Starting phenix.real_space_refine on Fri Jul 3 05:57:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x2u_32971/07_2026/7x2u_32971_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x2u_32971/07_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_32971/07_2026/7x2u_32971_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x2u_32971/07_2026/7x2u_32971_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7x2u_32971/07_2026/7x2u_32971.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x2u_32971/07_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-6108/lib/python3.11/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: 112 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: 115 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: 2.17, per 1000 atoms: 0.18 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: 0.92 Conformation dependent library (CDL) restraints added in 428.0 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: 0.29 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: 1.48 Time building geometry restraints manager: 1.16 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.950 Find NCS groups from input model: 0.170 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 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/Z covalent geometry : bond 0.01029 / 0.46 (12107) covalent geometry : angle 0.91955 / 0.50 (16336) hydrogen bonds : bond 0.17432 / 11.88 ( 761) hydrogen bonds : angle 7.73515 / 5.49 ( 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 : 0.293 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: 0.1019 time to fit residues: 25.8698 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 : 0.437 ------------------------------------------------------------------------------- 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... 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 = 0.3423 r_free = 0.3423 target = 0.136911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.093107 restraints weight = 13441.003| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 1.56 r_work: 0.2701 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2570 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12107 Z= 0.169 Angle : 0.577 7.026 16336 Z= 0.304 Chirality : 0.042 0.201 1881 Planarity : 0.004 0.051 2020 Dihedral : 9.332 59.619 1815 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % 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: 0.60 (0.16), residues: 1023 sheet: None (None), residues: 0 loop : -0.97 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 637 TYR 0.012 0.001 TYR A 322 PHE 0.023 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/Z covalent geometry : bond 0.00399 / 0.17 (12107) covalent geometry : angle 0.57711 / 0.30 (16336) hydrogen bonds : bond 0.04836 / 3.36 ( 761) hydrogen bonds : angle 5.09612 / 3.66 ( 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 : 0.274 Fit side-chains REVERT: A 505 ASP cc_start: 0.7899 (t0) cc_final: 0.7697 (t0) REVERT: C 56 GLU cc_start: 0.7911 (pm20) cc_final: 0.7426 (pm20) REVERT: C 188 LYS cc_start: 0.8537 (ptmt) cc_final: 0.8145 (ptmt) REVERT: D 56 GLU cc_start: 0.8176 (pm20) cc_final: 0.7723 (pm20) REVERT: D 135 LEU cc_start: 0.7694 (tp) cc_final: 0.7354 (tp) outliers start: 6 outliers final: 1 residues processed: 171 average time/residue: 0.1170 time to fit residues: 27.9110 Evaluate side-chains 159 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 158 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 17 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 49 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 103 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 125 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 HIS B 76 HIS C 195 HIS D 60 ASN D 195 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.138725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.097881 restraints weight = 13385.171| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.54 r_work: 0.2776 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12107 Z= 0.157 Angle : 0.537 6.625 16336 Z= 0.283 Chirality : 0.041 0.147 1881 Planarity : 0.003 0.049 2020 Dihedral : 8.363 59.961 1808 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.25 % Allowed : 12.06 % Favored : 86.69 % 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: 0.48 (0.22), residues: 1435 helix: 0.85 (0.16), residues: 1030 sheet: None (None), residues: 