle : 0.491 6.353 16336 Z= 0.260 Chirality : 0.039 0.132 1881 Planarity : 0.003 0.047 2020 Dihedral : 7.469 58.606 1808 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.49 % Allowed : 13.08 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.22), residues: 1435 helix: 1.22 (0.16), residues: 1022 sheet: None (None), residues: 0 loop : -0.97 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 65 TYR 0.009 0.001 TYR A 322 PHE 0.014 0.001 PHE B 200 TRP 0.005 0.000 TRP B 366 HIS 0.005 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00260 (12107) covalent geometry : angle 0.49067 (16336) hydrogen bonds : bond 0.03974 ( 761) hydrogen bonds : angle 4.45681 ( 2253) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 189 time to evaluate : 0.467 Fit side-chains REVERT: A 208 VAL cc_start: 0.8765 (t) cc_final: 0.8525 (t) REVERT: A 621 GLN cc_start: 0.7491 (tm-30) cc_final: 0.7255 (pt0) REVERT: B 208 VAL cc_start: 0.8756 (t) cc_final: 0.8538 (t) REVERT: B 348 THR cc_start: 0.9097 (OUTLIER) cc_final: 0.8843 (m) REVERT: B 621 GLN cc_start: 0.7647 (tm-30) cc_final: 0.7340 (pt0) REVERT: C 56 GLU cc_start: 0.7840 (pm20) cc_final: 0.7429 (pm20) REVERT: C 135 LEU cc_start: 0.7699 (tp) cc_final: 0.7367 (tp) REVERT: C 168 ASP cc_start: 0.5996 (m-30) cc_final: 0.5492 (t0) REVERT: D 45 THR cc_start: 0.7925 (t) cc_final: 0.7677 (m) REVERT: D 56 GLU cc_start: 0.7970 (pm20) cc_final: 0.7512 (pm20) REVERT: D 168 ASP cc_start: 0.5811 (m-30) cc_final: 0.5466 (t0) outliers start: 19 outliers final: 12 residues processed: 199 average time/residue: 0.1133 time to fit residues: 32.2662 Evaluate side-chains 182 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 169 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 136 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 91 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 chunk 77 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 95 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 117 optimal weight: 0.3980 chunk 131 optimal weight: 3.9990 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 76 HIS B 76 HIS C 195 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.141041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.097827 restraints weight = 13302.079| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 1.51 r_work: 0.2764 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12107 Z= 0.142 Angle : 0.520 8.913 16336 Z= 0.271 Chirality : 0.040 0.157 1881 Planarity : 0.003 0.047 2020 Dihedral : 7.506 59.148 1808 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.88 % Allowed : 13.47 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.22), residues: 1435 helix: 1.12 (0.16), residues: 1052 sheet: None (None), residues: 0 loop : -0.95 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 65 TYR 0.010 0.001 TYR A 322 PHE 0.016 0.001 PHE B 200 TRP 0.006 0.001 TRP A 366 HIS 0.005 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00335 (12107) covalent geometry : angle 0.51991 (16336) hydrogen bonds : bond 0.04123 ( 761) hydrogen bonds : angle 4.45870 ( 2253) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 179 time to evaluate : 0.450 Fit side-chains REVERT: A 208 VAL cc_start: 0.8754 (t) cc_final: 0.8540 (t) REVERT: A 621 GLN cc_start: 0.7472 (tm-30) cc_final: 0.7198 (pt0) REVERT: B 208 VAL cc_start: 0.8761 (t) cc_final: 0.8552 (t) REVERT: B 348 THR cc_start: 0.9097 (OUTLIER) cc_final: 0.8827 (m) REVERT: B 380 VAL cc_start: 0.9010 (t) cc_final: 0.8699 (m) REVERT: B 621 GLN cc_start: 0.7613 (tm-30) cc_final: 0.7297 (pt0) REVERT: C 56 GLU cc_start: 0.7806 (pm20) cc_final: 0.7396 (pm20) REVERT: C 135 LEU cc_start: 0.7702 (tp) cc_final: 0.7376 (tp) REVERT: C 142 MET cc_start: 0.8905 (ttp) cc_final: 0.8646 (ttp) REVERT: C 168 ASP cc_start: 0.5993 (m-30) cc_final: 0.5462 (t0) REVERT: D 45 THR cc_start: 0.7940 (t) cc_final: 0.7712 (m) REVERT: D 56 GLU cc_start: 0.7780 (pm20) cc_final: 0.7444 (pm20) REVERT: D 168 ASP cc_start: 0.5875 (m-30) cc_final: 0.5503 (t0) outliers start: 24 outliers final: 16 residues processed: 191 average time/residue: 0.1125 time to fit residues: 30.3653 Evaluate side-chains 189 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 172 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 93 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 7 optimal weight: 0.0770 chunk 78 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 135 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 105 optimal weight: 0.3980 chunk 136 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS B 76 HIS C 195 