0 loop : -0.88 (0.31), residues: 405 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 0.019 0.002 PHE B 200 TRP 0.006 0.001 TRP A 507 HIS 0.006 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (12107) covalent geometry : angle 0.53746 / 0.28 (16336) hydrogen bonds : bond 0.04486 / 3.11 ( 761) hydrogen bonds : angle 4.75489 / 3.43 ( 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 189 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 173 time to evaluate : 0.382 Fit side-chains REVERT: A 381 TYR cc_start: 0.9245 (m-80) cc_final: 0.8971 (m-10) REVERT: A 505 ASP cc_start: 0.7963 (t0) cc_final: 0.7731 (t0) REVERT: B 339 MET cc_start: 0.8990 (mtt) cc_final: 0.8748 (mtt) REVERT: B 381 TYR cc_start: 0.9222 (m-80) cc_final: 0.8948 (m-10) REVERT: C 56 GLU cc_start: 0.8093 (pm20) cc_final: 0.7603 (pm20) REVERT: C 135 LEU cc_start: 0.7836 (tp) cc_final: 0.7571 (tp) REVERT: D 56 GLU cc_start: 0.8180 (pm20) cc_final: 0.7712 (pm20) REVERT: D 123 ASP cc_start: 0.6227 (t0) cc_final: 0.5661 (t0) REVERT: D 135 LEU cc_start: 0.7741 (tp) cc_final: 0.7389 (tp) outliers start: 16 outliers final: 12 residues processed: 178 average time/residue: 0.1118 time to fit residues: 28.2445 Evaluate side-chains 178 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 166 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.7980 chunk 51 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 133 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 54 optimal weight: 0.0050 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 HIS B 76 HIS C 109 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 = 0.3463 r_free = 0.3463 target = 0.140444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.096938 restraints weight = 13330.823| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 1.54 r_work: 0.2754 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1979 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= 0.135 Angle : 0.506 6.349 16336 Z= 0.267 Chirality : 0.040 0.132 1881 Planarity : 0.003 0.048 2020 Dihedral : 7.739 59.466 1808 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.64 % Allowed : 12.92 % 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: 0.78 (0.22), residues: 1435 helix: 1.10 (0.16), residues: 1030 sheet: None (None), residues: 0 loop : -0.88 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 65 TYR 0.010 0.001 TYR A 322 PHE 0.017 0.001 PHE B 200 TRP 0.006 0.001 TRP B 366 HIS 0.006 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (12107) covalent geometry : angle 0.50645 / 0.27 (16336) hydrogen bonds : bond 0.04162 / 2.89 ( 761) hydrogen bonds : angle 4.54611 / 3.29 ( 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 204 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 0.460 Fit side-chains REVERT: A 505 ASP cc_start: 0.7958 (t0) cc_final: 0.7715 (t0) REVERT: A 621 GLN cc_start: 0.7487 (tm-30) cc_final: 0.7237 (pt0) REVERT: B 348 THR cc_start: 0.9096 (OUTLIER) cc_final: 0.8821 (m) REVERT: B 621 GLN cc_start: 0.7594 (tm-30) cc_final: 0.7254 (pt0) REVERT: C 56 GLU cc_start: 0.8018 (pm20) cc_final: 0.7566 (pm20) REVERT: C 135 LEU cc_start: 0.7743 (tp) cc_final: 0.7438 (tp) REVERT: C 168 ASP cc_start: 0.6142 (m-30) cc_final: 0.5591 (t0) REVERT: D 45 THR cc_start: 0.7926 (t) cc_final: 0.7684 (m) REVERT: D 56 GLU cc_start: 0.8007 (pm20) cc_final: 0.7513 (pm20) REVERT: D 135 LEU cc_start: 0.7635 (tp) cc_final: 0.7235 (tp) REVERT: D 141 MET cc_start: 0.7574 (ttt) cc_final: 0.7229 (ttt) REVERT: D 168 ASP cc_start: 0.5852 (m-30) cc_final: 0.5476 (t0) outliers start: 21 outliers final: 13 residues processed: 194 average time/residue: 0.1070 time to fit residues: 29.4289 Evaluate side-chains 185 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 171 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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 465 VAL 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 465 VAL Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 124 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: 3.9990 chunk 26 optimal weight: 1.9990 chunk 105 optimal weight: 0.4980 chunk 48 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 87 optimal weight: 0.5980 chunk 117 optimal weight: 0.0050 chunk 131 optimal weight: 0.6980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3479 r_free = 0.3479 target = 0.141791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.098328 restraints