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.140914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.099603 restraints weight = 13327.466| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 1.49 r_work: 0.2734 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12107 Z= 0.137 Angle : 0.512 7.358 16336 Z= 0.267 Chirality : 0.040 0.171 1881 Planarity : 0.003 0.047 2020 Dihedral : 7.362 58.261 1808 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.19 % Allowed : 13.86 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.22), residues: 1435 helix: 1.23 (0.16), residues: 1050 sheet: None (None), residues: 0 loop : -0.84 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 637 TYR 0.010 0.001 TYR A 322 PHE 0.015 0.001 PHE A 200 TRP 0.006 0.001 TRP A 366 HIS 0.005 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00320 (12107) covalent geometry : angle 0.51161 (16336) hydrogen bonds : bond 0.04035 ( 761) hydrogen bonds : angle 4.42137 ( 2253) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 179 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: A 208 VAL cc_start: 0.8808 (t) cc_final: 0.8597 (t) REVERT: A 380 VAL cc_start: 0.9047 (t) cc_final: 0.8750 (m) REVERT: A 621 GLN cc_start: 0.7481 (tm-30) cc_final: 0.7181 (pt0) REVERT: B 208 VAL cc_start: 0.8810 (t) cc_final: 0.8605 (t) REVERT: B 348 THR cc_start: 0.9153 (OUTLIER) cc_final: 0.8906 (m) REVERT: B 380 VAL cc_start: 0.9046 (t) cc_final: 0.8751 (m) REVERT: B 621 GLN cc_start: 0.7603 (tm-30) cc_final: 0.7277 (pt0) REVERT: C 56 GLU cc_start: 0.7892 (pm20) cc_final: 0.7498 (pm20) REVERT: C 93 ILE cc_start: 0.7682 (OUTLIER) cc_final: 0.7422 (tp) REVERT: C 135 LEU cc_start: 0.7810 (tp) cc_final: 0.7490 (tp) REVERT: C 142 MET cc_start: 0.8919 (ttp) cc_final: 0.8696 (ttp) REVERT: C 168 ASP cc_start: 0.6041 (m-30) cc_final: 0.5505 (t0) REVERT: D 56 GLU cc_start: 0.7852 (pm20) cc_final: 0.7494 (pm20) REVERT: D 93 ILE cc_start: 0.7658 (OUTLIER) cc_final: 0.7433 (tp) REVERT: D 168 ASP cc_start: 0.5862 (m-30) cc_final: 0.5497 (t0) outliers start: 28 outliers final: 17 residues processed: 192 average time/residue: 0.1068 time to fit residues: 29.4138 Evaluate side-chains 189 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 169 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 GLN Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 629 GLN Chi-restraints excluded: chain B residue 649 ASP Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 93 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 96 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 136 optimal weight: 0.5980 chunk 78 optimal weight: 0.0060 chunk 123 optimal weight: 8.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS B 76 HIS C 195 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.142573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.101935 restraints weight = 13242.505| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.48 r_work: 0.2859 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12107 Z= 0.132 Angle : 0.513 6.726 16336 Z= 0.268 Chirality : 0.040 0.144 1881 Planarity : 0.003 0.047 2020 Dihedral : 7.204 58.516 1808 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.27 % Allowed : 14.80 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.22), residues: 1435 helix: 1.33 (0.16), residues: 1050 sheet: None (None), residues: 0 loop : -0.89 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 65 TYR 0.009 0.001 TYR A 322 PHE 0.017 0.001 PHE A 200 TRP 0.006 0.001 TRP A 507 HIS 0.006 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00305 (12107) covalent geometry : angle 0.51270 (16336) hydrogen bonds : bond 0.03978 ( 761) hydrogen bonds : angle 4.39417 ( 2253) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 177 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8104 (tp30) cc_final: 0.7766 (tp30) REVERT: A 208 VAL cc_start: 0.8807 (t) cc_final: 0.8596 (t) REVERT: A 348 THR cc_start: 0.9163 (OUTLIER) cc_final: 0.8913 (m) REVERT: A 621 GLN cc_start: 0.7403 (tm-30) cc_final: 0.7128 (pt0) REVERT: B 48 GLU cc_start: 0.8130 (tp30) cc_final: 0.7804 (tp30) REVERT: B 208 VAL cc_start: 0.8850 (t) cc_final: 0.8638 (t) REVERT: B 348 THR cc_start: 0.9138 (OUTLIER) cc_final: 0.8911 (m) REVERT: B 621 GLN cc_start: 0.7496 (tm-30) cc_final: 0.7293 (pt0) REVERT: C 93 ILE cc_start: 0.7629 (OUTLIER) cc_final: 0.7405 (tp) REVERT: C 135 LEU cc_start: 0.7818 (tp) cc_final: 0.7461 (tp) REVERT: C 168 ASP cc_start: 0.6144 (m-30) cc_final: 0.5494 (t0) REVERT: D 16 GLU cc_start: 0.7592 (mp0) cc_final: 0.7239 (mp0) REVERT: D 93 ILE cc_start: 0.7661 (OUTLIER) cc_final: 0.7429 (tp) REVERT: D 142 MET cc_start: 0.8893 (ttp) cc_final: 0.8650 (ttp) REVERT: D 168 ASP cc_start: 0.5943 (m-30) cc_final: 0.5580 (t0) outliers start: 29 outliers final: 16 residues processed: 192 average time/residue: 0.1191 time to fit residues: 32.0708 Evaluate side-chains 186 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 GLN Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 649 ASP Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 124 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 143 optimal weight: 4.9990 chunk 133 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 107 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 110 optimal weight: 5.9990 chunk 68 optimal weight: 0.0870 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS B 76 HIS C 195 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.141741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.098570 restraints weight = 13243.103| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 1.53 r_work: 0.2784 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12107 Z= 0.130 Angle : 0.511 6.870 16336 Z= 0.267 Chirality : 0.040 0.139 1881 Planarity : 0.003 0.047 2020 Dihedral : 7.093 58.525 1808 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.35 % Allowed : 14.64 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.22), residues: 1435 helix: 1.43 (0.16), residues: 1042 sheet: None (None), residues: 0 loop : -0.83 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 65 TYR 0.009 0.001 TYR A 322 PHE 0.017 0.001 PHE B 200 TRP 0.007 0.001 TRP B 507 HIS 0.006 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00302 (12107) covalent geometry : angle 0.51100 (16336) hydrogen bonds : bond 0.03953 ( 761) hydrogen bonds : angle 4.36617 ( 2253) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 175 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8066 (tp30) cc_final: 0.7665 (tp30) REVERT: A 208 VAL cc_start: 0.8757 (t) cc_final: 0.8549 (t) REVERT: A 348 THR cc_start: 0.9118 (OUTLIER) cc_final: 0.8918 (m) REVERT: A 621 GLN cc_start: 0.7407 (tm-30) cc_final: 0.7128 (pt0) REVERT: B 48 GLU cc_start: 0.8116 (tp30) cc_final: 0.7723 (tp30) REVERT: B 208 VAL cc_start: 0.8792 (t) cc_final: 0.8586 (t) REVERT: B 348 THR cc_start: 0.9106 (OUTLIER) cc_final: 0.8870 (m) REVERT: C 93 ILE cc_start: 0.7597 (OUTLIER) cc_final: 0.7377 (tp) REVERT: C 135 LEU cc_start: 0.7649 (tp) cc_final: 0.7247 (tp) REVERT: C 168 ASP cc_start: 0.6142 (m-30) cc_final: 0.5495 (t0) REVERT: D 93 ILE cc_start: 0.7630 (OUTLIER) cc_final: 0.7407 (tp) REVERT: D 149 ASP cc_start: 0.7218 (m-30) cc_final: 0.6314 (p0) REVERT: D 168 ASP cc_start: 0.5896 (m-30) cc_final: 0.5532 (t0) outliers start: 30 outliers final: 18 residues processed: 191 average time/residue: 0.1218 time to fit residues: 32.8273 Evaluate side-chains 190 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 GLN Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 629 GLN Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 124 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 104 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 64 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 108 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS B 76 HIS C 195 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.139328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.097987 restraints weight = 13223.325| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 1.59 r_work: 0.2755 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12107 Z= 0.165 Angle : 0.540 7.424 16336 Z= 0.281 Chirality : 0.041 0.147 1881 Planarity : 0.003 0.047 2020 Dihedral : 7.350 59.257 1808 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.27 % Allowed : 15.35 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.22), residues: 1435 helix: 1.27 (0.16), residues: 1048 sheet: None (None), residues: 0 loop : -0.77 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 65 TYR 0.011 0.001 TYR A 129 PHE 0.017 0.002 PHE A 200 TRP 0.008 0.001 TRP A 507 HIS 0.006 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00397 (12107) covalent geometry : angle 0.54033 (16336) hydrogen bonds : bond 0.04237 ( 761) hydrogen bonds : angle 4.48702 ( 2253) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8060 (tp30) cc_final: 0.7826 (tp30) REVERT: A 348 THR cc_start: 0.9117 (OUTLIER) cc_final: 0.8866 (m) REVERT: A 621 GLN cc_start: 0.7348 (tm-30) cc_final: 0.7063 (pt0) REVERT: B 48 GLU cc_start: 0.8115 (tp30) cc_final: 0.7894 (tp30) REVERT: B 348 THR cc_start: 0.9092 (OUTLIER) cc_final: 0.8863 (m) REVERT: C 135 LEU cc_start: 