weight = 13263.948| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 1.56 r_work: 0.2780 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12107 Z= 0.123 Angle : 0.501 9.135 16336 Z= 0.261 Chirality : 0.039 0.134 1881 Planarity : 0.003 0.047 2020 Dihedral : 7.351 58.216 1808 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.88 % Allowed : 13.86 % Favored : 84.26 % 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: 0.99 (0.22), residues: 1435 helix: 1.35 (0.16), residues: 1028 sheet: None (None), residues: 0 loop : -1.09 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 336 TYR 0.010 0.001 TYR A 322 PHE 0.014 0.001 PHE B 200 TRP 0.006 0.001 TRP A 507 HIS 0.005 0.001 HIS A 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (12107) covalent geometry : angle 0.50076 / 0.26 (16336) hydrogen bonds : bond 0.03972 / 2.76 ( 761) hydrogen bonds : angle 4.40917 / 3.20 ( 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 218 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 194 time to evaluate : 0.391 Fit side-chains REVERT: A 505 ASP cc_start: 0.7901 (t0) cc_final: 0.7695 (t0) REVERT: A 621 GLN cc_start: 0.7465 (tm-30) cc_final: 0.7171 (pt0) REVERT: B 348 THR cc_start: 0.9082 (OUTLIER) cc_final: 0.8813 (m) REVERT: B 621 GLN cc_start: 0.7624 (tm-30) cc_final: 0.7314 (pt0) REVERT: C 56 GLU cc_start: 0.7805 (pm20) cc_final: 0.7337 (pm20) REVERT: C 135 LEU cc_start: 0.7632 (tp) cc_final: 0.7304 (tp) REVERT: C 168 ASP cc_start: 0.5961 (m-30) cc_final: 0.5436 (t0) REVERT: D 45 THR cc_start: 0.7892 (t) cc_final: 0.7674 (m) REVERT: D 56 GLU cc_start: 0.7906 (pm20) cc_final: 0.7441 (pm20) REVERT: D 135 LEU cc_start: 0.7646 (tp) cc_final: 0.7199 (tp) REVERT: D 168 ASP cc_start: 0.5860 (m-30) cc_final: 0.5486 (t0) outliers start: 24 outliers final: 15 residues processed: 205 average time/residue: 0.1035 time to fit residues: 30.3150 Evaluate side-chains 191 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 175 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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 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 93 ILE Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain D residue 14 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 7 optimal weight: 0.7980 chunk 78 optimal weight: 0.0770 chunk 121 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 135 optimal weight: 0.0020 chunk 103 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 105 optimal weight: 0.2980 chunk 136 optimal weight: 0.9990 chunk 120 optimal weight: 0.6980 overall best weight: 0.3746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3492 r_free = 0.3492 target = 0.143014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.099791 restraints weight = 13305.463| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 1.56 r_work: 0.2807 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2468 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= 0.116 Angle : 0.503 9.888 16336 Z= 0.261 Chirality : 0.039 0.147 1881 Planarity : 0.003 0.047 2020 Dihedral : 7.102 58.536 1808 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.96 % Allowed : 14.10 % 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: 1.21 (0.22), residues: 1435 helix: 1.50 (0.16), residues: 1028 sheet: None (None), residues: 0 loop : -0.96 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 65 TYR 0.009 0.001 TYR A 322 PHE 0.013 0.001 PHE B 200 TRP 0.005 0.001 TRP A 507 HIS 0.005 0.001 HIS A 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (12107) covalent geometry : angle 0.50298 / 0.26 (16336) hydrogen bonds : bond 0.03834 / 2.66 ( 761) hydrogen bonds : angle 4.33185 / 3.14 ( 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 216 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 191 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 501 ASN cc_start: 0.7439 (t0) cc_final: 0.7121 (t0) REVERT: A 505 ASP cc_start: 0.7883 (t0) cc_final: 0.7678 (t0) REVERT: A 621 GLN cc_start: 0.7420 (tm-30) cc_final: 0.7114 (pt0) REVERT: B 348 THR cc_start: 0.9089 (OUTLIER) cc_final: 0.8836 (m) REVERT: B 621 GLN cc_start: 0.7562 (tm-30) cc_final: 0.7243 (pt0) REVERT: C 56 GLU cc_start: 0.7871 (pm20) cc_final: 0.7499 (pm20) REVERT: C 93 ILE cc_start: 0.7576 (OUTLIER) cc_final: 0.7348 (tp) REVERT: C 135 LEU cc_start: 0.7709 (tp) cc_final: 0.7371 (tp) REVERT: C 149 ASP cc_start: 0.7097 (m-30) cc_final: 0.6296 (p0) REVERT: C 168 ASP cc_start: 0.6048 (m-30) cc_final: 0.5443 (t0) REVERT: D 13 GLU cc_start: 0.4934 (pm20) cc_final: 0.4438 (pm20) REVERT: D 16 GLU cc_start: 0.7565 (mp0) cc_final: 0.7186 (mp0) REVERT: D 135 LEU cc_start: 0.7529 (tp) cc_final: 0.7052 (tp) REVERT: D 142 MET cc_start: 0.8830 (ttp) cc_final: 0.8563 (ttp) REVERT: D 168 ASP cc_start: 0.5938 (m-30) cc_final: 0.5500 (t0) outliers start: 25 outliers final: 18 residues processed: 204 average time/residue: 0.0976 time to fit residues: 28.7354 Evaluate side-chains 196 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 93 LEU 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 341 MET 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 33 SER Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain D residue 64 ASP 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: 1.9990 chunk 6 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 136 optimal weight: 0.9990 chunk 78 optimal weight: 0.0060 chunk 123 optimal weight: 0.0770 overall best weight: 0.4754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 HIS ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3494 r_free = 0.3494 target = 0.143138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.099851 restraints weight = 13219.398| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 1.55 r_work: 0.2807 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12107 Z= 0.122 Angle : 0.505 7.451 16336 Z= 0.262 Chirality : 0.039 0.158 1881 Planarity : 0.003 0.047 2020 Dihedral : 6.993 58.456 1808 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.80 % Allowed : 15.90 % Favored : 82.30 % 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: 1.29 (0.22), residues: 1435 helix: 1.55 (0.16), residues: 1028 sheet: None (None), residues: 0 loop : -0.92 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 65 TYR 0.009 0.001 TYR A 322 PHE 0.016 0.001 PHE B 200 TRP 0.006 0.001 TRP B 507 HIS 0.005 0.001 HIS A 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (12107) covalent geometry : angle 0.50453 / 0.26 (16336) hydrogen bonds : bond 0.03856 / 2.67 ( 761) hydrogen bonds : angle 4.31120 / 3.12 ( 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 208 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 185 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8030 (tp30) cc_final: 0.7635 (tp30) REVERT: A 348 THR cc_start: 0.9111 (OUTLIER) cc_final: 0.8877 (m) REVERT: A 501 ASN cc_start: 0.7313 (t0) cc_final: 0.7047 (t0) REVERT: A 505 ASP cc_start: 0.7903 (t0) cc_final: 0.7694 (t0) REVERT: A 621 GLN cc_start: 0.7413 (tm-30) cc_final: 0.7114 (pt0) REVERT: B 348 THR cc_start: 0.9102 (OUTLIER) cc_final: 0.8854 (m) REVERT: B 501 ASN cc_start: 0.7612 (t0) cc_final: 0.7237 (t0) REVERT: B 621 GLN cc_start: 0.7442 (tm-30) cc_final: 0.7208 (pt0) REVERT: C 93 ILE cc_start: 0.7579 (OUTLIER) cc_final: 0.7354 (tp) REVERT: C 135 LEU cc_start: 0.7734 (tp) cc_final: 0.7367 (tp) REVERT: C 149 ASP cc_start: 0.7238 (m-30) cc_final: 0.6397 (p0) REVERT: C 168 ASP cc_start: 0.6110 (m-30) cc_final: 0.5462 (t0) REVERT: D 13 GLU cc_start: 0.4710 (pm20) cc_final: 0.4489 (pm20) REVERT: D 135 LEU cc_start: 0.7500 (tp) cc_final: 0.6967 (tp) REVERT: D 142 MET cc_start: 0.8878 (ttp) cc_final: 0.8600 (ttp) REVERT: D 168 ASP cc_start: 0.5896 (m-30) cc_final: 0.5563 (t0) outliers start: 23 outliers final: 15 residues processed: 199 average time/residue: 0.1008 time to fit residues: 28.9512 Evaluate side-chains 196 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 178 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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 341 MET 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 93 ILE 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: 0.6980 chunk 19 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 41 optimal weight: 0.5980 chunk 120 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.140845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.099584 restraints weight = 13246.985| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.51 r_work: 0.2788 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12107 Z= 0.149 Angle : 0.525 7.572 16336 Z= 0.272 Chirality : 0.040 0.155 1881 Planarity : 0.003 0.048 2020 Dihedral : 7.175 59.198 1808 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.11 % Allowed : 15.74 % Favored : 82.15 % 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: 1.22 (0.22), residues: 1435 helix: 1.46 (0.16), residues: 1036 sheet: None (None), residues: 0 loop : -0.88 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 637 TYR 0.010 0.001 TYR B 322 PHE 0.016 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/Z covalent geometry : bond 0.00353 / 0.15 (12107) covalent geometry : angle 0.52451 / 0.27 (16336) hydrogen bonds : bond 0.04077 / 2.82 ( 761) hydrogen bonds : angle 4.40394 / 3.19 ( 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 199 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8082 (tp30) cc_final: 0.7678 (tp30) REVERT: A 348 THR cc_start: 0.9142 (OUTLIER) cc_final: 0.8892 (m) REVERT: A 380 VAL cc_start: 0.8990 (t) cc_final: 0.8712 (m) REVERT: A 621 GLN cc_start: 0.7362 (tm-30) cc_final: 0.7075 (pt0) REVERT: B 48 GLU cc_start: 0.8117 (tp30) cc_final: 0.7720 (tp30) REVERT: B 348 THR cc_start: 0.9099 (OUTLIER) cc_final: 0.8854 (m) REVERT: C 93 ILE cc_start: 0.7628 (OUTLIER) cc_final: 0.7398 (tp) REVERT: C 135 LEU cc_start: 0.7685 (tp) cc_final: 0.7302 (tp) REVERT: C 149 ASP cc_start: 0.7231 (m-30) cc_final: 0.6376 (p0) REVERT: C 168 ASP cc_start: 0.6134 (m-30) cc_final: 0.5479 (t0) REVERT: D 13 GLU cc_start: 0.4663 (pm20) cc_final: 0.4410 (pm20) REVERT: D 135 LEU cc_start: 0.7535 (tp) cc_final: 0.7018 (tp) REVERT: D 168 ASP cc_start: 0.5887 (m-30) cc_final: 0.5523 (t0) outliers start: 27 outliers final: 15 residues processed: 188 average time/residue: 0.1148 time to fit residues: 30.5741 Evaluate side-chains 185 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 167 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 341 MET 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 93 ILE Chi-restraints excluded: chain D residue 16 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 104 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 97 optimal weight: 0.9990 chunk 131 optimal weight: 0.7980 chunk 26 optimal weight: 0.2980 chunk 108 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 100 optimal weight: 0.4980 chunk 95 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3475 r_free = 0.3475 target = 0.141484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.098053 restraints weight = 13196.649| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 1.55 r_work: 0.2783 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2493 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= 0.133 Angle : 0.514 7.327 16336 Z= 0.267 Chirality : 0.040 0.152 1881 Planarity : 0.003 0.047 2020 Dihedral : 7.093 59.680 1808 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.80 % Allowed : 16.44 % Favored : 81.75 % 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: 1.52 (0.16), residues: 1034 sheet: None (None), residues: 0 loop : -0.87 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 637 TYR 0.009 0.001 TYR B 322 PHE 0.016 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/Z covalent geometry : bond 0.00312 / 0.13 (12107) covalent geometry : angle 0.51436 / 0.27 (16336) hydrogen bonds : bond 0.03977 / 2.75 ( 761) hydrogen bonds : angle 4.37455 / 3.17 ( 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 198 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 175 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8060 (tp30) cc_final: 0.7841 (tp30) REVERT: A 348 THR cc_start: 0.9130 (OUTLIER) cc_final: 0.8928 (m) REVERT: A 621 GLN cc_start: 0.7332 (tm-30) cc_final: 0.7048 (pt0) REVERT: B 48 GLU cc_start: 0.8074 (tp30) cc_final: 0.7680 (tp30) REVERT: B 348 THR cc_start: 0.9097 (OUTLIER) cc_final: 0.8865 (m) REVERT: C 93 ILE cc_start: 0.7615 (OUTLIER) cc_final: 0.7385 (tp) REVERT: C 128 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7407 (tp30) REVERT: C 135 LEU cc_start: 0.7638 (tp) cc_final: 0.7248 (tp) REVERT: C 149 ASP cc_start: 0.7227 (m-30) cc_final: 0.6376 (p0) REVERT: C 168 ASP cc_start: 0.6133 (m-30) cc_final: 0.5474 (t0) REVERT: D 128 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7319 (tp30) REVERT: D 135 LEU cc_start: 0.7500 (tp) cc_final: 0.6993 (tp) REVERT: D 168 ASP cc_start: 0.5893 (m-30) cc_final: 0.5515 (t0) outliers start: 23 outliers final: 17 residues processed: 188 average time/residue: 0.1106 time to fit residues: 29.1703 Evaluate side-chains 185 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 93 LEU 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 B residue 629 GLN 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 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: 10.0000 chunk 35 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 115 optimal weight: 0.0570 chunk 57 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 120 optimal weight: 0.0980 chunk 19 optimal weight: 1.