0.7601 (tp) cc_final: 0.7216 (tp) REVERT: C 168 ASP cc_start: 0.6192 (m-30) cc_final: 0.5508 (t0) REVERT: D 16 GLU cc_start: 0.7725 (mp0) cc_final: 0.7456 (mp0) REVERT: D 142 MET cc_start: 0.8856 (ttp) cc_final: 0.8638 (ttp) REVERT: D 168 ASP cc_start: 0.5931 (m-30) cc_final: 0.5497 (t0) outliers start: 29 outliers final: 17 residues processed: 185 average time/residue: 0.1143 time to fit residues: 29.7974 Evaluate side-chains 187 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 GLN Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain D residue 93 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 5 optimal weight: 0.7980 chunk 142 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 115 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 122 optimal weight: 6.9990 chunk 120 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS B 76 HIS C 195 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.140549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.097046 restraints weight = 13370.178| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 1.55 r_work: 0.2763 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12107 Z= 0.144 Angle : 0.526 7.557 16336 Z= 0.274 Chirality : 0.040 0.140 1881 Planarity : 0.003 0.047 2020 Dihedral : 7.249 59.076 1808 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.57 % Allowed : 16.21 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.22), residues: 1435 helix: 1.41 (0.16), residues: 1038 sheet: None (None), residues: 0 loop : -0.83 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 65 TYR 0.010 0.001 TYR B 322 PHE 0.018 0.001 PHE B 200 TRP 0.007 0.001 TRP A 507 HIS 0.006 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00340 (12107) covalent geometry : angle 0.52643 (16336) hydrogen bonds : bond 0.04077 ( 761) hydrogen bonds : angle 4.43175 ( 2253) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8074 (tp30) cc_final: 0.7863 (tp30) REVERT: A 208 VAL cc_start: 0.8784 (t) cc_final: 0.8574 (t) REVERT: A 621 GLN cc_start: 0.7298 (tm-30) cc_final: 0.7030 (pt0) REVERT: B 48 GLU cc_start: 0.8120 (tp30) cc_final: 0.7909 (tp30) REVERT: B 208 VAL cc_start: 0.8812 (t) cc_final: 0.8607 (t) REVERT: B 339 MET cc_start: 0.8908 (mtt) cc_final: 0.8672 (mtt) REVERT: B 348 THR cc_start: 0.9096 (OUTLIER) cc_final: 0.8870 (m) REVERT: C 135 LEU cc_start: 0.7575 (tp) cc_final: 0.7196 (tp) REVERT: C 168 ASP cc_start: 0.6146 (m-30) cc_final: 0.5541 (t0) REVERT: D 93 ILE cc_start: 0.7622 (OUTLIER) cc_final: 0.7413 (tp) REVERT: D 128 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7404 (tp30) REVERT: D 142 MET cc_start: 0.8879 (ttp) cc_final: 0.8670 (ttp) REVERT: D 149 ASP cc_start: 0.7244 (m-30) cc_final: 0.6359 (p0) REVERT: D 168 ASP cc_start: 0.5830 (m-30) cc_final: 0.5483 (t0) outliers start: 20 outliers final: 15 residues processed: 183 average time/residue: 0.1210 time to fit residues: 31.0948 Evaluate side-chains 182 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 165 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 GLN Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain D residue 93 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 5 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 139 optimal weight: 0.9990 chunk 129 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 50 optimal weight: 0.3980 chunk 135 optimal weight: 0.1980 chunk 136 optimal weight: 0.8980 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 76 HIS B 76 HIS C 60 ASN C 195 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.141195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.097575 restraints weight = 13326.672| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 1.56 r_work: 0.2771 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12107 Z= 0.136 Angle : 0.521 7.371 16336 Z= 0.272 Chirality : 0.040 0.140 1881 Planarity : 0.003 0.047 2020 Dihedral : 7.154 59.955 1808 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.64 % Allowed : 16.44 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.22), residues: 1435 helix: 1.47 (0.16), residues: 1044 sheet: None (None), residues: 0 loop : -0.79 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 65 TYR 0.010 0.001 TYR A 322 PHE 0.018 0.001 PHE A 484 TRP 0.007 0.001 TRP A 507 HIS 0.006 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00319 (12107) covalent geometry : angle 0.52150 (16336) hydrogen bonds : bond 0.04017 ( 761) hydrogen bonds : angle 4.38397 ( 2253) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2768.81 seconds wall clock time: 48 minutes 8.12 seconds (2888.12 seconds total)