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3472 r_free = 0.3472 target = 0.141295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.097837 restraints weight = 13350.379| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 1.57 r_work: 0.2785 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2543 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 : 0.515 7.409 16336 Z= 0.267 Chirality : 0.040 0.150 1881 Planarity : 0.003 0.047 2020 Dihedral : 7.038 59.729 1808 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.57 % Allowed : 16.68 % Favored : 81.75 % 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: 1.30 (0.22), residues: 1435 helix: 1.51 (0.16), residues: 1040 sheet: None (None), residues: 0 loop : -0.83 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 637 TYR 0.009 0.001 TYR B 322 PHE 0.017 0.001 PHE B 200 TRP 0.006 0.001 TRP B 507 HIS 0.006 0.001 HIS A 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (12107) covalent geometry : angle 0.51509 / 0.27 (16336) hydrogen bonds : bond 0.03954 / 2.73 ( 761) hydrogen bonds : angle 4.35547 / 3.16 ( 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 193 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 173 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8046 (tp30) cc_final: 0.7827 (tp30) REVERT: A 348 THR cc_start: 0.9131 (OUTLIER) cc_final: 0.8927 (m) REVERT: A 621 GLN cc_start: 0.7344 (tm-30) cc_final: 0.7049 (pt0) REVERT: B 48 GLU cc_start: 0.8073 (tp30) cc_final: 0.7872 (tp30) REVERT: B 348 THR cc_start: 0.9097 (OUTLIER) cc_final: 0.8866 (m) REVERT: B 430 LYS cc_start: 0.8326 (mttt) cc_final: 0.8027 (mtpt) REVERT: C 93 ILE cc_start: 0.7623 (OUTLIER) cc_final: 0.7417 (mt) REVERT: C 128 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7349 (tp30) REVERT: C 135 LEU cc_start: 0.7579 (tp) cc_final: 0.7184 (tp) REVERT: C 149 ASP cc_start: 0.7187 (m-30) cc_final: 0.6396 (p0) REVERT: C 168 ASP cc_start: 0.6105 (m-30) cc_final: 0.5523 (t0) REVERT: D 128 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7301 (tp30) REVERT: D 135 LEU cc_start: 0.7528 (tp) cc_final: 0.7018 (tp) REVERT: D 168 ASP cc_start: 0.5906 (m-30) cc_final: 0.5515 (t0) REVERT: D 188 LYS cc_start: 0.8448 (ptmt) cc_final: 0.8230 (ptpt) outliers start: 20 outliers final: 15 residues processed: 185 average time/residue: 0.1188 time to fit residues: 31.0263 Evaluate side-chains 188 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 170 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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 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 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 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 122 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 chunk 95 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 chunk 117 optimal weight: 0.0010 chunk 50 optimal weight: 0.5980 chunk 135 optimal weight: 9.9990 chunk 136 optimal weight: 0.9980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3474 r_free = 0.3474 target = 0.141501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.098019 restraints weight = 13336.323| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 1.57 r_work: 0.2790 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2579 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= 0.132 Angle : 0.515 7.320 16336 Z= 0.267 Chirality : 0.040 0.149 1881 Planarity : 0.003 0.047 2020 Dihedral : 6.994 59.257 1808 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.57 % Allowed : 16.84 % Favored : 81.60 % 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: 1.35 (0.22), residues: 1435 helix: 1.53 (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 0.001 0.000 ARG A 637 TYR 0.009 0.001 TYR B 322 PHE 0.017 0.001 PHE A 200 TRP 0.007 0.001 TRP B 507 HIS 0.006 0.001 HIS A 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (12107) covalent geometry : angle 0.51463 / 0.27 (16336) hydrogen bonds : bond 0.03958 / 2.74 ( 761) hydrogen bonds : angle 4.35852 / 3.16 ( 2253) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2667.13 seconds wall clock time: 46 minutes 34.28 seconds (2794.28 seconds total)